Preservation of the y transcriptome in a 10-million-year-old plant sex chromosome system

Current Biology

Volumn 21, Issue 17, 2011, Pages 1470-1474

  Bergero, Roberta ^a   Charlesworth, Deborah ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CHROMOSOME MAP; DNA SEQUENCE; EVALUATION; GENE EXPRESSION REGULATION; GENETIC LINKAGE; GENETICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT CHROMOSOME; PLANT GENE; POLYMERASE CHAIN REACTION; SEX CHROMOSOME; SILENE; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENETIC LINKAGE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SEX CHROMOSOMES; SILENE; TRANSCRIPTOME;

ANIMALIA; SILENE; SILENE LATIFOLIA;

EID: 80052816495     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2011.07.032     Document Type: Article

References (34)

1. D. Bachtrog A dynamic view of sex chromosome evolution Curr. Opin. Genet. Dev. 16 2006 578 585 (Pubitemid 44738528)
2. D. Bachtrog, and B. Charlesworth Reduced adaptation of a non-recombining neo-Y chromosome Nature 416 2002 323 326 (Pubitemid 34260246)
3. D. Bachtrog Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila Genome Res. 15 2005 1393 1401 (Pubitemid 41400906)
4. D. Bachtrog Expression profile of a degenerating neo-y chromosome in Drosophila Curr. Biol. 16 2006 1694 1699 (Pubitemid 44691786)
5. Q. Yu, S. Hou, F.A. Feltus, M.R. Jones, J.E. Murray, O. Veatch, C. Lemke, J.H. Saw, R.C. Moore, and J. Thimmapuram Low X/Y divergence in four pairs of papaya sex-linked genes Plant J. 53 2008 124 132 (Pubitemid 350265248)
6. Z. Liu, P.H. Moore, H. Ma, C.M. Ackerman, M. Ragiba, Q. Yu, H.M. Pearl, M.S. Kim, J.W. Charlton, and J.I. Stiles A primitive Y chromosome in papaya marks incipient sex chromosome evolution Nature 427 2004 348 352 (Pubitemid 38133661)
7. R.B. Spigler, K.S. Lewers, and T.L. Ashman Genetic architecture of sexual dimorphism in a subdioecious plant with a proto-sex chromosome Evolution 65 2011 1114 1126
8. T. Yin, S.P. Difazio, L.E. Gunter, X. Zhang, M.M. Sewell, S.A. Woolbright, G.J. Allan, C.T. Kelleher, C.J. Douglas, M. Wang, and G.A. Tuskan Genome structure and emerging evidence of an incipient sex chromosome in Populus Genome Res. 18 2008 422 430 (Pubitemid 351347085)
9. R. Bergero, A. Forrest, E. Kamau, and D. Charlesworth Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: Evidence from new sex-linked genes Genetics 175 2007 1945 1954 (Pubitemid 46789975)
10. D.A. Filatov, V. Laporte, C. Vitte, and D. Charlesworth DNA diversity in sex-linked and autosomal genes of the plant species Silene latifolia and Silene dioica Mol. Biol. Evol. 18 2001 1442 1454 (Pubitemid 32735092)
11. I. Atanassov, C. Delichre, D.A. Filatov, D. Charlesworth, I. Negrutiu, and F. Monéger A putative monofunctional fructose-2,6-bisphosphatase gene has functional copies located on the X and Y sex chromosomes in white campion (Silene latifolia) Mol. Biol. Evol. 18 2001 2162 2168
12. D.A. Filatov, F. Monéger, I. Negrutiu, and D. Charlesworth Evolution of a plant Y-chromosome: Variability in a Y-linked gene of Silene latifolia Nature 404 2000 388 390 (Pubitemid 30164339)
13. J.E. Ironside, and D.A. Filatov Extreme population structure and high interspecific divergence of the Silene Y chromosome Genetics 171 2005 705 713 (Pubitemid 43156458)
14. S. Qiu, R. Bergero, A. Forrest, V.B. Kaiser, and D. Charlesworth Nucleotide diversity in Silene latifolia autosomal and sex-linked genes Proc. Biol. Sci. 277 2010 3283 3290
