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The genome diversity and karyotype evolution of mammals

Graphodatsky AS, Trifonov VA, Stanyon R - Mol Cytogenet (2011)

Bottom Line: 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.

Affiliation: Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia. vlad@mcb.nsc.ru.

ABSTRACT

The past decade has witnessed an explosion of genome sequencing and mapping in 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. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results.

Conservation of chromosome banding pattern between mammals. A. Conservation of chromosomes between opossum (Metatheria) and some eutherians based on alignments and painting data. The high degree of conservation in G-banding patterns between the homologous segments of opossum and placental mammals. MDO - short-tailed opossum, Monodelphis domestica (Metatheria, Marsupialia); HSA - human, Homo sapiens (Eutheria, Euarchontoglires, Primates); OAF - aardvark, Orycteropus afer (Eutheria, Afrotheria, Tubulidentata); LAF - African Savannah elephant, Loxodonta africana (Eutheria, Afrotheria, Proboscidea); FCA - domestic cat, Felis catus (Eutheria, Laurasiatheria, Carnivora); GMA - short-finned pilot whale, Globicephala macrorhynchus (Eutheria, Laurasiatheria, Cetartiodactyla); OCU - Old World rabbit. Oryctolagus cuniculus (Eutheria, Euarchontoglires, Lagomorpha); CBA- Bactrian camel, Camelus bactrianus (Eutheria, Laurasiatheria, Cetartiodactyla); SSC - domestic pig, Sus scrofa (Eutheria, Laurasiatheria, Cetartiodactyla); CFA - domestic dog, Canis familiaris (Eutheria, Laurasiatheria, Carnivora); MVI - American mink, Mustela vison (Eutheria, Laurasiatheria, Carnivora); SVU - European squirrel, Sciurus vulgaris (Eutheria, Euarchontoglires, Rodentia). B. Banding patterns for some characteristic eutherian signatures. a. HSA 19/3/21 signature of Carnivora. MVI -mink, Mustela vison; AFU - lesser panda, Ailurus fulgens b. HSA 9/11 and 10p/1q signatures of Glires. OCU - Old World rabbit. Oryctolagus cuniculus; TSI - Siberian chipmunk, Tamias sibiricus c. HSA 1/19 signature of Afrotheria. LAF - African savannah elephant, Loxodonta africana; OAF - aardvark, Orycteropus afer d. Putative HSA 10/14/15 signature of Pegasoferae taxa. EAS - donkey, Equus asinus; MAL- Szechwan myotis, Myotis altarium e. Conservation and putative inversions of HSA4/8p mammalian signature, inferred by localizations of some human and dog chromosomes painting probes. HSA - human, Homo sapiens; CFA - domestic dog, Canis familiaris; OCU - Old World rabbit, Oryctolagus cuniculus; FCA - domestic cat, Felis catus; MVI- American mink, Mustela vison; OAF - aardvark, Orycteropus afer; CCR - spotted hyena, Crocuta crocuta; PLA - masked palm civet, Paguma larvata; AFU - lesser panda, Ailurus fulgens
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Figure 6: Conservation of chromosome banding pattern between mammals. A. Conservation of chromosomes between opossum (Metatheria) and some eutherians based on alignments and painting data. The high degree of conservation in G-banding patterns between the homologous segments of opossum and placental mammals. MDO - short-tailed opossum, Monodelphis domestica (Metatheria, Marsupialia); HSA - human, Homo sapiens (Eutheria, Euarchontoglires, Primates); OAF - aardvark, Orycteropus afer (Eutheria, Afrotheria, Tubulidentata); LAF - African Savannah elephant, Loxodonta africana (Eutheria, Afrotheria, Proboscidea); FCA - domestic cat, Felis catus (Eutheria, Laurasiatheria, Carnivora); GMA - short-finned pilot whale, Globicephala macrorhynchus (Eutheria, Laurasiatheria, Cetartiodactyla); OCU - Old World rabbit. Oryctolagus cuniculus (Eutheria, Euarchontoglires, Lagomorpha); CBA- Bactrian camel, Camelus bactrianus (Eutheria, Laurasiatheria, Cetartiodactyla); SSC - domestic pig, Sus scrofa (Eutheria, Laurasiatheria, Cetartiodactyla); CFA - domestic dog, Canis familiaris (Eutheria, Laurasiatheria, Carnivora); MVI - American mink, Mustela vison (Eutheria, Laurasiatheria, Carnivora); SVU - European squirrel, Sciurus vulgaris (Eutheria, Euarchontoglires, Rodentia). B. Banding patterns for some characteristic eutherian signatures. a. HSA 19/3/21 signature of Carnivora. MVI -mink, Mustela vison; AFU - lesser panda, Ailurus fulgens b. HSA 9/11 and 10p/1q signatures of Glires. OCU - Old World rabbit. Oryctolagus cuniculus; TSI - Siberian chipmunk, Tamias sibiricus c. HSA 1/19 signature of Afrotheria. LAF - African savannah elephant, Loxodonta africana; OAF - aardvark, Orycteropus afer d. Putative HSA 10/14/15 signature of Pegasoferae taxa. EAS - donkey, Equus asinus; MAL- Szechwan myotis, Myotis altarium e. Conservation and putative inversions of HSA4/8p mammalian signature, inferred by localizations of some human and dog chromosomes painting probes. HSA - human, Homo sapiens; CFA - domestic dog, Canis familiaris; OCU - Old World rabbit, Oryctolagus cuniculus; FCA - domestic cat, Felis catus; MVI- American mink, Mustela vison; OAF - aardvark, Orycteropus afer; CCR - spotted hyena, Crocuta crocuta; PLA - masked palm civet, Paguma larvata; AFU - lesser panda, Ailurus fulgens

