Ambystoma laterale–jeffersonianum complex that can optionally incorporate genetic material from locally adapted sexual hosts through genomic exchanges. More specifically, we compared environmentally induced epigenetic changes between lineages strictly reproducing clonally vs. those incorporating a locally adapted genome. The results revealed that both lineage and sample site components, as well as their interaction, affected epigenetic variation. When lineages were analysed separately, differences among sample sites were only detected in lineages impervious to genomic exchanges. Sample sites had no significant effect on the epigenetic variation of lineages that performed genomic exchanges. These results suggest that environmentally induced epigenetic variation among sites depends more on the lack of locally adapted alleles than on the level of genetic variation.Both genetic variation and environmentally induced epigenetic changes allow organisms to persist through the heterogeneity of their habitats. Selection on genetic variation can promote local adaptation of populations. However, in absence of genetic variation, clonal organisms mostly rely on epigenetics to respond to environmental heterogeneity. We used the potential of unisexual organisms in incorporating their host genome, to empirically assess whether the presence of a locally adapted genome affects environmentally induced epigenetic changes in clonal organisms. We addressed this problematic by using unisexual lineages of the kleptogen vertebrate  Organisms have developed a wide range of adaptive strategies to face environmental fluctuations . Most haEpigenetics consists of enzyme-mediated chemical modifications of histones, DNA and RNA. These changes modify the properties of these molecules while the amino/nucleic acids sequence remains unchanged . These cThe relative importance of epigenetic vs. genetic variation is comparable to the question of the relationship between phenotypic plasticity and genetic diversity which has been strongly debated in the literature. Some authors have argued that phenotypic plasticity is negatively correlated with genetic diversity because phenotypic plasticity evolves to display phenotypes acclimated to different environments without resorting to genetic variation . Others To empirically assess the relative importance of genetic and epigenetic variation, one could compare genetically similar individuals with or without the presence of a locally adapted genome. This allows isolation of the genetic effects from environmentally induced epigenetic variation. A locally adapted genome results of a long-term selection on genetic variation, providing to a population a higher fitness in their native environment than in other environments.Such particular system can naturally occur in unisexual vertebrates. These organisms reproduce clonally while they need sperm of a host species to trigger egg’s development. However, they can occasionally acquire a haplome of the sexual host via paternal leakage; when the sperm’s genome is incorporated to the egg’s pronucleus . If the vice versa—leads to the same outcome as genome replacement, but over several reproduction events. Genome exchange is the term used to designate the resulting haplome permutation, regardless of whether it occurred in one reproduction event or over many generations [Kleptogenesis is an example of a mechanism used by unisexual organisms to occasionally incorporate genetic material of a closely related species . Kleptogerations .Ambystoma laterale–jeffersonianum complex was used as a biological model because genome exchange has been inferred in multiple locations [The objective of this study was to assess whether the presence of a locally adapted genome affects environmentally induced epigenetic variation in a kleptogen vertebrate. The unisexual of the ocations , 24–27. ocations . The preIndividuals of a given GE− lineage are expected to display distinct epigenetic profiles in response to the environmental conditions of different sampling sites. However, since the locally adapted haplome incorporated through genome exchange might be partly responsible for the phenotype of a GE+ lineage, we predict a lower contribution of environmentally induced epigenetic variation among sites.et al. [Ambystoma laterale–jeffersonianum harbored a hybrid genome including at least one haplome from A. laterale and one from A. jeffersonianum. An additional haplome of A. laterale, the unique host species in this region, characterized most of the individuals captured. Lineages were previously discriminated using microsatellite loci [Individuals were collected in a study previously conducted by Beauregard and Angers . Samplinet al. . The uniite loci . Strictlite loci .A representative subsample of 125 unisexuals was selected for epigenetic analyses to maximizing comparison of lineages among sites . Most siTo determine whether environmental conditions among sampling sites of a given lineage were different, we performed an environmental characterization of the aquatic and terrestrial environments of the sites. First, environmental conditions were measured during the first sampling season. All sites  were visited four times during the larval development period from May to August 2014 . We measDucks Unlimited Canada was also used to further characterize the reproductive pond: type of wetland , superficies, and permanence. Finally, the soils characterization databank (Institut de recherche et de développement en agroenvironnement) was used to extract data about the tilt profile; soil drainage; granulometry; pH; dominance of clay, loam, silt, or sand; soil alkalinity, and humidity indices; and the percentage of coarse fragments, very fine sand, sand, silt, clay, and organic carbon. Data were only available for sites M01-05, M07, and E03.We completed the characterization with other sources of public data. The forest maps  provided data on age class, density, height, and inclination indices, as well as main and second tree essence near the site. Tree essences were related to a sunlight, soil acidity, and humidity indices. Detailed mapping of wetlands by All data-sets included various types of data. Quantitative data were not transformed otherwise. Semi-quantitative data in the form of descriptor indices were associated with a number from 0 to the higher descriptor. Semi-quantitative data in the form of different numerical classes were converted to the median of each class. Unordered qualitative data were split into as many columns as there were categories and converted to binary data .vegan [The four different databanks were analysed separately, since they do not all include data of the same sites . A globavegan . The relet al. [The Methylation Sensitive Amplified Polymorphism (MSAP) method was chosen because it allows the coverage of a large-spectrum portrait of the epigenetics of a large number of individuals. A total of 125 individuals were selected to conduct MSAP analysis according to a protocol modified from Xiong et al. . The Mspcmdscale in R.The epigenetic matrix was obtained by removing all the loci in the presence–absence HpaII matrix that matched loci in the MspI matrix to avoid variation correlated with genetics (Supplementary : Sheet S1). The simple-matching coefficient was used to calculate the distance matrix from the presence–absence AFLP matrix to account for both double presences and double absences. To visualize the repartition of the individuals according to their epigenetic patterns, the inter-individual distance was represented via a principal coordinates analysis (PCoA) using the function varpart of the package vegan. Sample sites, ploidy level, and genetics were considered as constraining matrices (Supplementary Sheets S2–S4). The descriptive genetic matrix was a compilation of presence–absence of the highly divergent microsatellites’ alleles  and therda and Rsquare Adj of the package vegan. For total environmental effect, only site of sampling was considered as a constraining matrix. For partial environmental effect, site of sampling, ploidy level, and intra-lineage genetics were all considered as constraining matrices. The P-value of partial and total environmental effect on epigenetic patterns was obtained with the function anova.cca of the package vegan. Total and partial environmental effect for all lineages with genome exchange  and all exclusively clonal lineages (A and D-2n) was computed using the same method.Total and partial environmental effect for each lineage was also tested with the functions The sites clustered differently according to the different datasets used for environmental characterization . Sites tAll sites could be assigned to one of the five categories of environmental conditions. Sites that included individuals from the same lineage belonged to different categories. M02 and E02 are semi-permanent ponds created by digging and connected to a drainage ditch. E01 and M06 are temporary ponds easily drained in the top of a small mountain. M07 is a large marshy stream with some fish. M01 and M04 are larger, better defined, and deeper arborescent swamps, while M03, M05, and E03 are a grouping of a few smaller arborescent swamps.A total of 52 loci of the methylation pattern were kept for analysis, of which 37 were variable and 27 were informative . PrincipVariance partitioning on all individuals supports these trends . The totWhen lineages are analysed separately, sampling sites have a significant effect on three lineages , whereas they are not significant for the lineages with genome exchange analysed together .When genetic variation and ploidy levels are taken into account, sampling sites are only significant for the exclusively clonal lineages analysed together  did not display significant epigenetic differences among sites once the effects of genetics and ploidy were removed. On the contrary, sample sites had a significant effect only on the clonal lineages (GE−: lineages A and D-2n).Difference in environmental conditions among sampling sites is a crucial factor to consider when assessing environmentally induced epigenetic variation . HoweverTo circumvent this, the sampling site was considered as a proxy for environmental conditions, and all pairwise comparisons between sites are different from the same extent. This appears as a reasonable compromise given the distribution of sites of a given lineage according to the different sets of environmental factors: The sites dominated by the same lineage are globally very different from each other. However, it can be noted that the sites dominated by lineage C (M04 and M05) are more similar, whereas those dominated by lineage D  are more different.Ambystoma salamanders [Ambystoma display strong fidelity to their breeding sites [A second crucial factor to consider is the genetic differentiation of populations, which must be comparable between GE+ and GE− lineages. Both sampling sites hosting individuals from lineages B and E are genetically isolated from each other since sites M01 and M02 are located on different islands. There is a large geographic distance between sites hosting lineage D , while the landscape between sites hosting lineage A is highly urbanized. Only the sites hosting lineage C are not completely isolated from each other, but M04 and M05 are still 3.6 km apart and separated by a road and grasslands, which are typically avoided by amanders . Salamanng sites , and theng sites , 39–42.Depending on whether they perform genome exchange or not, lineages are characterized by different genetic diversity among sites according to microsatellite markers . Clonal The results revealed a marked difference in epigenetic variation between lineages with and without genome exchange. When genetics and ploidy level are taken into account, sample sites have a significant effect only on the environmentally induced epigenetic variation of clonal lineages A and D-2n. The three lineages that performed genome exchange  did not display significant epigenetic differences among sites once the effects of genetics and ploidy were removed.Individuals of lineage A are triploids; their genome includes a haplome from a paternal leakage in addition to the hybrid genome. It appears difficult to determine when the genome from paternal leakage was incorporated in this lineage. However, highly divergent alleles from the main microsatellite allele’s distribution of unisexuals were found in the sexual sympatric individuals . Those hIt is however more straightforward with lineage D-2n. Despite their relative remoteness from the other unisexual populations, individuals of lineage D-2n harbor a hybrid genome genetically equidistant from other lineages. Since genome exchange events did not occur locally , the hybIndividuals of the other lineages are likely not impervious to environmentally induced epigenetic variation, but they relied less on plasticity than clonal individuals. Lineages performing genome exchange can create genetic variation by replacing one of their haplomes with the haplome from a sexual species. This process has numerous advantages: It can purge deleterious alleles and increase genetic variation at the population scale. However, an important benefit is to gain a locally adapted haplome.Several authors have argued that no relationship exists between phenotypic plasticity and genetic diversity since they are both traits that act independently to cope with different levels of environmental changes , 43–45. Kleptogenetic lineages, as partially sexual organisms, can use either genetic or epigenetic variation, as well as their potential interactions. So, why do GE+ lineages put plasticity apart? One possible answer could be the cost of plasticity. Plasticity is expected to increase fitness by producing alternative phenotypes according to environmental conditions. However, this strategy is profitable only when conditions are fluctuating and when the changes are predictable , 46. MorLineages with and without genome exchange provide a useful model to assess the role of genetic variation in plasticity. Clonal organisms strongly rely on plasticity to adjust their phenotypes to a given environment. On the contrary, organisms that have the opportunity to use locally adapted alleles to generate their phenotypes depend less on plasticity. The importance of plasticity in an organism’s strategy seems to depend not only on the amount of genetic diversity but also on the adequacy of alleles for the local environment.Supplementary DataClick here for additional data file.