15. D.A. Filatov Evolutionary history of Silene latifolia sex chromosomes revealed by genetic mapping of four genes Genetics 170 2005 975 979 (Pubitemid 40980697)
16. D. Honys, and D. Twell Comparative analysis of the Arabidopsis pollen transcriptome Plant Physiol. 132 2003 640 652 (Pubitemid 36715064)
17. S. Matsunaga, M. Hizume, S. Kawano, and T. Kuroiwa Cytological analyses in Melandrium album: Genome size, chromosome size and fluorescence in situ hybridization Cytologia (Tokyo) 59 1994 135 141 (Pubitemid 2081708)
18. K. Yamada, J. Lim, J.M. Dale, H. Chen, P. Shinn, C.J. Palm, A.M. Southwick, H.C. Wu, C. Kim, and M. Nguyen Empirical analysis of transcriptional activity in the Arabidopsis genome Science 302 2003 842 846 (Pubitemid 37339620)
19. V.B. Kaiser, R. Bergero, and D. Charlesworth Slcyt, a newly identified sex-linked gene, has recently moved onto the X chromosome in Silene latifolia (Caryophyllaceae) Mol. Biol. Evol. 26 2009 2343 2351
20. G.A. Marais, M. Nicolas, R. Bergero, P. Chambrier, E. Kejnovsky, F. Monéger, R. Hobza, A. Widmer, and D. Charlesworth Evidence for degeneration of the Y chromosome in the dioecious plant Silene latifolia Curr. Biol. 18 2008 545 549
21. B. Charlesworth, and D. Charlesworth The degeneration of Y chromosomes Philos. Trans. R. Soc. Lond. B Biol. Sci. 355 2000 1563 1572
22. D. Bachtrog The temporal dynamics of processes underlying Y chromosome degeneration Genetics 179 2008 1513 1525
23. N.J. Tourasse, and W.H. Li Selective constraints, amino acid composition, and the rate of protein evolution Mol. Biol. Evol. 17 2000 656 664 (Pubitemid 30210710)
24. D. Honys, and D. Twell Transcriptome analysis of haploid male gametophyte development in Arabidopsis Genome Biol. 5 2004 R85
25. S.D. Tanksley, D. Zamir, and C.M. Rick Evidence for extensive overlap of sporophytic and gametophytic gene expression in Lycopersicon esculentum Science 213 1981 453 455 (Pubitemid 11023967)
26. J.R. Stinson, A.J. Eisenberg, R.P. Willing, M.E. Pe, D.D. Hanson, and J.P. Mascarenhas Genes expressed in the male gametophyte of flowering plants and their isolation Plant Physiol. 83 1987 442 447
27. C. Correns Die rolle der männlichen Keimzellen bei der Geschlechtsbestimmung der gynodioecishen Pflanzen Ber. Dtsch. Bot. Ges. 26A 1908 626 701
28. G.A.B. Marais, A. Forrest, E. Kamau, J. Käfer, V. Daubin, and D. Charlesworth Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene PLoS ONE 6 2011 e20077
29. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
30. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M.A. DePristo The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Genome Res. 20 2010 1297 1303
31. Z. Zhang, J. Li, X.Q. Zhao, J. Wang, G.K. Wong, and J. Yu KaKs-Calculator: Calculating Ka and Ks through model selection and model averaging Genomics Proteomics Bioinformatics 4 2006 259 263
32. M. Nei, and T. Gojobori Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions Mol. Biol. Evol. 3 1986 418 426 (Pubitemid 16010523)
33. W.A. Pearson Rapid and sensitive sequence comparison with FASTP and FASTA R. Doolittle, Methods in Enzymology Volume 183 1990 Academic Press San Diego, CA 63 98
34. D.A. Filatov, and D. Charlesworth Substitution rates in the X- and Y-linked genes of the plants, Silene latifolia and S. dioica Mol. Biol. Evol. 19 2002 898 907 (Pubitemid 34602959)