This Article Full Text Full Text (PDF) Monodelphis domestica Genome Supplemental Research Data All Versions of this Article: gr.6093907v1 17/7/969    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Goodstadt, L. Articles by Ponting, C. P. Search for Related Content PubMed PubMed Citation Articles by Goodstadt, L. Articles by Ponting, C. P. Related Content Related Articles Social Bookmarking                   What's this?

Letter

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

MRC Functional Genetics Unit, University of Oxford, Department of Physiology, Anatomy, and Genetics, South Parks Road, Oxford OX1 3QX, UK

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.

E-mail leo.goodstadt{at}dpag.ox.ac.uk; fax 44-1865-272420.

[Supplemental material is available online at www.genome.org.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6093907

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

Related Articles

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica

Andrew J. Gentles, Matthew J. Wakefield, Oleksiy Kohany, Wanjun Gu, Mark A. Batzer, David D. Pollock, and Jerzy Jurka
Genome Res. 2007 17: 992-1004. [Abstract] [Full Text] [PDF]

This article has been cited by other articles:

				P. B. Samollow The opossum genome: Insights and opportunities from an alternative mammal Genome Res., August 1, 2008; 18(8): 1199 - 1215. [Abstract] [Full Text] [PDF]

				A. Heger and C. P. Ponting Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes Genome Res., December 1, 2007; 17(12): 1837 - 1849. [Abstract] [Full Text] [PDF]