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Genome diversity and karyotype evolution of mammals

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Genome diversity and karyotype evolution of mammals
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The 2000s witnessed an explosion of genome sequencing and mapping in Wikipedia:evolutionary diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosome regions from more than a few species is still not possible. The intense focus on building of comparative maps for companion (dog and cat), laboratory (mice and rat) and agricultural (cattle, pig, and horse) animals has traditionally been used as a means to understand the underlying basis of disease-related or economically important phenotypes. However, these maps also provide an unprecedented opportunity to use multispecies analysis as a tool for inferring karyotype evolution. Comparative chromosome painting and related techniques are now considered to be the most powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH) on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders. In most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. The number of rearrangements that have become fixed in evolutionary history seems comparatively low, bearing in mind the 180 million years of the mammalian radiation. Comparative chromosome maps record the history of karyotype changes that have occurred during evolution.

Mammalian phylogenomics[edit]

An evolutionary tree of mammals[3]

Modern mammals (class Mammalia) are divided into three distinct groups. The subclass Wikipedia:Prototheria (monotremes) comprises three species of egg-laying mammals: Wikipedia:platypus and two Wikipedia:echidna species. The infraclasses Wikipedia:Metatheria (marsupials) and Wikipedia:Eutheria (placentals) together form the subclass Wikipedia:Theria. In the 2000s our understanding of the relationships among eutherian mammals has experienced a virtual revolution. Wikipedia:Molecular phylogenomics, new fossils finds and innovative morphological interpretations now group the more than 4600 extant species of eutherians into four major super-ordinal clades: Wikipedia:Euarchontoglires (including Wikipedia:Primates, Wikipedia:Dermoptera, Wikipedia:Scandentia, Wikipedia:Rodentia, and Wikipedia:Lagomorpha), Wikipedia:Laurasiatheria (Wikipedia:Cetartiodactyla, Wikipedia:Perissodactyla, Wikipedia:Carnivora, Wikipedia:Chiroptera, Wikipedia:Pholidota, and Wikipedia:Eulipotyphla), Wikipedia:Xenarthra, and Wikipedia:Afrotheria (Wikipedia:Proboscidea, Wikipedia:Sirenia, Wikipedia:Hyracoidea, Wikipedia:Afrosoricida, Wikipedia:Tubulidentata, and Wikipedia:Macroscelidea).[4] This modern phylogenetic tree serves as a useful scaffold for combining the various parts of a puzzle in comparative mammalian cytogenetics.

Karyotypes: a global view of the genome[edit]

Genes provide instructions to build living organisms and each gene maps to the same chromosome in every cell. Linkage is provided by the co-localization of two or more loci on the same chromosome and the largest linkage group is an entire chromosome. The entire chromosome set of a species is known as a karyotype, which can be thought of as a global map of the nuclear genome.

A seemingly logical consequence of descent from common ancestors is that more closely related species should have more similar chromosomes. However, it is now widely appreciated that species may have phenetically similar karyotypes because they are genomically conservative. Therefore in Wikipedia:comparative cytogenetics, phylogenetic relationships should be determined on the basis of the polarity of chromosome differences (derived traits).

Historical development of comparative cytogenetics[edit]

Mammalian comparative cytogenetics, an indispensable part of Wikipedia:phylogenomics, has evolved in a series of steps from a purely descriptive science to a heuristic science of the genomic era. Technical advances have marked the various developmental steps of cytogenetics.

Classical phase of cytogenetics[edit]

Examples of mammalian chromosomes[5]

It can be argued that the first step of the Wikipedia:Human Genome Project took place when Tjio and Levan in 1956 finally reported the correct Wikipedia:diploid number of humans as 2n = 46.[6]

During this phase of cytogenetics, data on the karyotypes of hundreds of mammalian species (including information on diploid numbers, relative length and morphology of chromosomes, presence of Wikipedia:B chromosomes) were described. Diploid numbers (2n) were found to vary from 2n = 6–7 in the Wikipedia:Indian muntjac[7] to over 100 in some rodents.[8]

Chromosome banding[edit]

The second step derived from the invention of C-, G-, R- and other banding techniques was marked by the Paris Conference (1971), which led to a standard nomenclature to recognize and classify each human chromosome.[9]

G- and R- banding[edit]

The most widely used banding methods are Wikipedia:G-banding (Giemsa-banding) and Wikipedia:R-banding (reverse-banding). These techniques produce a characteristic pattern of contrasting dark and light transverse bands on the chromosomes. Banding made it possible to identify homologous chromosomes and construct chromosomal nomenclatures for many species. With banding homologous chromosomes, chromosome segments and rearrangements could be identified. The banded karyotypes of 850 mammalian species were summarized in the Atlas of Mammalian Chromosomes.[10] These basic data present an invaluable resource for the contemporary comparative genomics era, and will assist in selection of new mammalian species for detailed study.