Candida krusei is a notable pathogenic fungus that causes invasive candidiasis, mainly due to its natural resistance to fluconazole. However, to date, there is limited research on the genetic population features of C. krusei. We developed a set of microsatellite markers for this organism, with a cumulative discriminatory power of 1,000. Using these microsatellite loci, 48 independent C. krusei strains of clearly known the sources, were analyzed. Furthermore, susceptibility to 9 antifungal agents was determined for each strain, by the Clinical and Laboratory Standards Institute broth microdilution method. Population structure analyses revealed that C. krusei could be separated into two clusters. The cluster with the higher genetic diversity had wider MIC ranges for six antifungal agents. Furthermore, the highest MIC values of the six antifungal agents belonged to the cluster with higher genetic diversity. The higher genetic diversity cluster might have a better adaptive capacity when C. krusei is under selection pressure from antifungal agents, and thus is more likely to develop drug resistance. Candida genus, Candida krusei attracts much medical attention because it is intrinsically resistant to fluconazole  developed a novel set of microsatellite markers for molecular typing and population genetic analysis of C. krusei; (2) used the developed assay to type 48 multicenter collected C. krusei clinical strains; and (3) analyzed the correlation between genetic diversity and drug susceptibility among the studied strains.However, to our best knowledge, no research targeting the genetic population features of This study was reviewed and approved by the ethics committee of the National Institute for Communicable Disease Control and Prevention, Chinese CDC. Written informed consent was obtained from patients for use of the samples in research.C. krusei isolates, each from a single patient, were collected from 15 hospitals distributed in 10 cities across China during the period 2009–2012, as part of the national surveillance program for invasive fungal infections  and incubated at 37°C for 24 h. Species identification of the isolates was confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry  as per manufacturer's instructions, and by sequence analysis of their rDNA internal transcribed spacer (ITS) regions .C. krusei genome ; second, the locus could be amplified relatively stable. The microsatellite loci would be abandoned if the loci was not amplified in more than two strains.The software SciRoKo was used to identify microsatellites in the Taq polymerase kit . Each of the amplification reactions was composed of 1 × PCR buffer, 0.2 μM dNTP, 0.5 U Taq polymerase, 0.2 μM each primer, and 2 μl genomic DNA (20–50 ng/μl). The thermocycler conditions were as follows: initial denaturation at 95°C for 5 min, followed by 35 cycles of denaturation at 94°C for 30 s, annealing at an optimized primer-specific annealing temperature for 30 s  broth microdilution method22. Minimum inhibitory concentration (MIC) results for fluconazole, voriconazole, caspofungin, micafungin, and anidulafungin, were interpreted using clinical breakpoints in accordance with the CLSI guidelines , effective number of alleles (ne), Shannon's Information Index (I), and Nei's unbiased gene diversity (HS), were calculated using GENALEX 6.5  MIC values were calculated using WHONET software .For antifungal susceptibility results, MICC. krusei, a total of 200 microsatellite loci were identified, and primers were designed (data not shown). Of these microsatellite loci, 33 polymorphic microsatellite loci (Cakr 001–Cakr 033) could be stably amplified in all C. krusei isolates (Table P < 0.05).Based on the genome of i Cakr 00–Cakr 033In addition, it must be noted that many isolates were heterozygote . The principal coordinate analysis (PCoA) supported the result of the STRUCTURE analyses  MIC, MICrs Table . For mosArabidopsis thaliana population with higher genetic diversity had better colonization success  was slightly higher than MLST, which exhibited a discriminatory index of 0.998 , or both in group A and group B . Meanwhile, there was no strain with the highest MIC value was observed in Cluster A. These findings suggest that the population with higher genetic diversity may have more diverse phenotypes, including drug resistance. When subjected to selective pressure from antifungal drugs, cluster B might have a better adaptive capacity, and thus would be more likely to develop drug resistance. This suggests that the C. krusei population or lineage with higher genetic diversity needs more attention in terms of fungal drug resistance.Cluster B had a higher genetic diversity which suggests a better adaptive capacity for survival in challenging conditions. As previously mentioned, the population with a higher genetic diversity is more likely to develop antimicrobial drug resistance. In our study, cluster B had a wider MIC range for 6 antifungal drugs, although there was no obvious difference in GM MIC, MICC. krusei was divided into two clusters by novel high-resolution microsatellite markers. The cluster with higher genetic diversity had wider MIC ranges for six antifungal agents, and the highest MIC values of the six antifungal agents belonged to the cluster of higher genetic diversity. It is plausible that the C. krusei cluster with higher genetic diversity might have better adaptive capacity when under the selection pressure of antifungal agents.In conclusion, JZ and Y-CX designed the experiments. JG, MX, HW, FZ, LH, and WW collected the samples and performed the experiments. JG, MX, TK, and YW analyzed data. JG, MX, and TK wrote the manuscript. All authors read and approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


It is the only species cultivated for turf among the eight species in Eremochloa. The center of origin for this species is southern to central China. Although centipedegrass is an excellent lawn grass and is most widely used in the southeastern United States, China has the largest reserve of centipedegrass germplasm in the world. Presently, the gene bank in China holds ~200 centipedegrass accessions collected from geographical regions that are diverse in terms of climate and elevation. This collection appears to have broad variability with regard to morphological and physiological characteristics. To efficiently develop new centipedegrass varieties and improve cultivated species by fully utilizing this variability, multiple approaches have been implemented in recent years to detect the extent of variation and to unravel the patterns of genetic diversity among centipedegrass collections. In this review, we briefly summarize research progress in investigating the diversity of centipedegrass using morphological, physiological, cytological, and molecular biological approaches, and present the current status of genomic studies in centipedegrass. Perspectives on future research on genetics and genomics and modern breeding of centipedegrass are also discussed.Genetic diversity is the heritable variation within and among populations, and in the context of this paper describes the heritable variation among the germplasm resources of centipedegrass. Centipedegrass is an important warm-season perennial C Eremochloa ophiuroides (Munro) Hack.] is a perennial warm-season (C4) grass that originated in China3. It is indigenous to Southeast Asia and is now widespread, with its distribution, including China (in the Yangtze River Basin and its southern area), Southeast Asia, the eastern and southern United States4, some parts of South America, the West Indies, and even parts of Africa5 and tropical northern and eastern Australia6. It has highly developed stolons during growth in the field and can form a dense canopy that provides continuous ground cover  provides an opportunity for plant breeders to develop new and improved cultivars with desirable characteristicsHere, we present overviews of the results of major studies on the genetic variation in centipedegrass and of the recent progress made in describing centipedegrass diversity, mainly in the United States and China. The information summarized in the present article is of potential value not only for understanding the drivers of genetic variation in centipedegrass, but also for promoting the breeding and improvement of centipedegrass varieties using modern genetic and genomic tools.Eremochloa in the family Poaceae or Gramineae, subfamily Panicoideae, tribe Andropogoneae, and subtribe Rottboelliinae18. It is the only species in the Eremochloa genus that is used as turfgrass12. Centipedegrass is a C4 plant, similar to maize and sorghum20.Centipedegrass belongs to the genus n = 2x = 1824 and a genome size of ~800 Mb25. Cytological observations of this species revealed that metaphase I of meiosis was mostly regular, with nine bivalents, but 1 to 15% of the microsporocytes had eight bivalents and two univalents due to a precociously dividing bivalent2. Centipedegrass is a sexually reproducing species with high-pollen stainability and normal sexual development involving megasporogenesis and an embryo sac, but it is self-incompatible9. An artificially induced tetraploid accession of centipedegrass can be generated by colchicine treatment, with an induction rate of 0.2%26. As polyploidization often results in the induction of chromosomal aberrations at the mitotic and/or meiotic level, such ploidy changes through artificial factors contribute to creating new centipedegrass germplasms, which are of high value in terms of sampling for cultivar improvement. However, cytogenetic information for natural accessions, as well as artificial lines of centipedegrass is currently limited. In addition, the above-mentioned findings were based on only a portion of centipedegrass samples, and such a small sample size might lead to an