Covalent organic frameworks (COFs) have been at the forefront of porous-material research in recent years. With predictable structural compositions and controllable functionalities, the structures and properties of COFs could be controlled to achieve targeted materials. On the other hand, the predesigned structure of COFs allows fruitful postsynthetic modifications to introduce new properties and functions. In this review, the postsynthetic functionalizations of COFs are discussed and their impacts towards structural qualities and performances are comparatively elaborated on. The functionalization involves the formation of specific interactions  and chemical reactions (oxidation/reduction reaction) with pendant groups, skeleton and reactive linkages of COFs. The chemical stability and performance of COFs including catalytic activity, storage, sorption and opto-electronic properties might be enhanced by specific postsynthetic functionalization. The generality of these strategies in terms of chemical reactions and the range of suitable COFs places them as a pivotal role for the development of COF-based smart materials. N. N3) andx-TPB-DMTP-COFs by reacting alkynyl (-C≡CH) pendant groups with azide-containing pyrrolidine (N3-Py) [S)-Py]x-TPB-DMTP-COFs contained chiral and catalytic active pyrrolidine moieties. Thus, they have potential as a chiral organocatalyst. Remarkably, [(S)-Py]x-TPB-DMTP-COFs were crystalline with a significant porosity intake. As a heterogeneous chiral organocatalyst, [(S)-Py]x-TPB-DMTP-COFs could catalyse the organic Michael-addition reaction—a basic C–C bond-formation reaction for synthesizing various important synthetics and natural products [S)-Py]x-TBP-DMTP-COFs were able to promote asymmetric C–C bond formation in water under ambient temperature with prominent activity, enantioselectivity, recyclability and environmental benignity compared to the other metal-based catalysts. For instance, [(S)-Py]0.17-TBP-DMTP-COF proceeded smoothly and cleanly to C–C bond formation with 100% conversion in 12 h (e.e. = 92% and d.r. = 90/10), which largely exceeded the molecular (S)-Py catalyst. Furthermore, several other COFs have been functionalized via triazole linkage, including the transformation from [CH≡C]x-H2P-COF into [Pyr]x-H2P-COF and [CH≡C]0.5-TPB-DMTP-COF into ([uracil]0.5-TPB-DMTP-COF) with preservation of crystallinity and enhanced performance for catalyst and adsorbent applications, respectively [60) has also been anchored on the pore surface of predesigned X%[N3]-ZnPc-COF to afford donor–acceptor heterojunction-based [C60]y-ZnPc-COF via covalent triazole linkage [60]y-ZnPc-COF exhibited a photoelectric phenomenon with segregated donor–acceptor alignment in which electron-accepting bucky-balls were spatially confined within the nanochannel via triazole units. In addition, it performed photo-induced electron transfer facilitated by an electron-donating COF scaffold and electron-accepting bucky-ball molecules. COFs with high energy-storage performance were achieved by the covalent introduction of redox-active species  (N3-Py) . The resproducts . In addiectively . Meanwhi linkage . As pred species . In anotproaches .x%-H2P-COFs) were synthesized and employed as scaffolds to demonstrate the structural functionalization of COF via an ester bond [2C]x%-H2P-COFs). This functionalization allows structural rigidity preservation with a well-organized functional constituent within the pore channel and substantial porosity intake. At the end, [HO2C]x%-H2P-COFs were employed as solid sorbents for CO2 storage and separation. Remarkably, the [HO2C]x%-H2P-COF sample demonstrated dramatic CO2-uptake enhancement relative to [HO]x%-H2P-COF. In addition, the ideal absorbed solution theory (IAST) calculation was performed based on their CO2 and N2 sorption isotherms, revealing high CO2-absorption selectivity (adsS) with 323 for [HOOC]100%-H2P-COF (at 0.1 kPa)—much greater than [HO]100%-H2P-COF (only 18). Indeed, this performance was much higher than for other reported adsorbents. On another occasion, a predesigned hydroxyl-appended 3D COF (3D-OH-COF) was prepared and further functionalized via an ester bond  and Fe3+ ions (IAST selectivity = 18) for a solution containing 5% Nd3+ ion and 95% Sr2+ or Fe3+ ions.Ester bonds have judiciously been applied to functionalize COFs, which were efficiently obtained under a mild and metal-free ring-opening reaction between anhydride and hydroxyl (-OH) groups Fig. b 22]. H. H22]. Hter bond . The rea2) and carbonyl groups 2 was designed by reducing its parent nitro-functionalized COF (TpBD(NO2)2) x%-Py-COFs afforded [Et4NBr]x%-Py-COFs (x = 25–100)  exhibited elevated CO2-uptake capacities and higher isosteric heat absorption (stQ) than those [HO]x%-Py-COFs samples and was able to catalyse the transformation of CO2 into value-added chemicals (N-formylation reaction). For instance, [Et4NBr]50%-Py-COF accounted for high CO2-uptake capacity , which was the highest value compared to several reported COFs. Meanwhile, with 5 mol% [Et4NBr]50%-Py-COF, a solely formylated product of N-methylaniline was obtained with an isolated yield of 94% under mild conditions, while [HO]50%-Py-COF could only exhibit 32% conversion under similar conditions. The generality of this postsynthetic functionalization was also demonstrated on other 2D COFs. For example, the functionalization of [OH]x%-TD-COFs into [BE]x%-TD-COFs transformed the neutral skeleton of the COF scaffold into zwitterionic-functionalized COF and the design of ionic-based [SO3−]-DhaTab COF was obtained by reacting DhaTab COF with 1,3-propanesulton in toluene -COFs) was also reduced (treated with PPh3 in methanol) to give the corresponding amine-containing COF (X%[NH2]-COFs) -COFs) ,51.Unlike the covalent bond that was formed through sharing electrons, coordination-bond formation involves the donor–acceptor electron transfer between the active sites of the components .Meanwhile, ionic interaction occurs on the dipolar region between the two active sites, establishing engagement forces between the components ,54. Thess- or p-type orbitals may facilitate the formation of coordination bonds with metals . For example, imine linkages found in imine-linked COFs are able to govern coordination bonds with metals or metal ions . I. I56]. Ireaction . Meanwhimethanol . Howevere Re-COF . The res2 at room temperature to afford Ni-DBA-3D-COF  in which the Pd ions were assumed to be coordinatively bonded on solely nitrogen of a particular imine linkage within the skeleton  ethylenediamine  has been considered as an attractive moiety for coordination chemistry due to its ability to hold metal ions . T. T2 at rskeleton . The X-rtal ions . In linetal ions . This trtalation . The JUC′-BPyPh was performed via sequential impregnation treatment, where MnCl2 was previously impregnated to give Mn@Py-2,2′-BPyPh and followed by treatment with Pd(OAc)2 to afford bimetal Mn/Pd@Py-2,2′-BPyPh  with the ability to catalyse a one-pot addition–oxidation reaction 17-COF by simply mixing the COF with the chloride salt solution of the respective metals and afforded [MOOC]17-COFs . As predicted, the resultant hybrids exhibited enhanced ammonia uptakes relative to the bare COF.The incorporation of a multi-metal component into the pore of COFs has also been demonstrated. The successful docking of bimetallic salts of Mn/Pd into the pore of a dual-coordinative site containing Py-2,2yPh Fig. c 67]. B. B′-BPyPreaction . Furtheromponent . VariousxOy@COF hybrids. The Au nanoparticles (Au(0)) were deposited within the channel of imine-linked TpPa-1 by reducing (using NaBH4 solution) the deposited Au(III) ions in Au(III)@TpPa-1 to give Au(0)@TpPa-1  and no catalytic activity was observed for the COF-TpPa-1 sample. Meanwhile, the Pd(0)@TpPa-1 has also been obtained under similar procedures and further employed as a catalyst for both C–C Sonogashira/Heck coupling and C–H activation reactions . T. TxOy@COeactions . Furthereactions ,76.3CN solution of ruthenium chloride (RuCl3) and further reduced by NaBH4. Notably, the hybrid showed enhanced catalytic performance for a one-pot solvent-free tandem reaction of imine synthesis from alcohols ,9089,90]-300-AR) . The red3.Et2O, chloranil and toluene for 72 h . T. T92]. Tfor 72 h . DrasticOF) Fig. c 94,95],953.Et2O2SO4, 14.8 M H3PO4 and 9 M H2SO4 in dimethyl sulfoxide (DMSO)) for 1 day. Although the linkage transformation discussed in this section mainly utilizes imine linkage, other linkages may also possibly be functionalized via a certain reaction or treatment.give thiazole-linked COF (COF-921) or with 2,5-diaminohydroquinone dihydrochloride in DMF under oxygen atmosphere to obtain oxazole-linked COF (LZU-192), respectively . These lAs highly porous materials, COFs are perfect porous confinement materials acting as hosts to accommodate guest molecules with controlled quantities via the host–guest chemistry approach. This confinement property involves weak forces that have been well studied in general supramolecular chemistry including van der Walls, π–π interaction and hydrophobic/hydrophilic interactions .60 molecules were incorporated into the channel of the highly stable, electronically conjugated 2D phenazine-linked COF (CS-COF) via host–guest chemistry to obtain donor–acceptor-based CS-COF⊃C60 , [Co(η5-C5H5)2] and [Ru(cod)(cot)] were loaded into the pore of COF-102 to obtain (FeCp2)4@COF-102, (CoCp2)4@COF-102 and [Ru(cod)(cot)]@COF-102 [Another piece of sophisticated work was loading ors Fig. b 109]. . N-heter in COFs . Meanwhi@COF-102 . InteresCOFs materials with tunable structural topologies and high thermal/chemical stabilities provide a versatile postsynthetic functionalization platform to enhance their psychochemical properties and performances toward specific applications. The manageable porosities and functionalities via the bottom-up design of COFs allow judicious incorporation of constituents that can be bonded by strong covalent bonds, ionic/coordination forces and host–guest chemistry interactions. Nevertheless, their linkages can also be postsynthetically functionalized to improve their structural stability. Furthermore, the resultant functionalized COFs with particular hybrid or composite fashions show outstanding performances in the field of catalyst, gaseous uptake–release, optics, energy storage and so on. In the future development of COFs, we assume that there are still many gaps left for further explorations, especially in functionalization of the available linkages that are less studied. In addition, incorporations of functional constituents via host–guest chemistry so far have been mainly developed for electronic and energy-storage applications, thus investigations in wider sophisticated applications are still highly demanded. Last but not least, the postsynthetic functionalization of 3D COFs is still less studied; thus, continuous efforts in the development of 3D COFs may need special concern.


