Cross-species chromosome painting between human and marsupial directly demonstrates the ancient region of the mammalian X

Glas, Robert; Graves, Jennifer A. Marshall; Toder, Roland; Ferguson-Smith, Malcolm; O’Brien, Patrícia C. M.

doi:10.1007/s003359901174

Cited by 70 publications

(49 citation statements)

References 10 publications

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“…Although a strict cladistic interpretation of our data is problematic (the appropriate outgroup to the Afrotheria would be a marsupial), we follow others in using commonality of a particular chromosomal state to reflect a common evolutionary origin (21,(25)(26)(27). [Thus far, chromosome painting across the Eutheria͞Metatheria boundary has proved intractable with the exception of the X chromosome, where a portion, Xp11.23Xqter, is conserved between the two lineages (28).] In determining primitive and derived associations, we used chromosome painting data from representatives of the Primates, Scandentia, Lagomorpha, Carnivora, Cetartiodactyla, Perissodactyla, Chiroptera, Insectivora (Eurylipotyphla), Xenarthra, and the two Afrotherian orders the Tubulidentata and Proboscidea (see ref.…”

Section: Methodsmentioning

confidence: 99%

Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype

Yang

Alkalaeva

Perelman

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

158

194

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The Afrotheria, a supraordinal grouping of mammals whose radiation is rooted in Africa, is strongly supported by DNA sequence data but not by their disparate anatomical features. We have used flow-sorted human, aardvark, and African elephant chromosome painting probes and applied reciprocal painting schemes to representatives of two of the Afrotherian orders, the Tubulidentata (aardvark) and Proboscidea (elephants), in an attempt to shed additional light on the evolutionary affinities of this enigmatic group of mammals. Although we have not yet found any unique cytogenetic signatures that support the monophyly of the Afrotheria, embedded within the aardvark genome we find the strongest evidence yet of a mammalian ancestral karyotype comprising 2n ‫؍‬ 44. This karyotype includes nine chromosomes that show complete conserved synteny to those of man, six that show conservation as single chromosome arms or blocks in the human karyotype but that occur on two different chromosomes in the ancestor, and seven neighbor-joining combinations (i.e., the synteny is maintained in the majority of species of the orders studied so far, but which corresponds to two chromosomes in humans). The comparative chromosome maps presented between human and these Afrotherian species provide further insight into mammalian genome organization and comparative genomic data for the Afrotheria, one of the four major evolutionary clades postulated for the Eutheria.

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Section: Methodsmentioning

confidence: 99%

Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype

Yang

Alkalaeva

Perelman

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

158

194

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“…comm.). mosome that are syntenic to the Monodelphis chromosomes 4 and 7 and that appear to have conjoined the rest of the X chromosome early in eutherian evolution (Glas et al 1999) (Figs. 2B, 3C; Supplemental Table 1).…”

Section: ‫3מ‬mentioning

confidence: 99%

An analysis of the gene complement of a marsupial,Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

Goodstadt¹,

Heger²,

Webber³

et al. 2007

Genome Res.

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The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of metatherians. Here, we compare Monodelphis with Homo sequences from alignments of single nucleotides, genes, and whole chromosomes. Using PhyOP, we have established orthologs in Homo for 82% (15,250) of Monodelphis gene predictions. Those with single orthologs in each species exhibited a high median synonymous substitution rate (d S = 1.02), thereby explaining the relative paucity of aligned regions outside of coding sequences. Orthology assignments were used to construct a synteny map that illustrates the considerable fragmentation of Monodelphis and Homo karyotypes since their therian last common ancestor. Fifteen percent of Monodelphis genes are predicted, from their low divergence at synonymous sites, to have been duplicated in the metatherian lineage. The majority of Monodelphis-specific genes possess predicted roles in chemosensation, reproduction, adaptation to specific diets, and immunity. Using alignments of Monodelphis genes to sequences from either Homo or Trichosurus vulpecula (an Australian marsupial), we show that metatherian X chromosomes have elevated silent substitution rates and high G+C contents in comparison with both metatherian autosomes and eutherian chromosomes. Each of these elevations is also a feature of subtelomeric chromosomal regions. We attribute these observations to high rates of female-specific recombination near the chromosomal ends and within the X chromosome, which act to sustain or increase G+C levels by biased gene conversion. In particular, we propose that the higher G+C content of the Monodelphis X chromosome is a direct consequence of its small size relative to the giant autosomes.

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“…Chromosome flow sorting followed by DOP-PCR leads to reciprocal and multi-directional chromosome painting between all extant placental mammal orders. The results permitted hypotheses about the architecture and content of the ancestral placental mammalian karyotype, which have proved to be amazingly heuristic (Chowdhary et al 1998;Glas et al 1999;Froenike et al 2003;Murphy et al 2003;Richard et al 2003;Yang et al 2003;Svartman et al 2004). Bioinformatics provided an alternative approach to reconstructing ancestral genomes (Bourque and Pevzner 2002).…”

mentioning

confidence: 99%

Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed

Rocchi¹,

Archidiacono²,

Stanyon³

2006

Genome Res.

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Cross-species chromosome painting between human and marsupial directly demonstrates the ancient region of the mammalian X

Cited by 70 publications

References 10 publications

Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype

Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype

An analysis of the gene complement of a marsupial,Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed

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