C-banding and heterochromatin[edit]

Examples of distribution of C-heterochromatin in mammalian chromosomes[11]

One important source of karyotype variability in mammals is related to Wikipedia:heterochromatin. Once the amount of heterochomatin is subtracted from total genome content, all mammals have very similar genome sizes.

Species of mammals differ considerably in the heterochromatin content and its location. Heterochromatin is most often detected using Wikipedia:C-banding,[12] and early studies using C-banding showed that differences in the fundamental number (i.e., the number of chromosome arms) could be entirely due to the addition of heterochromatic chromosome arms. It is well documented that heterochromatin may consists of different types of repetitive DNA, not all seen with C-banding, and it can vary greatly between karyotypes of even closely related species. The differences of heterochromatin amount among congeneric rodent species may reach 33% of nuclear DNA in Wikipedia:Dipodomys species,[13] 36% in Wikipedia:Peromyscus species,[14] 42% in Wikipedia:Ammospermophilus[15] and 60% in Wikipedia:Thomomys species where Wikipedia:C-value (haploid DNA content) ranges between 2.1 and 5.6 pg.[16][17] The Wikipedia:red viscacha rat (Tympanoctomys barrerae) has a record C-value among mammals—9.2 pg.[18] Although tetrapoidy was first proposed to be a reason for its high genome size and diploid chromosome number, Svartman et al.[19] showed that the high genome size was due to the enormous amplification of heterochromatin. Although one single copy number gene was found to be duplicated in the red viscacha rat genome,[20] data on absence of large genome segment duplications (single paints of most Octodon degu probes) and repetitive DNA hybridization evidence rules against tetraploidy. The study of heterochromatin composition, repeated DNA amount and its distribution on chromosomes of octodontids is absolutely necessary to define exactly what heterochromatin fraction is responsible for the large genomes of the red viscacha rat.[21]

In comparative cytogenetics, chromosome homology between species was proposed on the basis of similarities in banding patterns. Closely related species often had very similar banding pattern and after 40 years of comparing bands it seems safe to generalize that karyotype divergence in most taxonomic groups follows their phylogenetic relationship although there are notable exceptions.[22][10]

The conservation of large chromosome segments makes comparison between species possible and worthwhile. On the whole chromosome banding has been a reliable indicator of chromosome homology, i.e. that the chromosome identified on the basis of banding actually carry the same genes. However, this is not always the case especially when phylogenetically distant species or species that have experienced extremely rapid chromosome evolution are compared. Banding after all is still morphology and is not always a foolproof indicator of DNA content.[21]

Comparative molecular cytogenetics[edit]

The third step occurred when molecular techniques were incorporated into cytogenetics. These techniques use DNA probes of diverse sizes to compare chromosomes directly at the DNA level. Therefore homology was more confidently compared even between phylogenetically distant species or highly rearranged species (gibbons). Using cladistic analysis rearrangements that have diversified the mammalian karyotype were then more precisely mapped and placed in a phylogenomic perspective. "Wikipedia:Comparative chromosomics" is a new term that was used to define the field of cytogenetics dealing with recent molecular approaches,[23] although "chromosomics" was originally introduced to define the research of chromatin dynamics and morphological changes in interphase chromosome structures.[24]

Chromosome painting or Zoo-FISH was the first technique to have a wide-ranging impact.[25][26][27][28][29] With this method the homology of chromosome regions between different species are identified by hybridizing DNA probes of 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 scenario of chromosomal evolution. When many species covering different mammalian orders are compared, the analysis provides 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 tiny homologous regions resulted from multiple rearrangements (as between mouse and human). Besides, the method fails to report internal inversions within large segments. Another limitation is that painting across great phylogenetic distance often results in a decreased efficiency. Nevertheless, use of painting probes derived form different species combined with comparative sequencing projects helps to increase the resolution of the method.[21]

