Comparative analysis of mammalian y chromosomes illuminates ancestral structure and lineage-specific evolution

Genome Research

Volumn 23, Issue 9, 2013, Pages 1486-1495

  Li, Gang ^a   Davis, Brian W ^a,b   Raudsepp, Terje ^a,b   Wilkerson, Alison J Pearks ^a   Mason, Victor C ^a,b   Ferguson Smith, Malcolm ^c   O'Brien, Patricia C ^c   Waters, Paul D ^d   Murphy, William J ^a,b  

^a TEXAS A AND M UNIVERSITY   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAT; CHROMOSOME ANALYSIS; DOG; EVOLUTION; GENE LOSS; MALE; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; Y CHROMOSOME;

CANIS FAMILIARIS; EUTHERIA; MAMMALIA;

ANIMALS; CATS; CHROMOSOMES, MAMMALIAN; DOGS; EVOLUTION, MOLECULAR; GENETIC LOCI; MALE; PHYLOGENY; SELECTION, GENETIC; Y CHROMOSOME;

EID: 84883727395     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.154286.112     Document Type: Article

References (45)

1. Alkan C, Sajjadian S, Eichler EE. 2011. Limitations of next-generation genome sequence assembly. Nat Methods 8: 61-65.
2. Bachtrog D. 2004. Evidence that positive selection drives Y-chromosome degeneration in Drosophila miranda. Nat Genet 36: 518-522.
3. Bourque G, Pevzner PA. 2002. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res 12: 26-36.
4. Carvalho AB, Koerich LB, Clark AG. 2009. Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet 25: 270-277.
5. Chang TC, Klabnik JL, Liu WS. 2011. Regional selection acting on the OFD1 gene family. PLoS ONE 6: e26195.
6. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S. 2004. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14: 1147-1159.
7. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
8. Cocquet J, Ellis PJ, Mahadevaiah SK, Affara NA, Vaiman D, Burgoyne PS. 2012. A genetic basis for a postmeiotic X versus Y chromosome intragenomic conflict in the mouse. PLoS Genet 8: e1002900.
9. Engstrom PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B. 2007. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res 17: 1898-1908.
10. Graves JAM. 2006. Sex chromosome specialization and degeneration in mammals. Cell 124: 901-914.
11. Hamilton CK, Revay T, Domander R, Favetta LA, King WA. 2011. A large expansion of the HSFY gene family in cattle shows dispersion across Yq and testis-specific expression. PLoS ONE 6: e17790.
12. Hughes JF, Skaletsky H, Pyntikova T, Minx PJ, Graves T, Rozen S, Wilson RK, Page DC. 2005. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature 437: 100-103.
13. Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SK, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463: 536-539.
14. Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, et al. 2012. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature 483: 82-86.
15. Irimia M, Tena JJ, Alexis M, Fernandez-Minan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gomez-Skarmeta JL, Fraser HB. 2012. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res 22: 2356-2367.
16. Kaiser VB, Bachtrog D. 2010. Evolution of sex chromosomes in insects. Annu Rev Genet 44: 91-112.
17. Katoh K, Toh H. 2010. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26: 1899-1900.
18. Koerich LB, Wang XY, Clark AG, Carvalho AB. 2008. Low conservation of gene content in the Drosophila Y chromosome. Nature 456: 949-951.
19. Kuroki Y, Toyoda A, Noguchi H, Taylor TD, Itoh T, Kim DS, Kim DW, Choi SH, Kim IC, Choi HH, et al. 2006. Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat Genet 38: 158-167.
20. Lahn BT, Page DC. 1999. Four evolutionary strata on the human X chromosome. Science 286: 964-967.
21. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
22. Liu ZY, Moore PH, Ma H, Ackerman CM, Ragiba M, Yu QY, Pearl HM, KimMS, Charlton JW, Stiles JI, et al. 2004. A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427: 348-352.
23. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, et al. 2006. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
24. Marin I, Baker BS. 1998. The evolutionary dynamics of sex determination. Science 281: 1990-1994.
25. Mazeyrat S, Saut N, Sargent CA, Grimmond S, Longepied G, Ehrmann IE, Ellis PS, Greenfield A, Affara NA, Mitchell MJ. 1998. The mouse Y chromosome interval necessary for spermatogonial proliferation is gene dense with syntenic homology to the human AZFa region. Hum Mol Genet 7: 1713-1724.
26. Meredith RW, Janecka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simao TLL, Stadler T, et al. 2011. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334: 521-524.
27. MillerW, Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708-715.
28. Murphy WJ, Wilkerson AJP, Raudsepp T, Agarwala R, Schaffer AA, Stanyon R, Chowdhary BP. 2006. Novel gene acquisition on carnivore Y chromosomes. PLoS Genet 2: 353-363.
29. Pearks Wilkerson AJ, Raudsepp T, Graves T, Albracht D, Warren W, Chowdhary BP, Skow LC, Murphy WJ. 2008. Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome. Genomics 92: 329-338.
30. Posada D, Crandall KA. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14: 817-818.
31. Raudsepp T, Das PJ, Avila F, Chowdhary BP. 2012. The pseudoautosomal region and sex chromosome aneuploidies in domestic species. Sex Dev 6: 72-83.
32. Repping S, van Daalen SKM, Brown LG, Korver CM, Lange J, Marszalek JD, Pyntikova T, van der Veen F, Skaletsky H, Page DC, et al. 2006. High mutation rates have driven extensive structural polymorphism among human Y chromosomes. Nat Genet 38: 463-467.
33. Rice WR. 1987. Genetic hitchhiking and the evolution of reduced geneticactivity of the Y-sex chromosome. Genetics 116: 161-167.
34. Rice WR. 1996. Evolution of the Y sex chromosome in animals. Bioscience 46: 331-343.
35. Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Page DC. 2003. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423: 873-876.
36. Schmittgen TD, Livak KJ. 2008. Analyzing real-time PCR data by the comparative C-T method. Nat Protoc 3: 1101-1108.
37. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. 2004. Human-mouse alignments with BLASTZ. Genome Res 13: 103-107.
38. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, et al. 2003. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825-837.
39. Stamatakis A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
40. Swanson WJ, Vacquier VD. 2002. The rapid evolution of reproductive proteins. Nat Rev Genet 3: 137-144.
41. Toure A, Grigoriev V, Mahadevaiah SK, Rattigan A, Ojarikre OA, Burgoyne PS. 2004. A protein encoded by a member of the multicopy Ssty gene family located on the long arm of the mouse Y chromosome is expressed during sperm development. Genomics 83: 140-147.
42. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
43. Vernet N, Mahadevaiah SK, Ojarikre OA, Longepied G, Prosser HM, Bradley A, Mitchell MJ, Burgoyne PS. 2011. The Y-encoded gene Zfy2 acts to remove cells with unpaired chromosomes at the first meiotic metaphase in male mice. Curr Biol 21: 787-793.
44. Washietl S, Hofacker IL, Stadler PF. 2005. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci 102: 2454-2459.
45. Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.