underestimation of the genetic diversity in this species. Therefore, it is necessary to use current cytogenetic approaches to carry out ploidy identification and karyotype analysis of more centipedegrass germplasms derived from different provenances or multiple breeding sources.Centipedegrass is a diploid species with a somatic chromosome number of 224. Currently, the Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, which is one of the most important turf research institutes in China, has the only Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses in the National Forestry and Grassland Administration (NFGA) and has the largest National Main Warm-season Turfgrass Gene Bank (NMWTGB) in China. The NMWTGB preserves centipedegrass genetic resources collected from different geographical regions in China and plant materials imported from the United States. To the best of our knowledge, the NMWTGB maintains the richest centipedegrass resources in the world, with ~192 accessions, including 11 cultivars initially registered and conserved ex situ 31, seed yield32, and phenological phases, which mainly include the regreening stage, booting stage, blossom stage, maturity stage, wilting stage, and green period34. The narrower genetic base of centipedegrass collections in the United States than in China is likely because most of the centipedegrass accessions in the United States originated from a single collection introduced from China9. In addition, variations in some morphological characteristics related to lawn appearance, such as leaf length, plant height, and internode length and diameter, were also detected in centipedegrass hybrid generations36  and DNA markers Table , respect22. For centipedegrass collections or populations in China, several studies were also carried out on the variation in isozymes. Ren et al.39 tested peroxidase isozymes and esterase isozymes in five native centipedegrass samples from different areas of Sichuan and found that all five samples showed variations in the two enzymes. Bai et al.40 clustered 15 centipedegrass accessions collected from six geographical regions in China into two categories and four groups based on peroxidase isozyme analysis. By comparing peroxidase isozymes, esterase, and malate dehydrogenase isozymes among six populations of centipedegrass derived from geographical regions of mainland China, Xuan, and Liu41 evaluated the genetic diversity in centipedegrass populations and drew the conclusion that the genetic diversity of centipedegrass in China was more abundant within populations than among populations. Liu and Liu42 also revealed abundant genetic diversity in 16 centipedegrass accessions sampled from East China by electrophoretic analysis of peroxidase and esterase isozymes. However, the genetic diversity in centipedegrass revealed by these isozyme markers still needs to be further verified by more accurate DNA markers. In fact, portions of these research findings have already been validated or corrected in subsequent studies using DNA markers.Isozymes were among the most widely used markers for genetic variation analysis within and between populations before DNA markers were applied. Although they have now been largely superseded by more informative DNA-based markers, they were an excellent choice for projects that sought only to identify low levels of genetic variation. Early studies on isozymes showed different isoenzyme patterns of esterase and peroxidase among 12 U.S. centipedegrass accessions43. Similarly, genetic variations among accessions and populations of centipedegrass that were collected from different geographical regions in China were also analyzed in subsequent studies using AFLP44, RAPD45, ISSR46, SRAP48, and SSR markers49. The Nei’s genetic distances between nine centipedegrass collections derived from different geographic regions in China ranged from 0.135 to 0.994 for AFLP markers44, indicating broad genetic variation among these accessions. Significant variation was also detected in six centipedegrass populations consisting of 50 accessions by RAPD analysis45 and among 60 centipedegrass collections from 13 different geographical regions by ISSR analysis46, with a much higher level of genetic variation within populations than among populations. However, it is worth mentioning that a higher level of diversity in U.S. cultivars than in Chinese collections was revealed using SRAP and SSR markers; meanwhile, a lack of overlap in the ranges of diversity between the U.S. and most Chinese groups were found, and genetic diversity did not differ quantitatively between the U.S. and Chinese materials but did differ qualitatively11. Recently, Li et al.49 developed a large number of SSR markers based on the next-generation sequencing (NGS) approach and detected considerable genetic diversity among centipedegrass accessions by systematically analyzing the genetic variation among accessions in one core collection of 43 centipedegrass accessions. All the accessions were clustered into six groups according to genetic variation, while the genetic relationship among the 43 accessions did not correspond exactly to their geographical locations, which suggested that centipedegrass experienced outward expansion from its origin site, leading to a complex genetic background and evolutionary history. These analyses depicted a high level of polymorphism within cultivars and a dramatic difference in diversity between/among centipedegrass populations.Molecular markers are short sections of DNA that differ among genotypes, and they are widely used for the identification of germplasm, assessment of genetic variation within and among populations, and determination of genetic relationships between various populations. The genetic relationships among five centipedegrass accessions (or cultivars) in the United States were assessed based on DNA amplification fingerprinting (DAF), and the relatively low levels of polymorphism among them suggested that these accessions are closely related and may share a common origin1 progenies of a cross between two centipedegrass ecotypes (E102 and E092-1). The maps consisted of a female linkage map with 89 loci (85 SRAPs and 4 EST-SSRs) and a male linkage map with 71 assigned SRAP loci50. The same research group subsequently produced another set of genetic maps using the same molecular markers from a population of 87 F1 plants derived from crossing two different ecotypes (E142 and E022) and detected a total of 14 QTLs on the nine linkage groups of the maps; the QTLs were associated with seed yield, vegetative traits and cold tolerance, and could explain 8.71–23.61% of the phenotypic variation51. With the rapid development of high-throughput sequencing technology, additional specific molecular markers for centipedegrass can be rapidly developed at low cost. Therefore, constructing high-density genetic maps in centipedegrass will be an important goal for future research and has the potential to identify the genes responsible for traits of interest.Owing to the high level of heterozygosity of centipedegrass plants, research progress on genetic map construction and quantitative trait locus (QTL) mapping of major economic traits in centipedegrass has been slow. The first genetic linkage maps of centipedegrass were constructed using SRAP and SSR markers and were based on 89 F52. For the cold-tolerant variety “TifBlair”, a normalized transcriptome library was prepared and sequenced from leaves of seedlings, resulting in a transcriptome with 45,575 unigenes and 84,781 contigs52. A second normalized library was constructed from various centipedegrass tissues, including leaf, stolon, and spike tissues, resulting in more gene clusters49. Furthermore, a comparative RNA-seq study revealed 329 putative gene products differentially expressed between red-purple and green stolons and 829 differentially expressed genes between red-purple and yellow-green spikes49. Owing to various environmental adversities during lawn growth, future research endeavors should be devoted to the transcriptomic analysis of centipedegrass in response to cold and drought stresses and of its tolerance to barren and acidic soils, among other environmental stressors.To date, the transcriptomes from one cultivar and two accessions of centipedegrass have been sequenced53 and perennial ryegrass54 via NGS techniques.With the rapid development and wide applications of NGS technologies, genomic research on several grass species has recently moved from small-scale analysis of genetic polymorphisms toward whole-genome sequencing and genome-wide polymorphism surveys. The availability of genomic sequences for a turfgrass species will greatly increase the number of genome-scale investigations of fundamental mechanisms of resistance to biotic and abiotic stresses. However, to date, there have been no reports on centipedegrass whole-genome sequencing or related genome-sequencing projects, while a few such studies have been performed in zoysia60 to studies of physiological traits related to turf quality66. However, systematic studies on genetic variability in drought tolerance among centipedegrass genotypes have rarely been performed, which severely restricts the breeding of drought-tolerant centipedegrass varieties. Nevertheless, there have been a few successful attempts to produce drought-resistant mutants by radiation-induced mutation in centipedegrass seeds69 and by culture-induced variation in somatic embryogenesis70. These mutant plants showed greater tolerance to drought stress and thus could be potential germplasm resources for breeding drought-tolerant centipedegrass. Hence, it will be important to understand genetic variability in drought tolerance within the centipedegrass gene pool in the future.Drought stress often occurs during the process of lawn growth and management, and it results in a decline in the