Journal of Zhejiang University SCIENCE
(ISSN 1009-3095, Monthly)

2005   Vol. 6B   No. 6   p.470-476

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

WEN Xiao¹, GUO Xing-yi², FAN Long-jiang^†1,2

(¹Institute of Crop Science, Zhejiang University, Hangzhou 310029, China)
(²Institute of Bioinformatics/IBM Biocomputational Lab, Zhejiang University, Hangzhou 310029, China)
^†E-mail: fanlj@zju.edu.cn
Received Nov. 16, 2004; revision accepted Feb. 19, 2005

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 (d_A<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.

Key words: Maximal length of exact match (MALE), Divergent time, Gene family, Minimal length of exact match (MILE), Genome alignment
doi:10.1631/jzus.2005.B0470             CLC number: Q81