In addition to sorting, Wikipedia:microdissection of chromosomes and chromosome regions was used to obtain probes for chromosome painting. Impressive results were obtained when a series of microdissection probes covering the total human genome was localized on anthropoid primate chromosomes via multicolor banding (MCB).[30][31] 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 chromosome set—have similar drawbacks and have had little application outside of clinical cytogenetics.[21]

A comparative chromosome map of birds' and mammals' inferred human homologies (right numbers) on chromosome Wikipedia:idiograms[38]

Comparative genomics data including chromosome painting confirmed the high extent of conservation for mammalian chromosomes.[29] Total human chromosomes or their arms can efficiently paint extended chromosome regions in many placentals down to Wikipedia:Afrotheria and Wikipedia:Xenarthra. Humans are most commonly used as a reference species in chromosome comparisons. Gene localization data on human chromosomes can be extrapolated to the homologous chromosome regions of other species with high reliability. Another surprising feature that facilitates the use of the human genome in comparative studies is that humans are a species with a conserved syntenic chromosome organization that is not so distant from the ancestral condition of all placentals.

Post-genomic time and comparative chromosomics[edit]

After the Human Genome Project was completed, researchers focused on evolutionary comparisons of the genome structures of different species. The whole genome of any species can be sequenced completely and repeatedly to obtain a comprehensive, single-nucleotide map. The method makes it possible to compare genomes for any two species regardless of their taxonomic distance.

Sequencing efforts provided a host of products that were put to good use in molecular cytogenetics. Fluorescence in situ hybridization (FISH) with DNA clones (BAC and YAC clones, Wikipedia:cosmids) allowed the construction of chromosome maps at a resolution of several megabases which could detect relatively small chromosome rearrangements. A resolution of several kilobases can be achieved on interphase chromatin. A limitation is that hybridization efficiencies drop off with increasing phylogenetic distance.

Radiation hybrid (RH) genome mapping is another efficient approach. This method includes the irradiation of cells to disrupt the genome into the desired number of fragments that are subsequently fused with Chinese hamster cells. The resulting somatic cell hybrids contain individual fragments of the genome of interest. Then, 90–100 (sometimes, more) clones covering the total genome are selected, and the sequences of interest are localized on the cloned fragments via the Wikipedia:polymerase chain reaction (PCR) or direct DNA–DNA hybridization. To compare the genomes and chromosomes of two species, RHs should be obtained for both of them.[21]

Sex chromosome evolution[edit]

In contrast to many other taxa, therian mammals and birds are characterized by highly conserved systems of genetic sex determination that lead to special chromosomes, i.e. the Wikipedia:sex chromosomes. Although the XX/XY sex chromosome system is the most common among eutherian species, it is not universal. In some species X-autosomal translocations result in the appearance of "additional Y" chromosomes (for example, XX/XY1Y2Y3 systems in Wikipedia:black muntjac[39][40]). In other species Y-autosomal translocations lead to appearance of additional X chromosomes (for example, in some Wikipedia:New World primates such as Wikipedia:howler monkeys). In this respect rodents again represent a peculiar, derived group, comprising the record number of species with non-classical sex chromosomes such as the Wikipedia:wood lemming, the Wikipedia:collared lemming, the Wikipedia:creep vole, the Wikipedia:spinous country rat, the Wikipedia:Akodon and the Wikipedia:bandicoot rat.[41]

See also[edit]

References[edit]