quality and productivity of turfgrasses. Studies investigating the effect of moisture deficits on the performance of centipedegrass plants ranged from studies of variability in key morphological characters and responses72. Generally, however, centipedegrass is a salinity-sensitive species, in contrast to other warm-season turfgrasses77.Salinity is a detrimental abiotic stressor for turfgrass plant growth in salt-affected soils. Some artificially bred cultivars of centipedegrass show intraspecific variations in morphological characteristics and turf quality related to salinity tolerance; for example, there is a difference in salt tolerance between “TifBlair”  and “Common” . Studies on physiological responses to salt stress have revealed significant differences between salt-tolerant and salt-sensitive cultivars/accessions80. A preliminary genetic analysis of aluminum tolerance revealed that aluminum tolerance in centipedegrass is not controlled by a single major gene81. Root exudation of citric acid is one of the key mechanisms for Al tolerance in centipedegrass82.Aluminum (Al) toxicity is a major limiting factor for plants growing in acidic soils. Wild centipedegrass is mainly distributed in acidic soils in tropical and subtropical regions, so investigating and documenting the effect of such soil conditions on centipedegrass production and productivity is worthwhile. It has been widely assumed that centipedegrass is well adapted to acidic soils and has excellent Al resistance. A high degree of genetic variation in Al tolerance in centipedegrass collections in China, as well as in the cultivars “TifBlair” and “Common”, was found based on plant growth and physiological responses to Al83. In contrast, several centipedegrass accessions in China showed great differences in cold tolerance85. The freezing tolerance of centipedegrass was positively correlated with the levels of polyamines (Pas) and antioxidants, the levels of proline and soluble carbohydrates, and the ratio of soluble carbohydrates to starch89. The inheritance of cold tolerance in centipedegrass is additive and dominant with epistatic effects and is controlled by two major genes90. To date, one QTL for cold tolerance has been identified by constructing a group of genetic linkage maps of centipedegrass91. Recently, several centipedegrass mutants have been produced by radiation86 and by somaclonal variation92, and the resultant mutants show good cold resistance. These mutants are valuable materials for both centipedegrass research and centipedegrass breeding purposes.Centipedegrass is sensitive to low temperatures, is vulnerable to freezing injury, and has a poor overwintering ability. Thus, its adaptation is limited to areas with mild winter temperatures. An early study revealed no measurable differences in cold resistance among centipedegrass plants from different sources in the United StatesThe value of germplasm resources is determined by their genetic diversity, availability, and utility. The wide spectrum of genetic diversity in growth phenotypes and stress-related traits in centipedegrass implies great opportunities for genetic improvement through either direct selection or hybridization between parental lines with desirable traits. Cytological and molecular methods have provided powerful tools for a deeper analysis of genetic variation in centipedegrass. Some mutagenized materials have been developed to supplement the natural diversity present in centipedegrass. As in the many studies that were reviewed here, many efforts have been made over the past few decades to estimate and utilize the genetic variation in centipedegrass populations grown in the United States. Nevertheless, due to the limited populations and genotypes of U.S. accessions, the actual diversity is not reflected in the available centipedegrass germplasm. Although wild resources of centipedegrass are abundant in China and have many unique and useful characteristics, such as a diversity of turf performance and levels of stress tolerance, the exploitation and utilization of resources based on their genetic diversity are still limited. Therefore, it is necessary and valuable to further explore the diversity of centipedegrass germplasms that are currently growing in China and other places in South Asia. Such further germplasm exploration and evaluation may lead to the identification of additional improved centipedegrass materials, which could be conducive to the expanded production of high-value turf. Molecular cytogenetic and new sequence-based approaches will provide opportunities for in-depth studies of the genetic variation and phylogenetic relationships among global collections of this species. In view of the above facts, future research should emphasize four aspects: (1) further collection of centipedegrass germplasm from all of its distribution areas, and especially from regions not sampled during previous collection trips, in order to construct a richer and more complete germplasm bank and an updated core collection; (2) cytogenetic studies on the chromosome structure and function of centipedegrass both for breeders and for other scientists interested in the analysis and manipulation of breeding material at the chromosomal level; (3) studies of genomics, transcriptomics, proteomics, and metabolomics in centipedegrass using high-throughput sequencing techniques; and (4) mining and functional research on the genes responsible for desirable traits such as strong aluminum tolerance and good tolerance to infertile soils, which will ultimately aid in cultivar improvement. With this article, the authors hope that the concerted efforts of all stakeholders in research, development, and funding can be united globally to promote the healthy development of the turf industry.Table S1


Early detection of the onset of a caldera collapse can provide crucial information to understand their formation and thus to minimize risks for the nearby population and visitors. Here, we analyse the 2007 caldera collapse of Piton de la Fournaise on La Réunion Island recorded by a broadband seismic station. We show that this instrument recorded ultra-long period (ULP) signals with frequencies in the range (0.003–0.01 Hz) accompanied by very-long period (VLP) signals (between 0.02 and 0.50 Hz) prior to and during the caldera formation suggesting it is possible to detect the beginning of the collapse at depth and anticipate its surface formation. Interestingly, VLP wave packets with a similar duration of 20 s are identified prior to and during the caldera formation. We propose that these events could result from repeating piston-like successive collapses occurring through a ring-fault structure surrounding a magma reservoir from the following arguments: the source mechanism from the main collapse, the observations of slow source processes as well as observations from the field and the characteristic ring-fault seismicity. Identifying the occurrence of the first collapse at depth is of major importance in evaluating the triggering factors and anticipating the caldera surface formation. This detection can help to predict or at least indicate early future caldera collapses and subsequent consequences such as explosive eruptions, , or atmospheric impacts3.Caldera collapses are rare (only seven events over the last 100 years) and particularly destructive volcanic events that can induce catastrophic changes in the shape of a volcanic edifice and its environment7. Laboratory experiments and numerical analyses predicted the occurrence of precursory collapses at depth before the onset of the surface subsidence12 but observations obtained from adequate broadband seismometers were lacking. Until the present study, the Miyake-jima caldera formation was the only known case with evidence of such deep collapses before the faults reached the surface. The deep collapses were suggested from observations of VLP seismic pulses of 20 s width13. However, the timing of the first collapse at depth was not reported. VLP signals observed at volcanoes are generally considered having frequencies between 0.01–0.5 Hz (ref.14) and until the 2000 Miyake-jima event, they were generally considered to result from inertial forces associated with changes in the flow of magma and gases through conduits14. The VLP signals detected during the Miyake-jima caldera formation were explained by different physical mechanisms: (i) a buried geyser model15, (ii) a piston-like model16, and (iii) ring-faulting mechanisms related to shear failure on curved or cone-shaped fault structures18. 