Faster evolution of Z-linked duplicate genes in chicken

Li Yan^{a, c, #},
Zhang Liqing^{d, #},
Zhang Dexiang^e,
Zhang Xiquan^e,
Lu Xuemei^{a, b
, ,}

a.
State Key Laboratory of Biocontrol and International Center for Evolutionary and Genomic Studies, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
b.
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 10029, China
c.
Key Laboratory of Conservation and Utilization of Bio-resource, Yunnan University, Yunnan 650091, China
d.
Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0106, USA
e.
Department of Animal Science, South China Agricultural University, Guangzhou 510642, China

More Information

Corresponding author: E-mail address: luxm@big.ac.cn (Lu Xuemei)

These authors contributed equally to this work.

摘要

- /
- /
- /
- /
Abstract: It has been shown that duplicate genes on the X chromosome evolve much faster than duplicate genes on autosomes inDrosophila melanogaster. However, whether this phenomenon is general and can be applied to other species is not known. Here we examined this issue in chicken that have heterogametic females (females have ZW sex chromosome). We compared sequence divergence of duplicate genes on the Z chromosome with those on autosomes. We found that duplications on the Z chromosome indeed evolved faster than those on autosomes and show distinct patterns of molecular evolution from autosomal duplications. Examination of the expression of duplicate genes revealed an enrichment of duplications on the Z chromosome having male-biased expression and an enrichment of duplications on the autosomes having female-biased expression. These results suggest an evolutionary trend of the recruitment of duplicate genes towards reproduction-specific function. The faster evolution of duplications on Z than on the autosomes is most likely contributed by the selective forces driving the fixation of adaptive mutations on Z. Therefore, the common phenomena observed in both flies and chicken suggest that duplicate genes on sex chromosomes have distinct dynamics and are more influenced by natural selection than autosomal duplications, regardless of the kind of sex determination systems.
- faster evolution /
- Z chromosome /
- gene duplication /
- gene expression /
- chicken genome
These authors contributed equally to this work.
注释:

HTML全文

参考文献(31)

[1]	Begun, D.J. Genetics, 145 (1997),pp. 375-382
[2]	Betran, E., Thornton, K., Long, M. Genome Res., 12 (2002),pp. 1854-1859
[3]	Borge, T., Lindroos, K., Nadvornik, P. et al. Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post-zygotic barriers to gene exchange J. Evol. Biol., 18 (2005),pp. 1416-1424
[4]	Charlesworth, B. The evolution of chromosomal sex determination Novartis Found Symp, 244 (2002),pp. 207-219
[5]	Charlesworth, B., Coyne, J.A., Barton, N.H. The relative rates of evolution of sex chromosomes and autosomes Am. Nat., 130 (1987),pp. 113-146
[6]	Chicken Genome Sequencing Consortium International Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Nature, 432 (2004),pp. 695-716
[7]	Emerson, J.J., Kaessmann, H., Betran, E. et al. Extensive gene traffic on the mammalian X chromosome Science, 303 (2004),pp. 537-540
[8]	Force, A., Lynch, M., Pickett, F.B. et al. Preservation of duplicate genes by complementary, degenerative mutations Genetics, 151 (1999),pp. 1531-1545
[9]	Gentleman, R.C., Carey, V.J., Bates, D.M. et al. Bioconductor: open software development for computational biology and bioinformatics Genome Biol., 5 (2004),p. R80
[10]	Hughes, A.L., Nei, M. Maintenance of MHC polymorphism Nature, 355 (1992),pp. 402-403
[11]	Irizarry, R.A., Hobbs, B., Collin, F. et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics, 4 (2003),pp. 249-264
[12]	Jaszai, J., Fargeas, C.A., Haase, M. et al. Robust expression of Prominin-2 all along the adult male reproductive system and urinary bladder Histochem. Cell. Biol., 130 (2008),pp. 749-759
[13]	Kaiser, V.B., Ellegren, H. Nonrandom distribution of genes with sex-biased expression in the chicken genome Evolution, 60 (2006),pp. 1945-1951
[14]	Kirkpatrick, M., Hall, D.W. Sexual selection and sex linkage Evolution, 58 (2004),pp. 683-691
[15]	Lee, M.L., Kuo, F.C., Whitmore, G.A. et al. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations Proc. Natl. Acad. Sci. USA, 97 (2000),pp. 9834-9839
[16]	Long, M., Langley, C.H. Science, 260 (1993),pp. 91-95
[17]	Mank, J.E., Axelsson, E., Ellegren, H. Fast-X on the Z: rapid evolution of sex-linked genes in birds Genome Res., 17 (2007),pp. 618-624
[18]	Nurminsky, D.I., Nurminskaya, M.V., De Aguiar, D. et al. Nature, 396 (1998),pp. 572-575
[19]	Pavlidis, P., Li, Q., Noble, W.S. The effect of replication on gene expression microarray experiments Bioinformatics, 19 (2003),pp. 1620-1627
[20]	Reeve, H.K., Pfennig, D.W. Genetic biases for showy males: are some genetic systems especially conducive to sexual selection? Proc. Natl. Acad. Sci. USA, 100 (2003),pp. 1089-1094
[21]	Ritchie, M.G., Phillips, S.D.F.
[22]	Stahl, E.A., Dwyer, G., Mauricio, R. et al. Nature, 400 (1999),pp. 667-671
[23]	Storchova, R., Divina, P. Nonrandom representation of sex-biased genes on chicken Z chromosome J. Mol. Evol., 63 (2006),pp. 676-681
[24]	Sundstrom, H., Webster, M.T., Ellegren, H. Reduced variation on the chicken Z chromosome Genetics, 167 (2004),pp. 377-385
[25]	Thornton, K., Long, M. Mol. Biol. Evol., 19 (2002),pp. 918-925
[26]	Thornton, K., Long, M. Mol. Biol. Evol., 22 (2005),pp. 273-284
[27]	Vallender, E.J., Lahn, B.T. How mammalian sex chromosomes acquired their peculiar gene content Bioessays, 26 (2004),pp. 159-169
[28]	Wang, W., Zhang, J., Alvarez, C. et al. Mol. Biol. Evol., 17 (2000),pp. 1294-1301
[29]	Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood Comput. Appl. Biosci., 13 (1997),pp. 555-556
[30]	Zhang, Z., Kishino, H. Genomic background predicts the fate of duplicated genes: evidence from the yeast genome Genetics, 166 (2004),pp. 1995-1999
[31]	Zhang, Z., Hambuch, T.M., Parsch, J. Mol. Biol. Evol., 21 (2004),pp. 2130-2139