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Received: 2004-11-16

Revision Accepted: 2005-02-19

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Journal of Zhejiang University SCIENCE B 2005 Vol.6 No.6 P.470~476

10.1631/jzus.2005.B0470


Maximal sequence length of exact match between members from a gene family during early evolution


Author(s):  WEN Xiao, GUO Xing-yi, FAN Long-jiang

Affiliation(s):  Institute of Crop Science, Zhejiang University, Hangzhou 310029, China; more

Corresponding email(s):   fanlj@zju.edu.cn

Key Words:  Maximal length of exact match (MALE), Divergent time, Gene family, Minimal length of exact match (MILE), Genome alignment


WEN Xiao, GUO Xing-yi, FAN Long-jiang. Maximal sequence length of exact match between members from a gene family during early evolution[J]. Journal of Zhejiang University Science B, 2005, 6(5): 470~476.

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Abstract: 
Mutation (substitution, deletion, insertion, etc.) in nucleotide acid causes the maximal sequence lengths of exact match (MALE) between paralogous members from a duplicate event to become shorter during evolution. In this work, MALE changes between members of 26 gene families from four representative species (Arabidopsis thaliana, Oryza sativa, Mus musculus and Homo sapiens) were investigated. Comparative study of paralogous’ MALE and amino acid substitution rate (dA<0.5) indicated that a close relationship existed between them. The results suggested that MALE could be a sound evolutionary scale for the divergent time for paralogous genes during their early evolution. A reference table between MALE and divergent time for the four species was set up, which would be useful widely, for large-scale genome alignment and comparison. As an example, detection of large-scale duplication events of rice genome based on the table was illustrated.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

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[7] Li, W.H., 1997. Molecular Evolution. Sinauer Associates, Sunderland, MA.

[8] Lynch, M., Conery, J.S., 2000. The evolutionary fate and consequences of duplicate genes. Science, 290:1151-1155.

[9] Ohno, S., 1970. Evolution by Gene Duplication. George Allen and Unwin, London.

[10] Paterson, A.H., Bowers, J.E., Chapman, B.A., 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. USA, 101:9903-9908.

[11] Yang, Z., 1999. Phylogenetic Analysis by Maximum Likelihood (PAML). Version 2., London, UK.

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