46 step-like tilt changes (TC) were observed during the Miyake-jima caldera formation and among them 39 were accompanied by the VLP seismic signals20. The origin of these TC associated with the VLP pulses have been attributed to either a piston model with a vertical rock column intermittently sinking into a magma reservoir21 or to a magma sheet model with a large sill-like magma reservoir expanding cyclically20. Step-like tilt changes accompanied by VLP seismic signals were only reported during and not prior to the 2000 Miyake-jima collapse21. Here, we report for the first-time, ULP seismic signals accompanied by VLP seismic signals associated to precursory collapse at depth. We show the possibility of constraining the timing of the onset of the first collapse at depth and that the 2007 Piton de la Fournaise Caldera collapse may correspond to a piston-like collapse occurring through a ring-fault system.In the past two decades only four caldera collapses have been monitored by dense geophysical networks: chronologically, the 2000 Miyake-jima, Japan; the 2007 Piton de la Fournaise, La Réunion/France; the 2014–2015 Bárðarbunga, Iceland; and the 2018 Kīlauea, Hawai‘i8. An important challenge for understanding and constraining the triggering factors of caldera formation in this range of roof aspect ratio (i.e. 2–4.5) is to detect the first collapse at depth before the surface subsidence8. This should improve volcano early-warning systems. In the case of the 2007 Piton de la Fournaise collapse, the aspect ratio is around 1.7/0.4 = 4.25 assuming a fault surface approximated by a cylinder with a height of 1.7 km and radius of 0.2 km. The radius is derived from photographs obtained just after the main collapse5 and from the extension of the seismicity at depth22. The height is estimated from the location of the shallowest compression compensated linear vector dipole (C-CLVD) earthquakes22. Interestingly, the roof aspect ratio was also high (between 1.9 and 3.8) for the 2000 caldera formation at Miyake-jima23. The historical Dolomieu Caldera collapse, which occurred at Piton de la Fournaise in April 2007, is an unusual case with records from a broadband seismic station and a dense, continuous monitoring network of geodetic and short-period seismic stations. It provides a rare opportunity to study the processes related to early steps of caldera formation.Laboratory-analogue experiments show for roof aspect ratio (i.e. roof depth/piston diameter) between 2 and 4.5 that surface subsidence occurs concurrently with collapse at depth24. A low-elevation fissure opening, possibly triggered by deep magma input24 started on April 2 at 6:00 , only three days before the Dolomieu Caldera collapse. From March 31 to April 2 a lateral magma migration occurred at depth toward the April eruptive vent. The lateral magma migration from the March 30 eruptive fissure to the April 2 eruptive fissure was suggested from GPS observations25. A single lateral magma migration was also proposed24 based on the kinematic continuity since March 30 highlighted by the tilt data, combined with the interferometric data showing a large flank deformation area connecting both March 30 and April 2 eruptive fissures26. A significant increase of seismicity below the Dolomieu summit and beneath the eastern slope of Piton de la Fournaise was observed from the short-period seismic network from March 31 to April 2 with several thousands of volcano tectonic events22. From April 1 at 13:20 to April 4 at 15:44, the seismic crisis was dominated by 315 C-CLVD earthquakes located beneath the summit between the sea level and 0.8 km above. The C-CLVD earthquakes were associated with fluid motion from vertical fluid-filled cracks to a magmatic reservoir22. These events were not coincident with ULP signals accompanied by VLP signals as reported in this study for later precursory collapse events (E2 to E5) occurring on April 5  and the collapse episode led to the development of a caldera volume of 9 × 107 m3 (ref.27).Piton de la Fournaise is a basaltic shield volcano built on the southeastern part of La Réunion Island Fig. , in the 29 and a Quanterra Q330 digitiser. The three seismometers recorded the three seismic components  of ground velocity. The corresponding instrumental responses of the broadband (BH) raw seismic channels (sampling rate of 20 Hz) are flat in velocity in the 1/360–5 Hz frequency range. Data from teleseismic stations of the global seismic network were also used to determine the moment tensor solution for the main collapse event (CE1) and for surface-wave magnitude estimates.We used the seismic station RER of the GEOSCOPE seismological network installed in a 4.7 km-long tunnel, 8.2 km north of the summit Fig. . In 200730.VLP signals displayed dominant frequencies of 0.14 Hz, 0.3 Hz and 0.4–0.5 Hz  were identified from the following procedure: (i) removing the mean signal, (ii) removing the trend, (iii) applying a 5% Hanning taper, and (iv) bandpass filtering between 0.005 and 0.2 Hz with a zero-phase 4-pole Butterworth filter. We use this low corner frequency to investigate if the duration of VLP wave packets reached around 30–65 s during the caldera collapse episode, as observed during the Miyake-jima Caldera collapseThe intervals between two consecutive events decreased from about two hours at the beginning of the sequence  to 30 minutes on April 6  from data recorded at teleseismic stations SUR , BOSA , LBTB , LSZ , KMBO , FURI , LSA , CRZF , DBIC , KMI , MBAR  and TSUM  for 42 collapse events occurring between April 5 at 20:48 and April 14 as six other collapse events records were contaminated with interference from teleseisms.We estimated the relative size of the collapse events from CE1 to CE48 using the surface-wave magnitude MS values are between 3.6 and 4.8  is the 95% confidence interval for the slope and (1.55 ± 0.31) is the 95% confidence interval for the intercept.The estimated .97 Fig. . TherefoE) of all collapse events and precursory collapse events is estimated using the MS values and the formula32 used for the 1968 caldera collapse of Fernandina in the Galápagos archipelago31. The energy release rate is nearly constant from about 20:48 on April 5 to April 7  suggesting a similar source. The best constrained vertical polarization angle (VPA) from the collapse event E2 is 96.5 ± 6.3 suggesting a source located 0.1 km below the sea level ± 1.0 km . This depth range is fully compatible with the relocated seismicity of Massin et al.22 who showed that around 70% of the hypocenters are between the sea level and 0.8 km above the sea level from February 5 to May 1, 200722. It is also consistent with depth range (∼0.5 ± 0.4 km above the sea level) of the first source of deformation located by the GPS analysis25  range recorded in olivine melt inclusions (1.7 km below the summit)33. The similar location, shape and duration of the observed VLP signals recorded before and during the Dolomieu Caldera collapse indicates a repeating process, which clearly started before the surface subsidence.Individual VLP seismic wave packets related to the Dolomieu Caldera collapse show similar waveforms prior to and during the caldera formation  suggests that the Dolomieu Caldera collapse involved several slow earthquakes with long source durations and slow ruptures.The CE2 event was greatly depleted in high-frequency energy content compared to standard earthquakes of similar magnitude  which corresponds to a MW ∼ 4.7 using the equation 3.17 from Aki and Richards37. This value is in the range estimated from the surface-wave magnitude using the Main and Burton39 formula (see Methods) for earthquakes in the Aegean area: between 3.97 × 1015–7.35 × 1017 Nm. We used this relation between MS and M0 to estimate the error bars on converting from M0 (or MW) to MS. We applied this formula38 to estimate the MS value from the M0 of the CE1 event. We used the ± values in this formula to provide a crude estimate of uncertainty in MS. If we assume M0 = 1.53 × 1016 (which was obtained in moment tensor inversion), then MS could be in the range between 3.5 and 5.3. This range is compatible with the MS value of the CE1 event MS ± 1σ ∼ 4.8 ± 0.2 directly determined from the amplitude of surface waves, which is an independent measurement.In order to constrain the mechanical processes occurring at depth during the caldera collapse, we performed moment tensor inversion (see Methods) from surface waves. We analysed the main collapse event (CE1) on April 5 and used horizontal and vertical seismograms Fig.  from 12 ism Fig.  show tha40. Therefore, to estimate the uncertainty of the isotropic, CLVD and DC components, we repeated the inversion using Jackknife method42 at the optimum depth (i.e. 5 km) as shallower depths are not resolved at these frequencies. We then plot the percentage of each component of the moment tensor against the number of stations used in the inversion  with λ1, λ2 and λ3 the eigenvalues of the deviatoric moment tensor and λ1 ≥ λ2 ≥ λ3. If ε = 0 it is a DC earthquake whereas for ε = −0.5 or ε = 0.5 it is a pure CLVD. The parameter ε is −0.42 in the case of the CE1 and the compression axis plunges more than 60°, which corresponds to a definition recently proposed for a vertical-CLVD earthquake18 with a dominant pressure axis. The parameter k defining the relative contribution of the isotropic component to the isotropic and deviatoric moment tensors18 is −0.63. Using the k-ε space  the focal mechanism of the deviatoric fraction of the full moment tensor is close to the closing tensile crack end-member.The estimated moment tensor consists of a dominant isotropic component (57%) and a strong CLVD component (36%) characterized by a near vertical axis of compression and a small double couple (DC) component (7%). Supplementary Fig. In summary, the CE1 earthquake shows a dominant non-double-couple component and both the isotropic and vertical CLVD components indicate a seismic source related to a near vertical pressure axis.43. Slip on curved normal faults can generate vertical-CLVD earthquakes with dominant pressure axes44. The existence of a ring-fault (i.e. curved or cone-shaped dip-slip fault) system can produce a vertical-CLVD earthquake18. Slip on ring-faults could also explain the anomalously long source duration time, a ring-fault seismicity, and observations of scarps of a ring-fault from the field.We can propose plausible source mechanisms to explain the combination of strong isotropic and vertical CLVD components based on our results and on published constraints from field geology, analogue and numerical modelling and seismology. The epicentral locations of earthquakes observed at a caldera can form roughly an elliptical annulus which is a characteristic of ring-fault seismicityτ and seismic moment M0 derived from body-wave waveform modelling for moderate-to-large shallow earthquakes is45τ ≈ 4.52 × 10−6M01/3 where τ is expressed in s and M0 in Nm. A duration of approximately 1–4 s is predicted for the CE1 earthquake with M0 in the range 3.97 × 1015–7.35 × 1017 Nm from this equation. Therefore, the estimated duration of about 20 s for the CE1 earthquake during the Dolomieu Caldera