The ubiquitin proteasome system (UPS) is a protein degradation machinery that is crucial for cellular homeostasis in eukaryotes. Therefore, it is not surprising that the UPS coordinates almost all host cellular processes, including host–pathogen interactions. This protein degradation machinery acts predominantly by tagging substrate proteins designated for degradation with a ubiquitin molecule. These ubiquitin tags have been involved at various steps of the innate immune response. Hence, herpesviruses have evolved ways to antagonize the host defense mechanisms by targeting UPS components such as ubiquitin E3 ligases and deubiquitinases (DUBs) that establish a productive infection. This review delineates how herpesviruses usurp the critical roles of ubiquitin E3 ligases and DUBs in innate immune response to escape host-antiviral immune response, with particular focus on retinoic acid-inducible gene I (RIG-I)-like receptors (RLR), cyclic-GMP-AMP (cGAMP) synthase (cGAS), stimulator of interferon (IFN) genes (STING) pathways, and inflammasome signaling. The Herpesviridae are a family of large viruses that contain double-stranded DNA genomes and ubiquitously cause a range of human diseases of varying levels of severity . They arThe UPS is completed through a cascade of three distinct enzymes that modify target proteins via conjugation of ubiquitin ,13,14,15Unlike E1 and E2 enzymes, the specific recognition of substrates mainly relies on E3 ubiquitin ligase. E3s, estimated to more than 600 different mammalian members, are currently classified into three major groups according to structural similarities of their domain and mechanisms of their catalytic activity. These groups are the really interesting new gene (RING)-type, the E3 ligase of the homologous to E6-associated protein (E6-AP) carboxyl terminus (HECT)-type, and the RING -between-RING (RBR)-type E3 ligase families ,26,27,28OTU) of fruit flies. In human, 16 members of OTUs have been identified that mainly regulate cell-signaling cascades. Generally, the OTUs are composed of catalytic OTU domain which possesses putative catalytic cysteine and histidine residues and the ubiquitin interaction domain, such as a UBA (ubiquitin associated) domain, UIM (ubiquitin interacting motif) domain, or ZnF (Zinc finger) domain [DUBs are proteases that catalyze either complete deubiquitination or trimming of Ub chains from proproteins, substrates, or their degradation remnants . As ment) domain ,48,49. T) domain ,51. The ) domain ,54,55,56) domain . While t) domain ,59. More) domain . Unlike ) domain ,61,62.Since DUBs are proteases, regulations of deubiquitination nearly depend on expression and localization of substrate cleavages. The expression levels of DUBs in the cell can be modulated at the transcriptional level in a stimulation-dependent manner . For insRIG-I like receptor (RLR) is a family of DExD/H box RNA helicases that functions as viral RNA sensors. The RLR family includes three members: RIG-I, melanoma differentiation-associated protein 5 (MDA5), and LGP2 (laboratory of genetics and physiology 2). All RLRs contain a C-terminal domain (CTD) and an intermediate RNA helicase domain. Except for LPG2, RIG-I and MDA5 harbor the N-terminal caspase activation recruitment domains (CARDs), and the CTD which is responsible for recognition and binding of RNA . InteresMounting results report that many E3 ubiquitin ligases have been involved in RLR signaling at various steps of signal transduction clearly pointing out their impact on signaling . For insAs shown in E3 ubiquitin ligases, DUBs have also been demonstrated as crucial factors in the regulation of RLR-mediated signaling. In the cases of upregulation of RLR-signaling by DUBs, deubiquitination of both RIG-I and MDA5 mediated by USP17 facilitates the induction of type I IFN . USP4 alHence, it is not surprising that herpesviruses evolutionally employ numerous strategies to subvert RLR-induced immune response. HSV-1 ICP0, a viral E3 ubiquitin ligase, inhibits host anti-viral response by blocking IRF3 (or IRF7)-mediated activation of interferon stimulating genes (ISG) . HSV-1 IcGAS is a major sensor of cytosolic DNA that is also critical for launching host immune response . Longer Ubiquitination has also been shown to be equally important for cGAS-STING signaling. For instance, the interaction between E3 ligase RNF185 and cGAS leads to the K27-linked polyubiquitination of cGAS on Lys173 and Lys384, which promotes its enzymatic activity and subsequently enhances IRF3 expression . TRIM56 USP29 has been reported to contribute to cGAS-mediated antiviral response via stabilization of cGAS through interaction between their UCH domain and the nucleotidyltransferase (NTase) upon HSV-1 infection . USP20 wViral infection-driven cGAS-STING mediated type I IFN signaling has clearly shown the crucial role of cGAS-mediated STING activation against several DNA viruses. Hence, it is notable to further confirm how DNA viruses evade cGAS-STING-mediated type I IFN signaling. EBV utilizes TRIM29 to induce K48-linked ubiquitination of STING at Lys379 site for protein degradation, thereby preventing the activation of cGAS-STING signaling and subsequently dampening the antiviral immune response . NotablyInflammasome, a large cytosolic multiprotein oligomer, is a part of the innate immune system which is activated by either PAMPs derived from infectious microbe or damage-associated molecular patterns (DAMPs) . Both PAMass spectrometry analysis and knockdown of MARCH using siRNA revealed MARCH7 to be responsible for dopamine-induced NLRP3 ubiquitination and degradation, leading to NLRP3 inflammasome inhibition . The E3 USP7 and USP47 have been reported to have functional redundancy in deubiquitinating NLRP3. Using CRISPR/Cas9 in the THP-1 cells, inflammasome activation was reduced when both USP7 and USP47 were knocked out . ConcurrHence, to perturb inflammasome signaling, KSHV ORF63 which has sequence homology with cellular NLRP1, interacts with NLRP1 and inhibits the association of NLRP1 with pro-caspase-1 to prevent the NLRP1 oligomerization . FurtherRecognition of herpesviruses by the host immune response begins through activation of diverse PRRs that produce type I IFN as well as pro-inflammatory cytokines. Thus, for every identified antiviral measure, herpesviruses employ numerous strategies to evade the innate immune response and establish their life cycle. Therefore, much work has been performed and more is still needed for better appreciation of the viral evading strategies via ubiquitination and deubiquitination. Herein, we have delineated our current knowledge on how herpesviruses manipulate the ubiquitin system to escape the host immune response, while efficiently establishing their life cycle. Especially, accumulated data show rapidly increasing examples of the human herpesviruses that not only modify ubiquitinated substrates but also employ viral ubiquitin E3 ligase as well as deubiquitinase to reshape host environment for their benefit . Notably


Deciphering nucleosome–nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available.We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools.https://github.com/Karimi-Lab/inucs/.Bioinformatics online. This allows iNucs to be integrated as a plugin to 4DN analysis pipeline in the future. In addition, the tool provides division and visualization of interaction pairs based on their orientation providing further spatial information about the conformation of chromatin fiber at genomic loci.In eukaryotes, DNA is packaged in the nucleus as a nucleoprotein complex called chromatin. The nucleosome is the fundamental unit of chromatin, around which 147 bp of DNA is wound. The packaging of chromatin in the nucleus is not linear. This results in different levels of 3-D genome folding and interaction. Deciphering genome organization within the nucleus is a multi-scale problem and while higher-order tertiary genome structures have been extensively studied using chromatin conformation capture technologies , the secondary structure of chromatin, i.e. nucleosomal interactions, remains elusive. Recently, new genome-wide chromatin conformation approaches have been introduced, allowing interactions at nucleosome level. However, the commonly utilized visualization tools such as HiGlass and Juicebox . TherefoiNucs consists of prepare and plot modules for which the processes, input and output files and formats are shown in Prepare module: This module takes in nucleosome genomic coordinates, ligation junctions (in pairs format) and chromosome names as input, and it produces a nucleosome interaction matrix (NIM) as output. The pairs’ input data are typically very large, particularly for human samples (n log n), where n is the larger of nucleosome counts and ligation junction counts reported in pairs file . The normalized value for each nucleosome pair (NP) is calculated as the observed interaction count for that NP divided by the expected count. The expected count for an NP is the average interaction count between nucleosome pairs whose distance is within the NP's average distance ± a given distance. The default value for the parameter distance is 200.iNucs also benefits from an optional feature to compute normalized values for nucleosome-nucleosome interaction counts and plot the original and normalized matrices side by side . We haveTo evaluate the performance of iNucs in terms of computational time and memory usage, we applied iNucs on two sets of data for yeast and human , executed on a MacBook Pro .Saccharomyces cerevisiae Hi-CO (S.cerevisiae and ligation junctions (pairs file) were provided by the authors of Hi-CO data. In the case of human data, the pairs file was publicly available in 4DN portal, but there were no matched nucleosome coordinates. Therefore, we downloaded nucleosome coordinates from NucMap repository (https://ngdc.cncb.ac.cn/nucmap/NucMap_FTP_Directory/Homo_sapiens/byDataType/Nucleosome_peaks_DANPOS/) for H1-hESC (Sample ID hsNuc0070101) (We used recently published 0070101)  and B. A0070101) . Also, i0070101) .btab698_Supplementary_DataClick here for additional data file.