Mentions: All new comparative genomics data including chromosome painting confirmed the high extent of conservation for mammalian chromosomes [23] (Figures 5, 6). Total human chromosomes or their arms can efficiently paint extended chromosome regions in many placentals down to Afrotheria and 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. In Figure 5 we present chromosomal maps of chicken, opossum, and some species of placentals with homologies to human chromosomes and putative mammalian ancestor chromosomes.

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The genome diversity and karyotype evolution of mammals

Graphodatsky AS, Trifonov VA, Stanyon R - Mol Cytogenet (2011)

Conservation of chromosome banding pattern between mammals. A. Conservation of chromosomes between opossum (Metatheria) and some eutherians based on alignments and painting data. The high degree of conservation in G-banding patterns between the homologous segments of opossum and placental mammals. MDO - short-tailed opossum, Monodelphis domestica (Metatheria, Marsupialia); HSA - human, Homo sapiens (Eutheria, Euarchontoglires, Primates); OAF - aardvark, Orycteropus afer (Eutheria, Afrotheria, Tubulidentata); LAF - African Savannah elephant, Loxodonta africana (Eutheria, Afrotheria, Proboscidea); FCA - domestic cat, Felis catus (Eutheria, Laurasiatheria, Carnivora); GMA - short-finned pilot whale, Globicephala macrorhynchus (Eutheria, Laurasiatheria, Cetartiodactyla); OCU - Old World rabbit. Oryctolagus cuniculus (Eutheria, Euarchontoglires, Lagomorpha); CBA- Bactrian camel, Camelus bactrianus (Eutheria, Laurasiatheria, Cetartiodactyla); SSC - domestic pig, Sus scrofa (Eutheria, Laurasiatheria, Cetartiodactyla); CFA - domestic dog, Canis familiaris (Eutheria, Laurasiatheria, Carnivora); MVI - American mink, Mustela vison (Eutheria, Laurasiatheria, Carnivora); SVU - European squirrel, Sciurus vulgaris (Eutheria, Euarchontoglires, Rodentia). B. Banding patterns for some characteristic eutherian signatures. a. HSA 19/3/21 signature of Carnivora. MVI -mink, Mustela vison; AFU - lesser panda, Ailurus fulgens b. HSA 9/11 and 10p/1q signatures of Glires. OCU - Old World rabbit. Oryctolagus cuniculus; TSI - Siberian chipmunk, Tamias sibiricus c. HSA 1/19 signature of Afrotheria. LAF - African savannah elephant, Loxodonta africana; OAF - aardvark, Orycteropus afer d. Putative HSA 10/14/15 signature of Pegasoferae taxa. EAS - donkey, Equus asinus; MAL- Szechwan myotis, Myotis altarium e. Conservation and putative inversions of HSA4/8p mammalian signature, inferred by localizations of some human and dog chromosomes painting probes. HSA - human, Homo sapiens; CFA - domestic dog, Canis familiaris; OCU - Old World rabbit, Oryctolagus cuniculus; FCA - domestic cat, Felis catus; MVI- American mink, Mustela vison; OAF - aardvark, Orycteropus afer; CCR - spotted hyena, Crocuta crocuta; PLA - masked palm civet, Paguma larvata; AFU - lesser panda, Ailurus fulgens
© Copyright Policy - open-access
