page_title: Genome diversity and karyotype evolution of mammals
section_title: Comparative molecular cytogenetics
hierarchical_section_title: Genome diversity and karyotype evolution of mammals / Historical development of comparative cytogenetics / Comparative molecular cytogenetics
caption_attribution_description: English: A comparative chromosome map of birds and mammals inferred human homologies (right numbers) on chromosome ideograms. a. Reconstructed karyotype of the ancestral Eutherian genome. Each chromosome is assigned a specific color. These colors are used for mark homologies in ideograms of chromosomes of other species (Figure 5b-5i) b. Ideogram of chicken (Gallus gallus domesticus, 2n = 78) chromosomes. The reconstruction is based on alignments of chicken and human genome sequences. c. Ideogram of short-tailed opossum (Monodelphis domestica, 2n = 18) chromosomes. The reconstruction is based on alignments of opossum and human genome sequences. d. Ideogram of aardvark (Orycteropus afer, 2n = 20) chromosomes. The reconstruction is based on painting data. e. Ideogram of mink (Mustela vison, 2n = 30) chromosomes. The reconstruction is based on painting data. f. Ideogram of the Red fox (Vulpes vulpes, 2n = 34 + 0-8 B's) chromosomes. The reconstruction is based on painting and mapping data. g. Reconstructed karyotype of the ancestral Sciuridae (Rodentia) genome, based on painting data (Li et al., 2004). h. Ideogram of the House mouse (Mus musculus, 2n = 40) chromosomes. The reconstruction is based on alignments of Mus and human genome sequences. i. Ideogram of human (Homo sapiens, 2n = 46) chromosomes.
context_page_description: The 2000s witnessed an explosion of genome sequencing and mapping in evolutionarily diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosomal regions from more than a few species is not yet possible. The intense focus on the building of comparative maps for domestic, laboratory and agricultural animals has traditionally been used to understand the underlying basis of disease-related and healthy phenotypes.
  These maps also provide an unprecedented opportunity to use multispecies analysis as a tool to infer karyotype evolution. Comparative chromosome painting and related techniques are very powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders.
  It was found that in most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates.
context_section_description: The third step occurred when molecular techniques were incorporated into cytogenetics. These techniques use DNA probes of diverse sizes to compare chromosomes at the DNA level. Homology can be confidently compared even between phylogenetically distant species or highly rearranged species (e.g., gibbons). Using cladistic analysis rearrangements that have diversified the mammalian karyotype are more precisely mapped and placed in a phylogenomic perspective. "Comparative chromosomics" defines the field of cytogenetics dealing with molecular approaches, although "chromosomics" was originally introduced to define the research of chromatin dynamics and morphological changes in interphase chromosome structures.
  Chromosome painting or Zoo-FISH was the first technique to have a wide-ranging impact. With this method the homology of chromosome regions between different species are identified by hybridizing DNA probes of an individual, whole chromosomes of one species to metaphase chromosomes of another species. Comparative chromosome painting allows a rapid and efficient comparison of many species and the distribution of homologous regions makes it possible to track the translocation of chromosomal evolution. When many species covering different mammalian orders are compared, this analysis can provide information on trends and rates of chromosomal evolution in different branches.
  However, homology is only detected qualitatively, and resolution is limited by the size of visualized regions. Thus, the method does not detect all minuscule homologous regions from multiple rearrangements (as between mouse and human). The method also fails to report internal inversions within large segments. Another limitation is that painting across great phylogenetic distance often results in a decreased efficiency. Nevertheless, the use of painting probes derived from different species combined with comparative sequencing projects help to increase the resolution of the method.
  In addition to sorting, microdissection of chromosomes and chromosome regions was also used to obtain probes for chromosome painting. Best results were obtained when a series of microdissection probes covering the total human genome were localized on anthropoid primate chromosomes via multicolor banding (MCB). However a limitation of MCB is that it can only be used within a group of closely related species ("phylogenetic" resolution is too low). Spectral karyotyping (SKY) and MFISH—the ratio labeling and simultaneous hybridization of a complete chromosomal set have similar drawbacks and little application outside of clinical studies.
  Comparative genomics data including chromosome painting confirmed the substantial conservation of mammalian chromosomes. Total human chromosomes or their arms can efficiently paint extended chromosome regions in many placentals down to Afrotheria and Xenarthra. Gene localization data on human chromosomes can be extrapolated to the homologous chromosome regions of other species with high reliability. Usefully, humans express conserved syntenic chromosome organization similar to the ancestral condition of all placental mammals.
caption: A comparative chromosome map of birds' and mammals' inferred human homologies (right numbers) on chromosome idiograms[29]
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