collapse is clearly not common for an earthquake of such magnitude. Such a long duration for a MS 4.8 seismic event supports a slow rupture on a ring-fault18. Interestingly, slow processes were also suggested during the 2000 Miyake-jima caldera collapse with source duration around 30–65 s17.The global average relationship between source duration 46.Several preserved polished surfaces were observed a few days after the first collapse on the scarps of a ring-fault indicating that the shallow subsidence was controlled by inward steep normal faults in sub-surface22 from February 5 to May 1, 2007 form roughly an elliptical annulus similar to that observed at the Rabaul caldera43 in Papua New Guinea during a seismic crisis period from late 1983 to mid-1985. The limits of the ring pattern may correspond to the caldera’s faults. The location of the epicenters observed at the Piton de la Fournaise volcano’s summit suggest an active ring-fault structure beneath the volcano’s summit between 0.8 km above the sea level and sea level.The location of the seismicity is represented in Supplementary Fig. 47:μ is the rigidity, u is the average slip and S is the fault surface.We tested if slip on ring-fault structures can explain the incremental Piton de la Fournaise collapse. The theoretical scalar seismic moment can be described as44. Assuming a ring-fault arc length of 360° and a dip of 85°, the composite scalar moment is 13% of that obtained by summing the scalar moments from each portion of the fault44. We also assume a fault surface approximated by a cylinder with a height of 1.7 km and radius of 0.2 km. The radius is derived from photographs obtained just after the CE15 and from the extension of the seismicity at depth22. The height is estimated from the location of the shallowest C-CLVD earthquakes22. The cumulative seismic moment of the collapse events (CE1 to CE48) and of the events occurring before the caldera formation (E2 to E5) is around 2.28 × 1016–3.04 × 1018 Nm. Using Eq.  where M0 = 2.28 × 1016–3.04 × 1018 Nm, μ = 3 × 1010 Pa, and S ~ 2.1 × 106 m2. Therefore, u is between 3 to 365 m. This estimated range of values is compatible with the observed final depth of the caldera (340 m)27 but the maximum value is lower than the estimated total collapse of 450 m computed by Michon et al.50 based on the final volume of the caldera divided by the observed surface of a piston. Due to the uncertainty on the dip angle, on the fault surface geometry and on the rigidity, this estimation above all shows that ring-fault structures can produce the incremental Piton de la Fournaise collapse. We applied the same approach to all the collapse events before and during the caldera formation. The results show a quasi-linear increase of the displacement from 16:19 on April 5 to April 7  where M is the isotropic part of the total seismic moment, λ and μ are the Lamé parameters and ΔVcrack is the volume change of the crack volume. In this equation, the isotropic component is considered to be 57% as for the CE1 event. This equation correspond to the case of a flat crack volume with arbitrary shape and curvature51. From this equation, we obtained ΔVcrack between 2.6 × 105 and 3.5 × 107 m3 using, and assuming λ = μ, μ = 30 GPa48 and using the isotropic part of the total seismic moment [2.28 × 1016–3.04 × 1018] × 57%~[1.30 × 1016–1.73 × 1018] Nm. This volume is up to around 39% of the 9 × 107 m3 final volume of the caldera27. Therefore, this mechanism may contribute partly to the CE1 event.The relationship between the moment tensor and the volumetric change for opening or closing cracks, expansion or contraction of a spherical source is described by several authors16 and 1.73 × 1018 Nm), the following equation51: M = ΔVsphere(λ + 2μ) where ΔVsphere is the volume change of the spherical reservoir, and assuming λ = μ and μ = 30 GPa. The total isotropic volume change of the reservoir associated with all collapses is between 1.4 × 105 and 1.9 × 107 m3, which is up to around 21% of the final caldera volume. Although, this mechanism may contribute partly to the CE1 earthquake, its potential contribution is around 54% of the closing tensile-crack mechanism.The isotropic volume change associated with all collapses can be estimated using the isotropic part of the estimated total seismic moment of all collapses  and the large CLVD component (36%) of the CE1 event indicates a downward contraction which could be due to the near vertical compression of the magma reservoir. A collapsing piston model may therefore explain this near vertical compression and is also compatible with a crack like geometry4 and with previous results from the analysis of the seismicity and of the GPS data.At Miyake-jima, the source of the VLP signals prior to and after the first caldera collapse was attributed to the pressurisation of a magmatic reservoir impacted by a falling rock columnst to 5th between the sea level and 0.8 km above the sea level22. Massin et al.22 considered the C-CLVD earthquakes as a precursor of the Dolomieu Caldera collapse. GPS data from the geodetic permanent network were processed by Peltier et al.25 using 3D elastic model based on the mixed boundary element method52 combined with the neighbourhood algorithm53. A migration of the source of deformation was observed from February 21st-March 29th 2007 to April 5th–6th  during magma withdrawal from the magma reservoir can explain the migration and change of shape determined with an elastic-deformation source. They proposed that deflation associated with host-rock fracturing can be the cause of the underestimation of the true magma reservoir depth on April 5th–6th. Holohan et al.12 proposed that the rock column above the magma reservoir experienced an initial phase of sub-surface fracturing from April 2nd–5th, then from April 5th–6th a piston-like collapse occurred through a ring-fault system.Earthquakes with C-CLVD and normal fault mechanisms occurred just before the main collapse event (CE1) from April 112 suggesting a possible piston-like collapse on April 5th–6th, 2007 during Piton de la Fournaise collapse once the through-going ring-fault system has developed.Slip on ring-faults could explain some observations such as anomalously slow source processes, observations from the field and the characteristic ring-fault seismicity. However, the dominant isotropic component obtained from the moment tensor inversion cannot be explained by a pure ring-fault mechanism whereas it could be explained by a piston-like model. Based on the previous arguments, our preferred model to explain the 2007 Piton de la Fournaise Caldera collapse is a piston-like collapse occurring through a ring-fault system. In this model, a rock column overlying a magma reservoir is delimited by ring-faults and collapsed due to the decrease of pressure of the magma reservoir associated with the lateral magma migration. This model is fully compatible with recent numerical modelling24. Tilt data24 permits the identification of several key seismic events that preceded the April 5 main caldera collapse . This deflation may be induced by magma lateral migration toward the April eruptive vent. The tilt signal related to the lateral magma migration is only characterized by a period of deflation whereas shorter tilt signals associated with the collapses events show inflation-deflation cycles , similar to those observed during the following collapse events (CE1 to CE48)  Figs  and 5a. 3/s from MODIS data56 and April 6 at 12:00 with a value higher than 200 m3/s from a field survey27. From April 8 to May 1 the eruption continued at a low intensity50. The time difference ∆t between two successive tilt signals related to collapse events was measured in a previous study50. ∆t clearly decreased, whereas the magma outflow rate increased from April 5 20:48 to April 6 at 12:00. ∆t then increased, whereas the magma outflow rate decreased until April 8 at 00:09. Our study  and incompatible trace element ratios (La/Sm) is observed in lavas57 erupted during the period April 4 to 6 with respect to those erupted during the whole 1999-March 2007 period  part of the plumbing system33.A previous studyiod Fig. . This doet al.8 highlight the importance of the roof aspect ratio (i.e. roof depth/piston diameter) in the fault formation and in the onset of the caldera formation. For low aspect ratio (≤1), the caldera collapsed as a coherent piston and the caldera surface subsidence is observed from the onset of the caldera formation. This was likely the case during the Fernandina caldera formation in 196831 where the reservoir diameter was around 3.2 km (ref.23) and the depth of the magma reservoir roof was estimated to be shallower around 1 km corresponding to a roof aspect ratio of around 0.3. For the 2014–2015 caldera development of Bárðarbunga, the depth of the magma reservoir was estimated to be much deeper (~12 km)6. This depth was constrained from lava chemistry, surface gas composition and geodetic modeling, providing a roof aspect ratio of 1.6 considering the diameter was around 7.5 km (ref.6). In the case of the 2007 Piton de la Fournaise collapse, we obtained a higher aspect ratio around 4.25. Interestingly, the roof aspect ratio was also high (between 1.9 and 3.8) for the 2000 caldera formation at Miyake-jima23. This therefore suggests that precursory collapses at depth at Piton de la Fournaise and at Miyake-jima are likely due to the roof aspect ratio.Precursory collapses at depth were only reported before the caldera formation of Miyake-jima and in this study we show their occurrence before the 2007 Dolomieu Caldera formation. What could explain their occurrence at both of these volcanoes and not prior to other caldera formation such as the 2014–2015 Bárðarbunga caldera development? As mentioned earlier, multiple analogue experiment of caldera formation from Roche 58, the caldera