Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li1,
- Brian W. Davis1,2,
- Terje Raudsepp1,2,
- Alison J. Pearks Wilkerson1,
- Victor C. Mason1,2,
- Malcolm Ferguson-Smith3,
- Patricia C. O'Brien3,
- Paul D. Waters4 and
- William J. Murphy1,2,5
- 1Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
- 2Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA;
- 3Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, CB3 0ES, United Kingdom;
- 4School of Biotechnology and Biomolecular Sciences, Faculty of Science, The University of New South Wales, Sydney, NSW 2052, Australia
Abstract
Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which different types of selection act to maintain genes within this unique genomic environment. Here, we present the first MSY (male-specific region of the Y chromosome) sequences from two carnivores, the domestic dog and cat. By combining these with other available MSY data, our multiordinal comparison allows for the first accounting of levels of selection constraining the evolution of eutherian Y chromosomes. Despite gene gain and loss across the phylogeny, we show the eutherian ancestor retained a core set of 17 MSY genes, most being constrained by negative selection for nearly 100 million years. The X-degenerate and ampliconic gene classes are partitioned into distinct chromosomal domains in most mammals, but were radically restructured on the human lineage. We identified multiple conserved noncoding elements that potentially regulate eutherian MSY genes. The acquisition of novel ampliconic gene families was accompanied by signatures of positive selection and has differentially impacted the degeneration and expansion of MSY gene repertoires in different species.
Footnotes
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↵5 Corresponding author
E-mail wmurphy{at}cvm.tamu.edu
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.154286.112.
- Received January 3, 2013.
- Accepted June 13, 2013.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.