Four, three, eleven, eleven MTAs for the flour whiteness, L* value, a* value, b* value, and one MTA for the dough sheet L* value were identified in more than one environment. Based on MATs, some important new candidate genes were identified. Of these, two candidate genes, TraesCS5D01G004300 and Gsp-1D, for BS00000020_51 were found in wheat, relating to grain hardness. Other candidate genes were associated with proteins, the fatty acid biosynthetic process, the ketone body biosynthetic process, etc.Flour whiteness and colour are important factors that influence the quality of wheat flour and end-use products. In this study, a genome wide association study focusing on flour and dough sheet colour using a high density genetic map constructed with 90K single nucleotide polymorphism arrays in a panel of 205 elite winter wheat accessions was conducted in two different locations in 2 years. Eighty-six significant marker-trait associations (MTAs) were detected for flour whiteness and the brightness index , the redness index , and the yellowness index  of flour and dough sheets (P < 10 Triticum aestivum L.) is one of the most important food crops worldwide, and it is also the source of major cooking foods in China. With the improvement of people’s living standards, the requirements for wheat colour have also increased significantly. Moreover, flour colour significantly influences the quality of wheat end-use products14. Therefore, it is necessary to pay attention to the study of flour colour to improve the quality of wheat products to meet the development needs of the market.Wheat , the redness index , and the yellowness index  could be used to evaluate flour colour7. In 2002, the CIE-L*, a*, b* colour system was introduced for the colour determination of Chinese flour and noodles8.Flour colour and whiteness are important indexes of wheat flour quality that can reflect flour quality and milling precision and are also important indicators of flour grading. Flour colour (whiteness) is a quantitative trait controlled by multiple genes with high heritability10, genetic dissection of the flour and dough sheet colours was rarely conducted at the same time. Through QTL mapping, some QTLs that control the stability of noodle colour traits were found on chromosomes 2A and 2D using DH populations11. The major QTLs/genes that affect the brightness of wheat flour were also detected on chromosomes 4D, 4A and 5D, ranging from 10 to 23.4% of PVE, and some QTLs associated with the yellowness of wheat flour were detected on chromosomes 7A and 4D12. However, for flour colour-related traits, the genotype rather than the environment was the main determinant13. In addition, the dough sheet colour is also important for noodle quality. The sheet colour score accounts for 9–45% of the total score when evaluating noodle quality14. With respect to dough sheet colour, the L* value is significantly affected by the protein content, and the a* value is highly correlated with the yellow pigment content. However, with respect to fresh dough sheets, PPO (polyphenol oxidase) activity significantly decreases the L* value, and highly significant positive correlations between the a* and b* values of fresh dough colour and PPO activity were reported from 4 to 24 h under resting conditions15. However, there is little information on the genetic dissection of the colour of dough sheets.Although there have been many studies on the quantitative trait locus (QTL) mapping of wheat flour quality-related traits16. Recently, GWAS has been widely used to study the complex traits of various plant species, such as Arabidopsis18, rice20, corn23 and durum wheat24. Although this method has also been used in wheat29, genome-wide association mapping of the colour-related flour and dough sheet traits has rarely been reported.A genome-wide association study (GWAS) is a powerful approach for mapping economically and biologically valuable traits of germplasm collections. This method has great potential in determining the locus responsible for a specific phenotype and for analysing the complex traits of cropsTherefore, the present study used GWAS to dissect the whiteness and colour-related traits of flour and dough sheets using 24,355 single nucleotide polymorphisms (SNPs) genotyped using the 90K Illumina iSelect array in a population of diverse winter wheat varieties. The objective of this study was to identify markers and candidate genes for loci associated with these traits to improve wheat flour and dough colour quality by breeding.h2 values of flour whiteness and the b* value were 98% and 99%, respectively  and the b* value of the dry dough sheets (DDS) were 50%, 48% and 46%, respectively  are shown in Tables 53. Twenty-two MTAs associated with flour whiteness (P < 10–4) were distributed on chromosomes 1A, 1B, 2B, 3A, 5D, 6A, and 7B  detected in two or more environments. The BS00000020_51 locus had the maximum phenotypic variation explained (PVE) with 15.95%. Alleles C and T of marker BS00000020_51 on chromosome 5D were associated with the largest phenotypic difference (2.13)  Table . The pheus Table .Table 3S–4)  were identified in more than one environment. The BS00000020_51 locus located on the 5D chromosome was detected in the four environments, with a maximum PVE of 12.28%. Alleles C and T of marker BS00000020_51 were associated with the largest phenotypic differences (0.57)  P < 10– (Table 47) Table .Table 4S–4) were distributed on chromosomes 1A, 3A, 6A, 6B, 7A, 7B and 7D. Among them, eleven MTAs were identified in two or more environments  were detected in three environments. Alleles A and G of marker Kukri_c65663_642 were associated with the largest phenotypic differences (0.38)   Table .Table 5S–4) (Table TA003858-0637 (6A) and BS00000020_51 (5D) were found in three and four environments, respectively. Alleles A and G of marker Kukri_c1214_437 on chromosome 5B were associated with the largest phenotypic differences (0.79). The phenotypic value of flour colour yellowness  associated with Kukri_c1214_437-G was significantly higher than that associated with Kukri_c1214_437-A across all four environments, indicating that Kukri_c1214_437-G was better than Kukri_c1214_437-A for the b* value   also participates in glycerol-3-phosphate O-acyltransferase activity and protein self-association. The marker BS00027770_51 on chromosome 6B had the candidate gene TraesCS6B01G419200, whose functions is related to the flavonoid biosynthetic process and regulation of jasmonic acid mediated signalling pathway. The candidate gene TraesCS5A01G003800 for the marker BS00099534_51 on chromosome 5A is related to the fucose metabolic process and protein phosphorylation. The marker TraesCS6A01G241200 on chromosome 6A had the candidate gene TA005690-1190, whose function is related to the ketone body biosynthetic process, leucine catabolic process and lipid metabolic process. These candidate genes may be related to flour colour, and their functions will be explored in future research.Markers with high PVE values were selected from loci significantly associated with flour whiteness and flour colour for prediction Table . Some imat Table . The funBS00065510_51 on chromosome 1D had the candidate gene TraesCS1D01G070200 from wheat  and Arabidopsis (mouse-ear cress). The functions of this gene are related to the response to oxidative stress, adenine salvage activity and the carbohydrate metabolic process. These candidate genes may be related to dough sheet colour, and their functions will be explored in future research.Markers with high PVE values were selected from loci significantly associated with dough sheet colour for prediction. Five new genes have been predicated. The marker at Table . The fun34 using QTL mapping methods, genome-wide association studies (GWAS) for these traits are rarely conducted using single nucleotide polymorphism markers (SNPs). Therefore, it is still important to find new major and stable loci introgressed into commercial cultivars using GWAS.Flour whiteness and flour and dough colour-related traits are critical determinants for the end-use product quality of wheat. Therefore, it is important to identify some major and stable loci for these traits and then transfer these favourable alleles into commercial varieties. Although some loci for these traits were found in previous studies in different populations34 constructed a genetic map that included 8227 SNP markers using an RIL population and found fifty-six QTLs. However, in the present study, a total of 24,355 SNP markers were mapped for MTA analysis using a panel of varieties, and more new loci were found than in a previous study. Some chromosomes for flour colour traits were involved in QTL mapping, including