floor subsidence was likely induced by the lateral withdrawal of magma from the summit reservoir system7 as proposed in this study. Similarly to for the Dolomieu Caldera collapse, the collapse episode was characterized by several collapse events and moment tensor inversions suggest a complex source mechanism associated with dominant changes in volume7.Although the 2018 Kīlauea Caldera collapse episode was not reported as a piston-like collapse59 collapse at depth were possibly triggered by the pressure decrease in the magma reservoir. Collapse at depth occurred following four cycles (E2 to E5) each characterised by two steps. Firstly, a downward motion of a rock column without visible surface rupture through a ring-fault system surrounding a magma reservoir that generated the first part of an ULP signal: a tilt-step signal accompanied by VLP signals  occurring at depth before the main event and 4 other events occurring at the end of the sequence (CE45–CE48) after April 8 at 00:09. This study demonstrates the possibility of detecting the first collapse (E2 event) at depth approximately 20 hours before the surface rupture and the caldera formation from the identification of ULP signals accompanied by VLP signals. Furthermore, the likely source mechanism of the caldera collapse can be identified from both records from this local very sensitive seismic station and teleseismic stations from the global seismic network. These observations are crucial for volcanic hazard assessment and particularly for volcano early-warning systems that may help in the decision of visitors and/or population evacuation at critical volcanoes. This study shows the importance of considering at least a broadband seismic station in volcano monitoring, particularly for those that can be potentially devastating by their eruptions or collapses.Analysis of ULP signals accompanied by VLP signals recorded by a nearby broadband seismic station can thus provide important constraints on the timing of the 2007 Piton de la Fournaise Caldera collapse onset. A total of 44 collapse events was reported before this studyMS was determined from the following classic equation37:A is the ground amplitude of Rayleigh wave in the vertical component in microns; T is the period near 20 s; and Δ is the epicentral distance in degrees.36 proposed to define the total scalar seismic moment as Mtot = MISO + MDEV where MISO = |(m1 + m2 + m3)/3| is the isotropic moment tensor and MDEV = max(|mj − (m1 + m2 + m3)/3|; j = 1, 2, 3) is the deviatoric moment tensor, and m1, m2, and m3 are the eigenvalues of the seismic moment tensor with m1 ≥ m3 ≥ m2.Bowers and HudsonMS values using the following formula39:We estimated the scalar seismic moment of each collapse event (CE1 to CE48) and of the events occurring prior to the caldera formation (E2 to E5) from the calculated To better constrain the seismic source associated with the main collapse event, we analysed three-component broadband data from permanent stations retrieved from the Incorporated Research Institutions for Seismology Data Management Center (IRIS DMC). Seismic stations with epicentral distances up to 60 degrees from the Dolomieu Caldera were selected. From an initial set of 50 stations only ones with signal–to–noise ratio (from the power spectrum) greater than 2 were considered. Subsequently, the quality of all waveforms was checked manually. The time window length is restricted to 2000 seconds from the origin time, which covers the full waveform for all seismic stations. We used a source time function with a triangle shape of 10–second half–duration, i.e. total duration of 20 seconds as an anomalously long source duration was suggested by the low frequency content of the CE1 event and as a grid-search for source time function duration provided an upper bound for the source duration of 20 s . The polarisation analysis was performed using a 667 s window around the onset of the signal. The covariance matrix resulting from this analysis was determined from the principal component analysis (PCA) applied to the three components seismic records69 (Supplementary Information). The horizontal and vertical polarisation angles were measured from PCA of the particle motion  and the vertical polarization angle (EVPA) were computed as described in the supplement text material following a formula proposed by D. Reymond70.We performed a polarisation analysis using the three-component seismic station RER. Repeating collapse events recorded at RER were characterised by notable ultra-long period signals . The presence of seismic anisotropy in the volcanic edifice could also result in a deviation of horizontal polarization angle69. However, the horizontal polarization angles of the E5-CE48 point toward the fissure of the March eruption (Supplementary Fig. Two other effects: the sensor misorientation and the presence of seismic anisotropy in the volcanic edifice could also disturb the signal polarisation. At RER permanent seismic station, the exact azimuths of the so-called N-S and E-W components have been checked with a gyrocompass and found to be N2.3° and N89.5°, respectively. This small sensor misorientation of each STS-1 horizontal component was neglected during the analysis. Power spectral densities computed at RER station show that the micro-seismic noise related to the swell activity occurred at higher frequencies than the frequencies considered during the polarisation analysis: mostly between 0.05 and 0.33 Hz (ref.The Supplementary Table Supplementary Information


Fermented broth has a long history of applications in the food, pharmaceutical and cosmetic industries. Recently, the use of fermented broth in skin care products is in ascendance. This review investigates the efficacy of fermented broth in inhibiting tyrosinase and melanogenesis. Possible active ingredients and hypopigmentation mechanisms of fermented broth are discussed, and potential applications of fermented broth in the cosmetic industry are also addressed. In the global beauty industry, multinational corporations such as L’Oreal, Estée Lauder, and Procter & Gamble earn billions of dollars every year by selling skin care products and cosmetics . The idel-tyrosine produces l-3,4-dihydroxyphenylalanine (l-DOPA), which is oxidized to the corresponding o-quinone [When humans are exposed to unlimited UV light, melanogenesis causes hyperpigmentation through the overproduction of melanin, which causes the skin to tan . Tyrosin-quinone . Tyrosin-quinone . Althoug-quinone , skin li-quinone ,15,16,17-quinone . Enhance-quinone ,20, and -quinone .l-ascorbic acid [l-ascorbic acid is heat sensitive and degrades easily [Tyrosinase inhibitors such as bic acid ,23,24, kbic acid ,26,27, ebic acid ,29,30, tbic acid ,32,33, abic acid ,35,36 has easily ; kojic as easily  and has s easily ,40; ellas easily ; the mels easily ,43. Epids easily , and ants easily . Becausein vitro, or they are not classified to hypopigmentation agents. This study investigates the difference between tyrosinase inhibitors and melanogenesis inhibitors of fermented broths including active ingredients, signal pathway regulators and mechanism.Mushroom tyrosinase has been used for prescreening hypopigmentation agents because it is commercially available. However, it was found that many melanogenesis inhibitors didn’t exhibit inhibitory effects on mushroom tyrosinase activity ,47,48,49Microorganisms such as bacteria, yeasts, and molds are commonly employed in fermentation . For exaFermentation is a metabolic process in which sugars are converted into acids, gases, and alcohol , mainly Aspergillus oryzae fermented broth [Eight of twenty five fermented broths were proved to be tyrosinase and melanogenesis inhibitors ,77,78,79ed broth  but whiled broth , 3'-ODI ed broth , indicatLactobacilli and Bifidobacteria are the two major genera of bacteria of which the broth is used to suppress melanogenesis; scientists have long used them to solve dermal problems [Lactobacilli and Bifidobacteria to inhibit melanogenesis. However, the mechanism of action of fermented broth in skin pigmentation regulation remains unclear. The possible active ingredients that could suppress melanogenesis are listed in The components of fermented broth include carbohydrates, alcohols, alditols, glycols, and other metabolic products . Accordiproblems . VariousLactobacillus rhamnosus is crucial to inhibit tyrosinase activity and can reduce melanogenesis [The lactic acid contained in ogenesis   and byelyankacin purified from fermented broths of seed medium/ectively ,76 (Tablectively ,76 (TablLeuconostoc mesenteroides isolated from kimoto induced a decrease in melanin content in B16F0 murine melanoma cells through inhibiting tyrosinase activity, tyrosinase translation, or accelerating its degradation but did not inhibit tyrosinase activity under cell-free conditions [L. mesenteroides has potential use as an effective anti-melanogenic agent. However, the active ingredient responsible has still not been determined.Autolysate of nditions . The autSaccharomycopsis fermented broth [Cosmetic products using probiotics such as bacteria and yeast include aftershaves, antiaging serums, face and body lotions, hydrating creams, toothpastes, sanitary napkins, tampons, shampoos, douche gels, and oral care gums . Howevered broth ,102 thated broth .This study verifies that fermented broth can be applied in reducing melanogenesis. Active ingredient levels of fermented broth are increased compared to unfermented broths. There are lots of fermented broths still needed to be tested as melanogenesis inhibitors. In addition to inhibiting tyrosinase activity, melanogenesis inhibitors can modulate different regulators of melanogenesis via the cAMP or MAPK signal pathways. In general, optimized fermented broth culture is promising for the development of novel skin whitening ingredients.