  1. ↑ W. J., ({{{year}}}). "Using genomic data to unravel the root of the placental mammal phylogeny," Genome Research, 17, 413–421.
  2. ↑ O. R., ({{{year}}}). "The delayed rise of present-day mammals," Nature, 446, 507–512.
  3. ↑ This tree depicts historic divergence relationships among the living orders of mammals. The phylogenetic hierarchy is a consensus view of several decades of molecular genetic, morphological and fossil inference (see for example,[1][2]). Double rings indicate mammalian supertaxa, numbers indicate the possible time of divergences.
  4. ↑ W. J., ({{{year}}}). "Molecular phylogenetics and the origins of placental mammals," Nature, 409, 614–618.
  5. ↑ a. Metaphase spread of the Wikipedia:Indian muntjac (Muntiacus muntjak vaginalis, 2n = 6, 7), the species with the lowest chromosome number. b. Metaphase spread of the Wikipedia:Viscacha rat (Tympanoctomys barrerae, 2n = 102), the species with the highest chromosome number. c. Metaphase spread of the Wikipedia:Siberian roe deer (Capreolus pygargus, 2n = 70 + 1-14 B's), the species with additional, or B- chromosomes. d. Metaphase spread of the Wikipedia:Transcaucasian Mole Vole female (Ellobius lutescens, 2n = 17, X0 in both sexes).
  6. ↑ HJ LA, ({{{year}}}). "The chromosome numbers of man," Hereditas, 42, 1–6.
  7. ↑ D. H., ({{{year}}}). "Indian muntjac, Muntiacus muntjak: a deer with a low diploid chromosome number," Science, 168, 1364–1366.
  8. ↑ L. C., ({{{year}}}). "The Largest Known Chromosome-Number for a Mammal, in a South-American Desert Rodent," Experientia, 46, 506–508.
  9. ↑ , ({{{year}}}). "Paris Conference (1971): Standardization in human cytogenetics," Cytogenetics, 11, 317–362.
  10. ↑ 10.0 10.1 W. G. N., ({{{year}}}). "Atlas of Mammalian Chromosomes," {{{journal}}}, {{{volume}}}, .
  11. ↑ a. C-banded chromosomes of the Eurasian shrew (Wikipedia:Sorex araneus, 2n = 21), example of the smallest amount of heterochromatic bands in mammalian genome. b. C-banded chromosomes of the ground squirrel (Wikipedia:Spermophilus erythrogenys, 2n = 36) with very large centomeric C-bands. c. C-banded chromosomes of the marbled polecat (Wikipedia:Vormela peregusna, 2n = 38) with the largest additional heterochromatic arms on some autosomes. d. C-banded chromosomes of the Amur hedgehog (Wikipedia:Erinaceus amurensis, 2n = 48) with the very large telomeric C-bands on autosomes. e. C-banded chromosomes of the Eversmann's hamster (Wikipedia:Allocricetulus eversmanni, 2n = 26) with pericentomeric C-bands on the X and Y chromosomes. f. C-banded chromosomes of the southern vole (Wikipedia:Microtus rossiaemeridionalis, 2n = 54) with very large C-bands on both sex chromosomes.
  12. ↑ T. C., ({{{year}}}). "Distribution of constitutive heterochromatin in mamalian chromosomes," Chromosoma, 34, 243–253.
  13. ↑ F. T., ({{{year}}}). "Satellite DNA and cytogenetic evolution. DNA quantity, satellite DNA and karyotypic variations in kangaroo rats (genus Dipodomys)," Chromosoma, 58, 155–168.
  14. ↑ L. L., ({{{year}}}). "Chromosomes of Peromyscus (rodentia, cricetidae). VI. The genomic size," Cytogenet Cell Genet, 19, 241–249.
  15. ↑ JT MJ, ({{{year}}}). "Chromosomes of antelope squirrels (genus Ammospermophilus): a systematic banding analysis of four species with unusual constitutive heterochromatin," Chromosoma, 64, 207–217.
  16. ↑ J. L., ({{{year}}}). "Genome evolution in pocket gophers (genus Thomomys). I. Heterochromatin variation and speciation potential," Chromosoma, 85, 149–162.
  17. ↑ S. W., ({{{year}}}). "Genome evolution in pocket gophers (genus Thomomys). II. Variation in cellular DNA content," Chromosoma, 85, 163–179.
  18. ↑ M. H., ({{{year}}}). "Discovery of tetraploidy in a mammal," Nature, 401, 341.
  19. ↑ M., ({{{year}}}). "Molecular cytogenetics discards polyploidy in mammals," Genomics, 85, 425–430.
  20. ↑ M. H., ({{{year}}}). "Molecular cytogenetics and allotetraploidy in the red vizcacha rat, Tympanoctomys barrerae (Rodentia, Octodontidae)," Genomics, 88, 214–221.