mainly homoeologous group 1, 2, 5, and 7 chromosomes, and chromosomes 3B, 4A, 4B and 6B35. Some QTLs detected for the a* value were found on the 1B and 3B chromosomes36, and other involved chromosomes were mainly 1B, 1D, 2D, 4A, 4D and 7B. In this study, loci associated with these traits were found on chromosomes 6A, 4A and 3A in addition to the above chromosomes. Zhai et al.37 performed GWAS on 166 bread wheat cultivars using the wheat 90 and 660K SNP arrays and 10 allele-specific markers, and identified 100 MTAs for flour color-related traits. This indicated that GWAS and QTL mapping could be complementary to each other.Zhai et al.40. Previous studies showed that PPO activity is mainly controlled by the genes on the homoeologous group 2 chromosomes, particularly 2A and 2D42. In the present study, significant SNP loci markers on chromosomes 2B, 2D and 2A were associated with flour whiteness, the flour L* value and dough sheet colour, but these SNP loci showed be different from PPO genes loci by comparing their physical positions. Excalibur_c4709_576 and TA001505-1171 on chromosome 2B were significantly associated with flour whiteness in two environments. Their candidate gene prediction indicated that the function was related to glycerol-3-phosphate O-acyltransferase activity, which participates in the fatty acid biosynthetic process. Previous research showed that lipoxygenase affects flour whiteness and colour43. Therefore, these loci may influence flour whiteness by lipoxygenase but not PPO activity. Kukri_c33486_128, on chromosome 2D, which was significantly associated with the flour L* value, was stably identified in three environments, but its candidate gene and function were not predicted in the BLAST search, which indicated that this locus is new and should be further studied in the future. GENE-1258_171 on chromosome 2A was significantly associated with the dough sheet L* value in two environments. Its predicted gene is TraesCS2A01G593500, whose function is related to protein kinase activity, so this locus affects the dough sheet colour, perhaps as a result of the grain protein content.PPO activity and the yellow pigment content have been reported to affect flour whiteness and colour45 In the present study, significantly associated loci were also found on these two chromosomes. Only one SNP marker associated with flour whiteness was detected on chromosome 7B. Although no loci were found on these two chromosomes for the flour b* value, nine SNP markers were significantly associated with the flour a* value. Moreover, they seemed to be stable in multiple environments. Three SNP markers were found on chromosome 7A, and their function is related to leucine rich repeat family protein expression. The other six SNP markers on chromosome 7B have one candidate gene, TraesCS7B01G482200, which is related to sucrose synthase activity. Therefore, the mechanism of their influence on flour colour is different from that of the Psy gene and yellow pigment content, which needs to be further studied in the future.Previous studies showed that the yellow pigment content is mainly controlled by chromosomes 7A and 7B; moreover, the Psy1 gene was reported to co-segregate with the b* value and yellow pigment content46. However, the milling characteristics are influenced by grain hardness, so the grain hardness affects the flour whiteness and colour. Zhai et al. identified the QTL QFL.caas-5D-1, which is close to the Pin-b gene, with a distance of 2.1 cM. The QTL for the L* value on chromosome 5DS coincided with the hardness (Ha) locus in previous studies46. In the present study, the SNP marker BS00000020_51 on chromosome 5D was significantly associated with flour whiteness and the L* and b* values and was stably detected in multiple environments. Therefore, this locus is important for flour whiteness and colour. Through a comparison of Zhai et al.’s results34, this SNP marker (BS00000020_51) was also found on their genetic map and was close to the closest marker BobWhite_s67669_117 of the QTL, with a distance of 2.1 cM. This indicated that the SNP marker BS00000020_51 controls flour whiteness and colour through grain hardness. We found two candidate genes, TraesCS5D01G004300 and Gsp-1D, by candidate gene prediction. Of these, Gsp-1D is the grain softness protein-1 gene that is linked to grain hardness, which affects flour particle size. Moreover, flour whiteness showed negatively correlated with flour particle size47, so it is possible that Gsp-1D affect the flour whiteness. Therefore, the accuracy of the results is confirmed.In addition, the flour whiteness colour is also affected by milling characteristicsRAC875_c34446_396 and GENE-4011_91 were at the same position, i.e., 49 cM, and were associated with flour whiteness and the flour L* value, respectively. The function of the candidate gene PUP88 was related to hydrolase activity and the hydrolysis of O-glycosyl compounds, participating in the carbohydrate metabolic process. However, at position 79 cM, five SNP markers detected in more than one environment were associated with the flour a* and b* values. The functions of the candidate gene TraesCS6A01G241200 of the SNP marker TA005690-1190 were different from those of other candidate genes. The TraesCS6A01G241200 gene participates in the ketone body biosynthetic process and lipid metabolic processes, which affect flour colour. Other candidate genes were mainly related to proteins. Moreover, the SNP marker BobWhite_c15802_72 on chromosome 6A was associated with dough sheet colour. Its function is related to peroxidase activity in soybean, but in wheat, the biological process is not clear. In addition, one special locus, the BS00027770_51 marker, associated with the flour a* value, was identified on chromosome 6B. Its candidate gene participates in the flavonoid biosynthetic process and regulation of jasmonic acid in Arabidopsis thaliana, but the function in wheat remains unknown. The above loci were not found in previous studies.Most interestingly, the SNP markers found on chromosome 6A were significantly associated with flour whiteness and colour. The markers 34. Their physical positions were seen in Table Flour whiteness and colour-related traits are inherently correlated. Three important loci on chromosomes 5D and 6A were identified. The SNP locus at genetic position 103 cM of chromosome 5D was involved in both flour whiteness and the b* value; the loci at genetic position 49 cM of chromosome 6A influenced flour whiteness and the flour L* value, and the last locus at genetic position 79 cM of chromosome 6A was associated with the flour a* and b* values. These relationships were reflected by the correlation coefficients Table , in agreThis study provided the important information about the influence of proteins, lipoxygenase and grain hardness on the flour whiteness and colour in addition to PPO activity and yellow pigment at the molecular level. GWAS is a good method for identifying new, important, stable loci. SNP markers significantly associated with flour whiteness and colour detected in this study provide opportunities for MAS of traits that are difficult to phenotype at the early stages of wheat breeding.All samples analysed in our study adhered to all local, national or international guidelines and legislation, and no ethical approval was required.48.The association mapping panel of 205 wheat genotypes for GWAS comprised 77 released cultivars, 55 landraces including two lines from Mexico and France, and 73 breeding lines from 10 provinces that represent the major winter wheat production regions in ChinaThe seeds used for the association mapping panel were planted in the 2015 and 2016 growing seasons in the experimental fields of two locations, that is, the Shandong Agricultural University, Tai’an (TA) location  and the Dezhou Institute of Agricultural Sciences, Dezhou (DZ) location . E1, E2, E3 and E4 represented Tai’an location in 2015 (TA 2015), Dezhou loction in 2015 (DZ 2015), Tai’an location in 2016 (TA 2016), and Dezhou location in 2016 (DZ 2016), respectively. The experimental field was arranged in a completely randomized block design, with two replicates in each environment. All lines were grown in 2 m plots with 3 rows spaced 25 cm apart, and 70 seeds were evenly broadcast in each row. During the growing seasons, all recommended local crop management practices were followed, and damage attributed to lodging, disease, or pests was not observed.Flour milling was carried out by using a Bühler experimental mill  with a flour extraction yield of approximately 70% in all samples stored for approximately 1 month after being harvested. The samples were tempered to 14%-16% moisture content according to grain texture overnight before milling.36. The working principle is to measure the absolute spectral diffuse reflectance using a photometry integrating sphere. The peak wavelength of the spectral power distribution of Y10 whiteness optical system is 475 nm and the half wave width is 44 nm. The standard of Y10 optical system accords with national standard GB3979 of China.Flour whiteness was determined by a WSB-IV intelligent whiteness determination meter 49 with minor modifications. Flour and water were mixed to achieve 44% absorption by slow mixing at a low speed for 5 min, followed by mixing at a medium speed for 2 min using a Kitchen Aid Professional Mixer . During the resting stage, crumbly dough was placed in a