Quercus spinosa, and evaluate the impacts of historical range shifts, climatic variation, and landscape factors on this species. The population topology and genetic divergence of the Cenozoic were inferred by a site frequency spectrum based composite-likelihood approach which is a novel strategy for maximizing the utility of linked SLAF markers. The overall genetic structure using model-based and model-free clustering methods was consistently identified as two geographically distinct genetic clusters. A deep divergence between two natural lineages  was observed. The demographic modeling and Niche reconstruction indicated that the two groups were diverged in the late Miocene and then presented as two distinct genetic lineages. With the Quaternary glacial climate fluctuation, two groups had continuous asymmetrical secondary contact and gene exchange in the Sichuan Basin during the last glacial maximum. Besides, a significant relationship between genetic distance and geography in all individuals was identified by the Mantel test. Overall, this study 1) contributes to a better understanding of the role played by Quaternary climatic fluctuation in the present-day distributions of Q. spinosa; 2) provides a comprehensive view of the genome-wide variation of sclerophyllous forests in ecological adaptive evolution; 3) indicates that dispersal limitation and ecological divergence contribute to the genome-wide differentiation of Q. spinosa, which supports a hypothesis that complex geography and climatic changes strongly influence the evolutionary origin and history of the species.Effectively identifying the genetic structure and related factors of a species can facilitate understanding the evolutionary history of the species. Phylogeographic patterns and genetic data are essential in investigating the species historical processes and diversification that response to environmental, climatic and geological influences. In this study, Specific Length Amplified Fragment Sequencing (SLAF-seq) data and ecological niche models (ENMs) are combined to identify the genetic structure and demographic modeling of  The genetic diversity and population structure of species are largely determined by intrinsic traits, external zoology environment including anthropogenic activities and historical events . PhylogeQuaternary glaciation (about 2–3 million years ago) involved multiple successive cycles of glacial and interglacial events, which brought dramatic changes in temperature and precipitation on earth . The resQuercus sect. Heterobalanus , the Qin-ling Mountains, and the subtropical regions of Central China. Q. spinosa has the intrinsic traits of long generation times, large effective population sizes, and limited dispersal distance  What is the population structure pattern of Q. spinosa within the whole genome? ii) Which differentiation model could be used to better explain the formation of the spatial distribution pattern of Q. spinosa? iii) Is there any evidence of local adaptation maintaining the genetic integrity of the species driven by geographical isolation and environmental factors?distance , which iQ. spinosa accessions from 38 wild populations, including all the relevant regions for the species that were described in Flora of China as a reference  in size were isolated and diluted for paired-end sequencing on the Illumina HiseqTM 2500 sequencing platform  at Beijing Biomarker Technologies Corporation. The raw reads were processed for each sample using the software Dual-index . In order to ensure the quality of sequencing, all paired-end reads were trimmed to 125bp×2 in length. These cleaned reads were stored in the NCBI SRA database (http://www.ncbi.nlm.nih.gov/sra/) under the BioProject ID PRJNA549662. Single nucleotide polymorphism (SNP) calling from multiple samples was performed using SAMtools (-6)  library sequencing according to the procedures described by Sun with a few modifications . In ordeal-index . After fSAMtools  and GenoSAMtools . The parSAMtools  and PLINSAMtools . In addiols (-6)  were scrQ. spinosa. For hierarchical population-clustering analyses, the maximum-likelihood-based clustering algorithm was implemented in the program ADMIXTURE (K) without a priori population designation. Then, a series of tests were conducted while the value of K was changed from 1 to 10, and accessions were assigned to a corresponding population based on their maximum membership probabilities. The most suitable K was determined by comparing threefold cross-validation (CV) error values across different values of K as described in the ADMIXTURE manual. For multivariate analyses, a discriminant analysis of principal components (DAPC)   was conds (DAPC)  prior ans (DAPC) . The DAPs (DAPC)  was impls (DAPC) . The opts (DAPC)  for sequanalysis .http://itol.embl.de/). In order to adopt a phylogenetic perspective, SNPs were used to generate maximum-likelihood trees. RAxML version 8.0.5  was usedQ. spinosa populations was calculated by the “ape” package in R studio  of the SNP alignment in the program δaδi v1.7 . SFS-basQ. spinosa across its whole range was registered in the Global Biodiversity Information Facility  and the China Virtual Herbarium  database. Google Earth (http://ditu.google.cn/) was used to determine the latitude and longitude when occurrence records lacked exact geo-coordinates. To avoid the impact of spatial autocorrelation on the results, the sample recorded the distance between latitude and longitude of which is below 0.4° were removed. In total, 211 unrepeatable geo-referenced occurrence records were collected.In order to verify whether the local adaptation could maintain the genetic structure of the species impelled by environmental factors, it is necessary to understand the climate niche of those plants and identify their suitable growing areas under current and future climate conditions. The geographical distribution of http://www.worldclim.org/) at 2.5-min resolution. This coarse resolution could leave out relevant small-scale environmental heterogeneity, which may be relevant to maintain divergence. The species distribution model (SDM) in current climate conditions was inferred with the maximum entropy approach implemented in MAXENT 3.3    and trueve (AUC) . The con-6) and used to investigate the genomic evolution of the population of 130 Q. spinosa accessions.After the raw data was qualified, it could be further used for data mining and additional analyses. Across the 130 accessions examined in this study, a total of 304.69M reads were obtained. The reads length of samples ranged from 1,125,840 to 6,844,685 bp . The GATQ. spinosa indicated that a value of K = 2 was associated with the lowest cross-validation procedure , and 25 populations clustered into another separate eastern group (cluster 2) Figure 22 = 0.2543, p < 0.001, 999 permutations)  detection of individuals from each group was implemented first. Based on the maximum value of SFS and the number of individuals of each group, the final dataset was projected to a size of 52 individuals from western group and 78 individuals from eastern group , yielding 58,353 SNPs. Regarding all levels of complexity, the Sec_contact_asym_mig_size model with the lowest AIC scores (Q. spinosa had divergence in isolation for a long time (T1 = 8.15). Then the two groups in recent periods had the secondary contact with asymmetrical gene flow (T2 = 0.11). The direction of gene flow was from the western group to the eastern group during this period (m12 = 12.58 migrants/generation with a 95% CI: 11.00–20.47 vs. m21 = 1.46 with a 95% CI: 0.82–1.50).According to the result of ADMIXTURE, the populations of Q. spinosa, the geographic distribution maps were generated to predict areas where Q. spinosa might emerge. The model performance for Q. spinosa was better than random (AUC = 0.996). Thus, the model performed well in predicting the suitable habitat for the species. The ENMs revealed that the suitable areas for Q. spinosa in last interglacial period were mainly located in Hengduan Mountains. At the beginning of the glacial period, the temperature decreased. The suitable areas of Q. spinosa were expanded during the last glacial maximum. The species had the most extensive habitat in this period. At present, the climate became much warmer than the glacial period. The suitable habitat areas for Q. spinosa were predicted to locate in the Qin-ling Mountains and HHM. In the region located between the two mountains, the suitable habitats were continuous, which presented a strip-shaped distribution in the Sichuan Basin. In other regions, the ecological niche presented a fragmentation distribution  could get the consistency of individual membership assignment   Figure 4Himalays  and Taxus region .The first uplift of Qinghai-Tibet Plateau (QTP) began around 40 Ma . Some stQuercus sect. Heterobalanus was closely related to the uplift of the HHM   . The enh10–8 Ma) . This mi10–8 Ma) , and be 10–8 Ma) , which iQ. spinosa. During the glacial periods, the monsoons were blocked by the North-South ranges in the HHM regions  to LGM (0.021–0.018 Ma), which was similar to other alpine plants reported in this region, e.g., Picea likiangensis, Picea wilsonii  , the cold climate might continue until the late Ionian stage (0.3–0.126 Ma) . However the HHM . Besideswilsonii , and Taxlichiana . The demlichiana . The suiarlesii) . The genQ. spinosa. All reads passed the quality controls. Finally, 58,353 consensus SNPs were developed for the population genetics analyses. The results indicated that large amounts of high quality reads almost covered the entire genome, which provided more comprehensive theoretical basis for the following research. The multidisciplinary approach combining molecular markers, ENMs, and demographic modeling strongly supported that the geological and climatic event since Miocene, and Quaternary climatic oscillations triggered the differentiation, evolution, and range shifts of Q. spinosa. The results promote deep insights into the diversification and evolutionary dynamics of sclerophyllous species in the HHM.This study used thousands of genome-wide SNPs to produce the first range-wide map of demographic model in http://www.ncbi.nlm.nih.gov/bioproject/549662. Publicly available datasets were analyzed in this study. These data can be found here: G-FZ and M-MJ contributed to the conception of the study. LF and JY collected the materials. M-MJ performed the data analyses and wrote the manuscript. LF, JY, Y-CY, and X-DC helped perform the analysis with constructive discussions. All authors contributed critically to the drafts and gave final approval for publication.This work was financially supported by the National Natural Science Foundation of China .The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.