  21. ↑ 21.0 21.1 21.2 21.3 21.4 A. S., (2011). "The genome diversity and karyotype evolution of mammals," Molecular Cytogenetics, 4, 22.
  22. ↑ A. S., ({{{year}}}). "Conserved and variable elements of mammalian chromosomes," Cytogenetics of animals, {{{volume}}}, 95–124.
  23. ↑ A. S., ({{{year}}}). "[Comparative chromosomics]," Mol Biol (Mosk), 41, 408–422.
  24. ↑ U., ({{{year}}}). "Chromosomics," Cytogenet Genome Res, 111, 101–106.
  25. ↑ J., ({{{year}}}). "Molecular cytotaxonomy of primates by chromosomal in situ suppression hybridization," Genomics, 8, 347–350.
  26. ↑ H., ({{{year}}}). "Cytogenetic Analysis by Chromosome Painting Using Dop-Pcr Amplified Flow-Sorted Chromosomes," Gene Chromosome Canc, 4, 257–263.
  27. ↑ H., ({{{year}}}). "Comparative Chromosome Painting Discloses Homologous Segments in Distantly Related Mammals," Nature Genetics, 6, 342–347.
  28. ↑ M. A., ({{{year}}}). "Genetic analysis by chromosome sorting and painting: phylogenetic and diagnostic applications," Eur J Hum Genet, 5, 253–265.
  29. ↑ 29.0 29.1 M. A., ({{{year}}}). "Mammalian karyotype evolution," Nat Rev Genet, 8, 950–962.
  30. ↑ K., ({{{year}}}). "Reconstruction of the female Gorilla gorilla karyotype using 25-color FISH and multicolor banding (MCB)," Cytogenetics and Cell Genetics, 93, 242–248.
  31. ↑ K., ({{{year}}}). "Detailed Hylobates lar karyotype defined by 25-color FISH and multicolor banding," International Journal of Molecular Medicine, 12, 139–146.
  32. ↑ 32.0 32.1 R., ({{{year}}}). "Reciprocal chromosome painting shows that squirrels, unlike murid rodents, have a highly conserved genome organization," Genomics, 82, 245–249.
  33. ↑ 33.0 33.1 33.2 Ensembl Genome Browser.
  34. ↑ H., ({{{year}}}). "Zoo-FISH analysis: the American mink (Mustela vison) closely resembles the cat karyotype," Chromosome Res, 5, 5–11.
  35. ↑ A. S., ({{{year}}}). "Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree," Cytogenetic and Genome Research, 96, 137–145.
  36. ↑ F., ({{{year}}}). "A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps," Genomics, 62, 189–202.
  37. ↑ A. S., ({{{year}}}). "The proto-oncogene C-KIT maps to canid B-chromosomes," Chromosome Research, 13, 113–122.
  38. ↑ a. Reconstructed karyotype of the ancestral Wikipedia:Eutherian genome.[32] Each chromosome is assigned a specific color. These colors are used for mark homologies in idiograms of chromosomes of other species (5b–5i) b. Idiogram of chicken (Gallus gallus domesticus, 2n = 78) chromosomes. The reconstruction is based on alignments of chicken and human genome sequences.[33] c. Idiogram of short-tailed opossum (Monodelphis domestica, 2n = 18) chromosomes. The reconstruction is based on alignments of opossum and human genome sequences.[33] d. Idiogram of aardvark (Orycteropus afer, 2n = 20) chromosomes. The reconstruction is based on painting data.[32] e. Idiogram of mink (Mustela vison, 2n = 30) chromosomes. The reconstruction is based on painting data.[34][35] f. Idiogram of the Red fox (Vulpes vulpes, 2n = 34 + 0-8 B's) chromosomes. The reconstruction is based on painting and mapping data.[36][37] g. Reconstructed karyotype of the ancestral Sciuridae (Rodentia) genome, based on painting data (Li et al., 2004). h. Idiogram of the House mouse (Mus musculus, 2n = 40) chromosomes. The reconstruction is based on alignments of Mus and human genome sequences.[33] i. Idiogram of human (Homo sapiens, 2n = 46) chromosomes.
  39. ↑ F., ({{{year}}}). "A comparative study of karyotypes of muntjacs by chromosome painting," Chromosoma, 103, 642–652.
  40. ↑ L., ({{{year}}}). "High-density comparative BAC mapping in the black muntjac (Muntiacus crinifrons): molecular cytogenetic dissection of the origin of MCR 1p+4 in the X1X2Y1Y2Y3 sex chromosome system," Genomics, 87, 608–615.
  41. ↑ K., ({{{year}}}). "Aberrant sex chromosome mechanisms in mammals. Evolutionary aspects," Differentiation, 23 Suppl, S23–30.
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