Figure 6: Conservation of chromosome banding pattern between mammals. A. Conservation of chromosomes between opossum (Metatheria) and some eutherians based on alignments and painting data. The high degree of conservation in G-banding patterns between the homologous segments of opossum and placental mammals. MDO - short-tailed opossum, Monodelphis domestica (Metatheria, Marsupialia); HSA - human, Homo sapiens (Eutheria, Euarchontoglires, Primates); OAF - aardvark, Orycteropus afer (Eutheria, Afrotheria, Tubulidentata); LAF - African Savannah elephant, Loxodonta africana (Eutheria, Afrotheria, Proboscidea); FCA - domestic cat, Felis catus (Eutheria, Laurasiatheria, Carnivora); GMA - short-finned pilot whale, Globicephala macrorhynchus (Eutheria, Laurasiatheria, Cetartiodactyla); OCU - Old World rabbit. Oryctolagus cuniculus (Eutheria, Euarchontoglires, Lagomorpha); CBA- Bactrian camel, Camelus bactrianus (Eutheria, Laurasiatheria, Cetartiodactyla); SSC - domestic pig, Sus scrofa (Eutheria, Laurasiatheria, Cetartiodactyla); CFA - domestic dog, Canis familiaris (Eutheria, Laurasiatheria, Carnivora); MVI - American mink, Mustela vison (Eutheria, Laurasiatheria, Carnivora); SVU - European squirrel, Sciurus vulgaris (Eutheria, Euarchontoglires, Rodentia). B. Banding patterns for some characteristic eutherian signatures. a. HSA 19/3/21 signature of Carnivora. MVI -mink, Mustela vison; AFU - lesser panda, Ailurus fulgens b. HSA 9/11 and 10p/1q signatures of Glires. OCU - Old World rabbit. Oryctolagus cuniculus; TSI - Siberian chipmunk, Tamias sibiricus c. HSA 1/19 signature of Afrotheria. LAF - African savannah elephant, Loxodonta africana; OAF - aardvark, Orycteropus afer d. Putative HSA 10/14/15 signature of Pegasoferae taxa. EAS - donkey, Equus asinus; MAL- Szechwan myotis, Myotis altarium e. Conservation and putative inversions of HSA4/8p mammalian signature, inferred by localizations of some human and dog chromosomes painting probes. HSA - human, Homo sapiens; CFA - domestic dog, Canis familiaris; OCU - Old World rabbit, Oryctolagus cuniculus; FCA - domestic cat, Felis catus; MVI- American mink, Mustela vison; OAF - aardvark, Orycteropus afer; CCR - spotted hyena, Crocuta crocuta; PLA - masked palm civet, Paguma larvata; AFU - lesser panda, Ailurus fulgens
Mentions: All new comparative genomics data including chromosome painting confirmed the high extent of conservation for mammalian chromosomes [23] (Figures 5, 6). Total human chromosomes or their arms can efficiently paint extended chromosome regions in many placentals down to Afrotheria and 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. In Figure 5 we present chromosomal maps of chicken, opossum, and some species of placentals with homologies to human chromosomes and putative mammalian ancestor chromosomes.

Bottom Line: 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.

Affiliation: Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia. vlad@mcb.nsc.ru.

ABSTRACT

The past decade has witnessed an explosion of genome sequencing and mapping in 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. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results.

View Similar Images In: Results  - Collection
View Article: PubMed Central - HTML -  PubMed
Show All Figures - Show MeSH
getmorefigures.php?pmc=3204295&rFormat=json&query=null&req=5