stainless steel bowl for 20 min at room temperature. The crumbly dough was then hand kneaded into a stiff mass and passed through an automatic noodle maker  three times to form a noodle sheet at a 2.0 mm roll gap-setting. The dough sheet was then folded twice and passed through six different roll gaps . Then, the fresh dough sheet was cut into approximately 6 small sheets . The fresh sheet was dried in the oven for 24 h at 40 °C.Dough making was performed according to50. The L* value indicates the lightness of flour with a range of 0–100 representing darkness to lightness . The a* value indicates the red-green direction, that is, it designates redness when positive but greenness when negative. The b* value indicates the degree of the flour yellow-blue colour, that is, the higher b* value denotes a greater amount of yellow51.The flour colour parameters  were measured with a Minolta colorimeter  using the commission Internationale de l’éclairage (CIE) L* a* b* colour system52.The dough sheet colour was also measured by a Minolta CR-300 colour meter. Three points were measured to determine the fresh dough sheet (FDS) (uncooked) at 0 h and the dry dough sheet colour at 24 h per noodle sheet, each at a different location on the same side of the surface of the noodle sheetThe colorimeter parameter of each sample was measured three times, and the mean values were used for subsequent statistical analysis.h2) was calculated as hB2 = σg2/(σg2 + σge2/r + σe2/re), where σg2, σge2, and σe2 are estimates of genotype, genotype × environment and residual error variances, respectively, r is replicates, and re is the product of replicates and number of environments. The estimates of σg2, σge2, and σe2 were obtained from variance estimates included in the ANOVA, which was performed using the PROC GLM procedure of SAS 8.0 .Analysis of variance (ANOVA) and correlations among phenotypic traits were carried out using the statistical software SPSS version 17.0 . Heritability  were identified using a mixed linear model (MLM) in TASSEL3.0. The P-value was used to determine whether a QTL was associated with a marker. The R2 value was used to evaluate the magnitude of the MTA effects. The genome-wide significance threshold  was given. SNPs with P-value ≤ 0.001 were considered to be significantly associated with phenotypic traits. When the MTA locus was detected in two or more environments, it was considered a stable association site48.SNP markers, genotyping and the population structure of the samples were reported previouslyhttp://www.wheatgenome.org/, 20th November 2020) using the sequence of the significant SNP markers identified by GWAS. When an SNP marker sequence from the IWGSC was 100% identical to any wheat contig, the sequence was extended 2 Mb for each marker using the IWGSC BLAST results. Then, the extended sequence was used to run a BLAST search at the National Center for Biotechnology Information (NCBI) database  and Ensembl Plants  to confirm possible candidate genes and functions.To identify the position of important MTA loci on a physical map and possible candidate genes, significant markers detected in this study were used to identify putative candidate genes. A BLAST  search was performed on the International Wheat Genome Sequencing Consortium database (IWGSC; Wheat is a common crop extensively cultivated in the world. This study does not contain any research requiring ethical consent or approval.Supplementary Information.


Fungal two-component regulatory systems incorporate receiver domains into hybrid histidine kinases (HHKs) and response regulators. We constructed a nonredundant database of 670 fungal receiver domain sequences from 51 species sampled from nine fungal phyla. A much greater proportion (21%) of predicted fungal response regulators did not belong to known groups than previously appreciated. Receiver domains in Rim15 response regulators from Ascomycota and other phyla are very different from one another, as are the duplicate receiver domains in group XII HHKs. Fungal receiver domains from five known types of response regulators and 20 known types of HHKs exhibit distinct patterns of amino acids at conserved and variable positions known to be structurally and functionally important in bacterial receiver domains. We inferred structure/activity relationships from the patterns and propose multiple experimentally testable hypotheses about the mechanisms of signal transduction mediated by fungal receiver domains. Two-component regulatory systems (TCSs) mediate signal transduction via transient protein phosphorylation. A generic TCS consists of a sensor kinase that monitors environmental conditions and a response regulator that implements appropriate responses to change. Conserved domains in both proteins catalyze phosphotransfer reactions. Transfer from ATP to a His residue on the sensor kinase transduces information into phosphoryl groups. Subsequent transfer to an Asp residue in the receiver domain of a response regulator modulates system output. Finally, transfer to water terminates the signal. In more complex versions, receiver and histidine-containing phosphotransfer (Hpt) domains inserted into the pathway between the sensor kinase and response regulator form a multistep phosphorelay. TCSs are organized differently in bacteria, archaea, fungi, and plants . BecauseSaccharomyces cerevisiae homologs. A narrow group of fungi closely related to Candida albicans encode Ssr1-type response regulators  stress response participate in phosphorelays . Here, w10.1128/mSphere.00722-21.1TEXT S1Text S1, PDF file, 0.1 MB.Supplemental materials and methods. Download Copyright © 2021 Bourret et al.2021Bourret et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 10.1128/mSphere.00722-21.2TEXT S2Text S2, PDF file, 0.2 MB.Fungal receiver domain sequences used in this study. Download Copyright © 2021 Bourret et al.2021Bourret et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 10.1128/mSphere.00722-21.3TABLE S1Table S1, PDF file, 0.04 MB.Fungal receiver domain inventory. Download Copyright © 2021 Bourret et al.2021Bourret et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 10.1128/mSphere.00722-21.9DATA SET S1Data Set S1, XLSX file, 0.2 MB.Spreadsheet of 25 selected characteristics for each of 670 individual fungal receiver domains. Download Copyright © 2021 Bourret et al.2021Bourret et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 5 structure featuring a central five-stranded parallel beta sheet flanked by five alpha helices  helices  and B  that stabilizes one of the phosphoryl group oxygens. Ser/Thr (T) and Lys (K) residues stabilize the other two oxygens of the phosphoryl group. About 10% of computationally identified receiver domains in bacteria lack one or more of the five conserved residues  or C (+) terminal to the conserved catalytic landmarks. Six variable positions are known to affect the rates of phosphorylation and dephosphorylation reactions in bacterial receiver domains. Five of these appear to be functionally linked, as revealed by sequence covariation . T+1 dirS. cerevisiae Sln1 exhibits Mg2+ coordination that is indistinguishable from that of bacterial receiver domains  with an oxidation-sensitive conformation promotes phosphorylation of a Ser/Thr at D+10 in α3 of Skn7. However, 9% of the Skn7s in our database lack a Ser/Thr at D+10. Strikingly, 98% of Skn7s contain a Cys residue at DD+17 in the α1β2 loop distal to the receiver domain active site  lack receiver domains entirely. The remaining Rim15 entries from Ascomycota contain a Glu residue instead of the Asp phosphorylation site and feature a His residue at DD+1 and a Leu residue at K–3. Half have a Pro residue at K+2. These residues are unique to Rim15 from Ascomycota. Descriptions of Rim15 receiver domains in the literature note the Asp-to-Glu substitution. In bacterial receiver domains, this often results in partial constitutive activity . We hypothesize that the signaling mechanisms used by Rim15 receiver domains differ between phyla and that there are likely to be both phosphorylation-dependent and -independent mechanisms. To the best of our knowledge, this is the first description of distinct types of Rim15 receiver domains. Finally, all Rim15 receiver domains in the database encode a modified α4 helix, most commonly shortened by 4 amino acids (one turn of a standard helix) compared to the length of C. albicans  how does Ssk1 separately bind to its upstream partner Ypd1, itself, or its downstream partner Ssk2 and (ii) how does phosphorylation of Ssk1 influence some these binding events but not others? r domain , formingr domain . When osr domain , 36.in silico studies suggest that the aromatic K–3 residue of Ssk1 remains exposed regardless of phosphorylation state  amino acid insertions in the α3β4 loop. The inserts are rich in Pro and Ser residues, consistent with intrinsically disordered protein regions often involved in protein/protein interactions , and aretructure . The factructure . Inclusitructure . Based otructure . In any  ± 16 amiOur database included 17 previously unclassified and 2 reclassified fungal HHKs . Figure 10.1128/mSphere.00722-21.7TABLE S5Table S5, PDF file, 0.04 MB.HHK group assignments made in this work. Download Copyright © 2021 Bourret et al.2021Bourret et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the E. coli CheY) in the α2β3 and/or α3β4 loop . The amino acids at T+2 are more diverse than at D+2 but are also mostly hydrophilic (with Asn/Ser being the most abundant). Hydrophilic residues at D+2 and T+2 are predicted to enhance dephosphorylation .Phe is the most common residue type at K+2 in bacteria. Five types of fungal HHK receiver domains contain Phe residues or functionally similar Tyr residues at K+2. However, 15 types of fungal HHK receiver domains contain primarily an Ile, Leu, or Val residue at K+2, which is likely to increase the fraction of the population in active conformations and enhance phosphorylation .E. coli CheY  is mostly Tyr or Phe residues in bacteria, as well as in most types of fungal HHK receiver domains. However, Val is most common in groups XI, XII Rec2, and XIII, and Trp is most common in groups VIII and XIV. Notably, a Trp residue at K–3 results in partial constitutive activity in oli CheY .Receiver domains in fungal HHKs frequently utilize amino acids that are uncommon at the equivalent positions in their bacterial counterparts . This prContinuing the trend observed in fungal response regulators, all fungal HHK receiver domain types exhibit different patterns of amino acid abundance across key residues . Groups About 73% of bacterial sensor kinases contain transmembrane regions , whereasFungi are major pathogens of plants, animals, and humans . Because47–


Rifted margins are the result of the successful process of thinning and breakup of the continental lithosphere leading to the formation of new oceanic lithosphere. Observations on rifted margins are now integrating an increasing amount of multi-channel seismic data and drilling of several Continent-Ocean Transitions. Based on large scale geometries and domains observed on high-quality multi-channel seismic data, this article proposes a classification reflecting the mechanical behavior of the crust from localized to diffuse deformation  and magmatic intensity leading to breakup from magma-rich to magma-poor margins. We illustrate a simple classification based on mechanical behavior and magmatic production with examples of rifted margins. We propose a non-exhaustive list of forcing parameters that can control the initial rifting conditions but also their evolution through time. Therefore, rifted margins are not divided into opposing types, but described as a combination and continuum that can evolve through time and space. They provide images of the deep levels of the crust, its internal geometries, structures and seismic facies, especially within the Continent-Ocean Transition (COT). Coupled with wide-angle seismic and gravity/magnetic data, which give an idea of the velocity/density gradient and layering of the crust, they allow a much better resolution of the large-scale character of a margin. Therefore, the structural diversity of rifted margins is now accessible. From the tilted blocks of the 1970′s, the detachments and mantle exhumation of the 1980′s–1990′s to the great variety of geometries now seen2 and Wernicke3 were developed based on observations from onshore and nearshore rifted basins. They were extrapolated to the entire margin and considered as references for the crustal thinning. Breakup was supposed to occur when the crustal stretching factor was reaching the value of 5 for a 30 km thick continental crust4, allowing magma to suddenly breach through the crust5.The extensional models of McKenzie6. In addition, alpine geologists highlighted the convergence with geological features observed in the Swiss Alps and developed original models integrating the complete evolution from the first increment of continental extension to oceanisation10. From these combined studies arose the magma-poor model of rifted margins, characterized by limited volumes of syn-rift magmatic rocks and exhumation of continental lithospheric mantle in the COT13.In the late 1980′s and 1990′s, an increasing collection of data  in the distal part of the Iberia-Newfoundland conjugate margins provided a better picture of the COT17 and onshore19 in the Northern Atlantic led to the development of a model for Volcanic, or magma-rich, Rifted Margins (VRM)21. These margins are characterized by thick wedges, up to 20 km, of Seaward Dipping Reflectors (SDR)23 mainly composed of basaltic flows interbedded with sediments and paleo-soils, all intruded by sills. VRM also possess overall high velocities (6–7 km/s) and High Velocity Lower Crustal Bodies 25. However, the different observations did not allow sufficient convergence of ideas to reach a consensual model30.In the meantime, other data collected offshoreThese spectacular observations tend to polarize rifted margins interpretation towards two opposite types based only on magmatic productivity.37. They recently allowed to explore these parameters in 3D40. In parallel, seismic profiles from several rifted margins revealed structures not predicted by neither the magma-poor nor the magma-rich models42. In agreement with previous numerical modelling results36, some authors proposed the existence of at least a third type of rifted margin, characterized by the inability of the deformation to localize until magmatic breakup occurs in a highly stretched crust.Since the 2000′s, many numerical models tried to test different physical parameters, especially the rheological strength of the crustAs a consequence, the mechanical behavior of the margin, that were not generally discussed in the magma-poor/magma-rich classification, became another axis for rifted margins description. Two endmembers were described  but, thanks to thermomechanical modelling, a wide spectrum of intermediate behaviors was explored.Based on the interpretation of deep seismic datasets across many margins and the existing knowledge, we present a classification based on two axes Fig. : MechaniThe main seismic characters, geometries and large-scale correlations are illustrated through four contrasting cases located along the Somalia, Uruguay, Gabon and Coral Sea margins Fig. . After dThe four presented sections illustrate striking geometries and large-scale organizations. Their description follows the methodology described in the Method and Terminology section.43. It displays only limited rift-related volcanism44 and developed in a context of carbonate sedimentation with little clastic input. We present a 210 km long and 12 s deep profile , the transparent upper crust (middle layer) is ~ 15 km thick while the lower layer is thin (~ 8 km) based on Pre-Stack Depth Migration seismic data. The inherited East African crust is said to be of Mesoproterozoic gneisses and meta-sediments reworked during the Panafrican OrogenyThe Proximal Domain underwent modest stretching. The brittle upper crust is cut by high-angle normal faults, bounding half-grabens with limited syn-rift strata packages. The Necking Domain is narrow  and Exhumation Line (EL), Fig. 10 in the Alps, are imaged. Both these blocks and exhumed mantle are further seaward covered by magmatic additions, an area interpreted as forming the COT. The COT corresponds to the onset of minor magmatic features  increase in frequency and size seaward and evolve finally towards a thin proto-oceanic crust prior to a 2 s (TWT) oceanic crust Although seismic imaging of the syn-rift and basement is limited due to very irregular post-rift sedimentary deposits, resulting from salt tectonics on the Latest Aptian salt layer, the continental crust appear stretched over more than 150 km Fig. . Thus, t27. The necking is associated to an up to 12 km thick syn-rift sequence of continental/lacustrine sediments  wedging towards the detachment faults and the core-complexes  and created local grabens with salt50.This line does not cover the large exhumation domain that, however, it is present further south together with increasing magmatism50 that intrudes the faulted late-rift sediments and evolves to a thin oceanic crust prior to a 2 s (TWT) thick mature oceanic crust ust Fig. .52, which is at least partly contemporaneous with the emplacement of the Parana-Etendeka large igneous province53. The austral South Atlantic Ocean opened across two generations of orogenic belts55: the Late Paleozoic Ventania-Cape Fold Belt to the south and the Pan-African/Brazilian Ediacaran orogenic belts to the north. We present a 255 km long and 14 s deep line from the South Namibia Margin  in the north57.The most striking structure of all these conjugate margins are SDR wedges Fig. . They we55. Small normal faults rooting in internal levels of this upper crust are bounding half-grabens filled by upper Lower Cretaceous sediments. The lower crustal layer shows the layered, high-amplitude seismic facies diagnostic of the lower crust.The Proximal Domain exhibits two crustal layers Fig. . The upp30 and high-amplitude features cutting the lower crustal levels suggests a strongly intruded crust and possible mafic underplating. This lower crustal layer presents highly reflective sigmoidal reflectors interpreted as sheared structure.The Necking Line corresponds to the onset of the SDR facies in association with a deepening of the Top-Basement/Base Rift horizon. The primary necking is rather short but followed by a wide crustal taper (> 100 km). The crustal layering is difficult to observe but the presence of both Seaward and Landward Dipping Reflectors 66. Locally, two basins are involved with a Late Cretaceous rifting for the subducted/obducted Emo Basin67 and Latest Cretaceous/Paleocene for the younger Coral Sea Basin. We present a 90 km long and 14 s deep line through the northern margin of the Coral Sea  involving progressive uplift of the detachment fault and of its rider blocks through a rolling hinge mechanism73. Several of these core-complexes and short normal faults rooting at the interface between the upper and middle crustal layers are visible along the profile. However, large scale correlations attribute these structures to the previous orogenic collapse74.Another striking feature is the scarcity of syn-rift deposits with some of them being even eroded before the deposition of post-tectonic sediments. Such patterns can be explained through a core-complex model in a thermally-supported setting  and rafting away elements of pre-rift sediments and upper crust  and strong  mechanical behaviors;The Breakup Axis considers the amount of magma involved from rifting to breakup, from a magma-poor to a magma-rich pole.The general and simple magma-rich/poor combined with the weak/strong crust classification can be efficiently used to classify the world’s rifted margins Fig. a:The RifA seismic lines shows the final structure and addressing the mechanical behavior of the rifted crust is uneasy as it results from the combination of several parameters that vary through time .A short Necking Domain in which the deformation is accommodated on very few structures;High-angle normal faults in the proximal margin, evolving in the Necking Domain into large listric faults rooted in the middle to lower crustal layer  of the crust are preserved82. On seismic, we can identify several geometrical characteristics that tend to suggest the existence of this type of behavior:The weak mechanical behavior have been widely explored by numerical modeling82. This wide Necking Domain is explained by the inability of the deformation to localize and couple with the mantle;A proximal and sharp onset of necking followed by a wide crustal taper  by a 3 km to 5 km-thick lower crust characterized by long and sub-horizontal reflectors. This lower crustal layer is particularly evocative of a ductile mechanical behavior, especially in the inter-boudin necks where it rises/bulges in between more resistant (upper/mid) crustal boudins. Similar structures83 can also be observed in magma-rich settings  and the presence of numerous low-angle normal faults is also a characteristic of the deformation associated to weak behavior .The key characteristic of magma-rich margin is the outer SDR domain, or Magmatic Domain. Its presence defines the magma-rich pole. Its width seems to be homogeneous  represent about 31% of the rifted margins107. These types of segments can be perceived as either inherited (reactivation of basement lineaments107) or newly formed (link between two divergent segments39).The obliquity of the margin is defined as the angle between the principal trends of the margin  and the involved plates motion. Most of the world’s rifted margins present a certain degree of obliquity. Indeed, modeling suggests that oblique extension facilitates rifting and continental breakupFrom the architecture, transform and high-obliquity margins occupied the strong position of the proposed classification Fig. . Indeed,110. With simple compositions , the wetness of the mineral assemblage will also influence the strength of the crust. In thermomechanical modeling, more complex compositions can be set up by multiplying layers of distinct mineral assemblage. The case of a mafic lower crust is often used leading to a general strengthening31. The composition, temperature and wetness of the lithospheric mantle will influence the magmatic productivity of the mantle. The richness in fertile elements and a higher content in water tend to favorize a high melt production114;Crust and mantle composition: the importance of the crustal chemical composition on the strength profile of the crust is known since several decades115. The lithospheric thickness increases with the age of the lithosphere (from Phanerozoic to Archean). Artemieva116 proposed a linear relation between age and thermal state of continental lithosphere. It is thus important to know when the last thermal event prior to the final rifting affected the future margin and its eventual intensity;Lithospheric thickness: this parameter represents the pre-rift thermal structure. In nature, little information is available on the geotherm before the last rifting event initiates. It is a function of the radiogenic heat production and the crustal/lithospheric thickness118 as both parameters will influence the radiogenic heat production. In a simple manner, the younger and thicker the crust is, the larger its temperature gradient will be;Thickness and age of the crust: crustal thermal state depends on the crustal age and crustal thickness119, giving the apparent effect of a stronger crust (fast coupling). In an opposite way, large deformed areas with important layering of the crust and numerous heterogeneities such as suture zones or arc settings may induce a more diffuse deformation and introduce several internal decoupling layers within the crust, weakening it119.Inherited structures may have either a positive or negative influence on mechanical behavior. Indeed, pre-existing faults  will help in localizing the rifting if optimally orientedThe inherited parameters are sorted in order of decreasing impact on the mechanical behavior of the crust and magmatic production of the mantle:120). This induces an increase of the partial melting rate within the mantle leading to a higher magma production. Secondly, it thins the lithospheric mantle through a rise of the asthenospheric mantle, heating the Moho. This in turn will increase the geothermal gradient and may weaken the crust 117;A mantle plume has two main effects. Firstly, the base lithosphere is hotter than usual due to deep mantle upwelling and can reach values over 1500 °C , which is generally the case during rifting, the rheology of the lithosphere is of primary importance105;Extension rate: in agreement with their numerical models, Brune et al.121. High erosion and sedimentation rates facilitate displacement on faults124. The increasing efficiency of surface processes during the initial phases of rifting results in localizing deformation and increasing fault-block size. Conversely, intermediate to high sedimentation rates over hot extending crustal sectors exert an effect of thermal blanketing that favors viscous/distributed deformation in the basement enhancing the effect of weak crustal rheologies121.High syn-rift sedimentation: surface processes promote the localization of the plastic deformation due to the reduction in topographic and flexural forces that oppose fault displacementThe following parameters are also sorted in order of decreasing impact on the mechanical behavior of the crust and magmatic production of the mantle. These parameters can impact before and during the formation of the rifted margin:This paper, supported by high-quality seismic examples, describes and enhances several key morphological and structural observations to propose a classification organized along two axes reflecting the mechanical behavior of the crust and the magmatic budget while rifting and breakup.The key observables are the presence or absence of certain domains. Magma-poor margins always present Coupling and Exhumation Domains, and the poorer in magma it is, the longer will be the Exhumation Domain with a very progressive magmatic input. On the contrary, magma-rich margins exhibit a magmatic domain with outer SDR.The width of the Necking Domain;79;The initial thickness and width of the Coupling DomainThe width of the Exhumation Domain;The initial thickness of the outer SDR (or Magmatic) Domain.Although this classification is a qualitative approach, some of its main propositions may be used quantitively, such as:105 and breakup mechanisms are symmetric to slightly asymmetric in terms of domain presence and width. However, having the conjugate margin would give more weight to the quantifiable elements.Because of a lack of data, we did not consider the conjugates to our examples. The descriptive approach would not change, as asymmetry is not necessarily linked to a certain mechanical behaviorIt is important to note that rifted margins may suffer several rifting events prior to finally breakup. The multiplicity of events is often related to changes in the external conditions  driving the formation of the rifted margins. In that case, the formation of the rifted margin could either be seen as a whole continuum or limited to the last event that successfully broke the crust up.Our work is based on a descriptive approach of the large-scale correlations, geometries and organization to define a set of observables from multi-channel seismic data. Even if we present a single margin, when available the conjugate has been interpreted jointly. The description of rifted margins is done firstly by defining its vertical layering and its horizontal zonation (domains). Then several key observables are defined.125 exhibit clear reflections within the mantle. These reflections can, in some cases, be continuous and consistent in 3D. Therefore, in areas where it is poorly defined or where there are multiple hypotheses, wide-angle seismic data or simple gravimetric/magnetic inversion may be needed to constrain the location of the Moho;The Moho reflection is amongst the deepest reflections visible along a seismic profile. In TWT, it is globally flat and generally around 9 to 11 s (TWT) deep. Its facies and amplitude may vary a lot along a profile. It may be a rather strong and continuous reflector but sometimes it disappears if the velocity contrast is not important enough or even absent . It is worth noticing that the Moho interpretation is not necessarily unique. Indeed, some multi-channel seismic linesConsidering that, in this article, the presented margins are all of Mesozoic/Cenozoic age, we chose to locate the Top Basement as the major consistent unconformity at the base of Mesozoic/Cenozoic basins or at the end of the last orogenic event. Therefore, the basement, as it stands here, may be composed of old sedimentary basins , metamorphosed/strongly folded sediments  or igneous rocks. It is generally easy to identify in the undeformed and proximal domain where it is well imaged and can be directly correlated to onshore geology. However, it is more difficult to interpret it in a rifted margin due to a poorer image quality . Also, the crust is often separated into sub-layers such as upper, middle and lower crust. In the Oceanic Domain, the Top Basement is the Top of the Oceanic Crust which also coincides with the base of the sediments;The Base Rift corresponds to the surface defining the onset of the rifting event. It is often an important unconformity between quite isopachous well-bedded sediments and typical syn-tectonic sequences (fault-controlled wedge-shaped layers). It is merely a matter of definition if layers defined between the Top Basement and the Base Rift, i.e. the Pre-Rift sedimentary unit, which may be composed of several internal layers depending on the geological history of the area (multiple rifting/cooling events) are considered as separate layers or if Top Basement and Base Rift are considered as the same surface, as it is done in this article;The Top Rift corresponds to the surface related to the breakup of the lithosphere. It is often named breakup unconformity. In this article, we choose to define the Top Rift as the most important onlap surface (unconformity) coeval with the first clearly observable oceanic crust. Therefore, the Top-Rift coincides laterally to the Top basaltic Oceanic Crust. It is characterized by a drowning or an acceleration of the drowning of the rifted margin recording a tilting associated to large scale subsidence of the margin. The Syn-Rift layer may be composed of several internal layers separated by regional or local unconformities that reflect the migration of the deformation during the rifting. Thus, the Syn-Rift layer represent the whole sedimentary package that registered the stretching, thinning and breakup of the lithosphere. Local or sub-basinal events along the margin are referred as pre-, syn- or post-tectonic sub-layers;The Seabed, or topography in onshore domain, defines the top of the Post-Rift sedimentary package. It reflects the balance between the lithospheric cooling following the rifting event and sediment input. This package is represented by wide and parallel reflections onlapping the rifted margin while subsiding. The post-rift package may be locally disturbed by salt and shale tectonics related to large deltaic provinces.The layering considers the presence and general shape of four layers. They are defined between five key surfaces, from bottom to top:127. This zonation is based on the relationship between the different layers and horizons defined in Sect. 5.1. and the presence of some characteristic geometries. Different domains can be seen along a rifted margin and are bounded by their onset lines. It is worth noticing that not all domains are observed in all different margins and their presence or absence depends greatly on the context:The Proximal Domain is where the crust is barely thinned. Moho reflection, Base-Rift, Top-Rift and Topography/Seabed are globally parallel. The syn-rift deformation is limited. Faulting may be observed in this domain but without any important thinning of the crust. The post-rift subsidence registered here is limited due to a little thinning of the lithospheric mantle during the rifting. This domain ends up at the Necking Line (NL);The Necking Domain onsets at the Necking Line (NL) and ends at different lines  depending on the type of rifted margin and context (see below). The Necking Line corresponds to the onset of crustal thinning and is characterized by a general convergence of Moho reflection with Base-Rift and Top Syn-Rift horizons. In depth section, both Moho and Top-Rift (+ Base Rift) form the typical triangular shape of this domain. In time section, the Moho being relatively flat, Top-Rift strongly dips toward the distal domains;79) that deform in a simple shear manner;The Coupling Line (CL), when existing, is characterized by the first faults cutting the whole crust down to the mantle. They might either root at Moho level or cut down into the mantle. The Coupling Domain onsets at this line and, similarly to the Necking line, ends up at different lines . The Coupling Domain exhibits also a triangular shape with converging Moho and Top Rift (+ Base Rift) horizons. This forms a distal necking accommodated by faults and detachments called Hyper-Extended Continental Wedge  corresponds to the point where identifiable continental crust elements are no longer visible. The Moho reflection is often lost or blurred and even sometimes doubled, thus geophysical Moho can be different from petrological Moho. Depending on the type of margin and the rapidity of the breakup processes, this limit also corresponds to the onset of either the exhumation domain (mantle exhumation at seafloor), or the Magmatic Domain (outer SDR wedge) or even directly the Oceanic Domain (oceanic crust);The Limit of Oceanic Crust (LOC) is defined by the point marking the first recognizable oceanic crust defined by parallel Moho and Top Basement and a thickness of 2 to 2.5 sTWT. In general, the upper seismic facies of the oceanic crust is made of chaotic to relatively flat lying reflections. In some particularly good multichannel seismic data, a lower layered facies and crust-cutting dykes might be observed. The first oceanic crust might form in an ultra-slow setting. Therefore, in term of facies and thickness, it is difficult to differentiate it from the exhumation domain. In that case the LOC is unclear.The morphology of a margin can be translated into its horizontal zonation or domainsThe observed domains. The large variability of rifted margins is illustrated at a first order by the presence or absence of some of the domains previously defined. Proximal and Necking domains are always present. Conversely, Magmatic (or Outer SDR), Coupling and Exhumation domains are not and are characteristic of certain types of margins. The presence of the Magmatic Domain is symptomatic of the magma-rich margin. It forms a distal necking accommodated by magmatic additions. On the other hand, the presence and width of the Exhumation domain is characteristic of magma-poor margins;79 but also at the scale of an ocean (notion of segments). The concept of coupling efficiency128 has been used to explain the necking variability along different segments of a single margin (e.g. Norway). The Necking Domain can be very short, even nearly absent, to extremely wide . In the case of a very wide Necking Domain, it can be divided into two sub-domains with a primary accentuated necking followed by a long flat to slightly converging taper often composed of several internal sub-basins (neck basins);The width of the Necking Domain: this domain is the most variable in terms of width and general shape. This variability is evident looking at worldwide rifted margins79. At a first glimpse, the taper angle of the Hyper-Extended Continental Wedge reflects the position of the taper relatively to the main detachment fault: a short taper characterizes the upper plate (above the detachment), a long taper with seaward dipping fault characterizes more generally the lower plate (below the detachment). At a second order, the width of the coupling domain is also dependent on the content of brittle material in the crust. The crustal thinning accommodated in the necking is made in a pure-shear manner and distributed between upper brittle crust and ductile mid to lower crust. Ultimately this ductile material is removed, and only brittle material is preserved in the coupling domain allowing faults to cut through the entire crust;The width of the Coupling Domain: this aspect has been well explored by Nirrengarten et al.The type of structures: The faults accommodating the rifting event can be described considering their shape  and their level of rooting within the crust. Their presence and repartition along a rifted margin and their timing are also key to understand the rifting processes;The syn-rift (either sedimentary and/or magmatic) infill. The relative thickness of the syn-rift package, its shape, layering and the identification of the period of tectonic activity of a group of faults or a sub-basin of the margin record the deformation and whether it is in-sequence  or not.Using the layering and the domains of rifted margins previously defined, we can focus secondly on several qualitative observables such as the presence or absence of certain elements or their relative width or thickness. They give key indication on the behavior during rifting and breakup periods. The listed observables are: