Full Text:
<3111>
CLC number: Q81
On-line Access: 2024-08-27
Received: 2023-10-17
Revision Accepted: 2024-05-08
Crosschecked: 0000-00-00
Cited: 1
Clicked: 5995
Maximal sequence length of exact match between members from a gene family during early evolution
| |||||||||||||
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(6): 470-476.
@article{title="Maximal sequence length of exact match between members from a gene family during early evolution",
author="WEN Xiao, GUO Xing-yi, FAN Long-jiang",
journal="Journal of Zhejiang University Science B",
volume="6",
number="6",
pages="470-476",
year="2005",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2005.B0470"
}
%0 Journal Article
%T Maximal sequence length of exact match between members from a gene family during early evolution
%A WEN Xiao
%A GUO Xing-yi
%A FAN Long-jiang
%J Journal of Zhejiang University SCIENCE B
%V 6
%N 6
%P 470-476
%@ 1673-1581
%D 2005
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2005.B0470
TY - JOUR
T1 - Maximal sequence length of exact match between members from a gene family during early evolution
A1 - WEN Xiao
A1 - GUO Xing-yi
A1 - FAN Long-jiang
J0 - Journal of Zhejiang University Science B
VL - 6
IS - 6
SP - 470
EP - 476
%@ 1673-1581
Y1 - 2005
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2005.B0470
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.
[1] Arratia, R., Gordon, L., Waterman, M.S., 1986. An extreme value theory for sequence matching. Ann. Stat., 14:971-993.
[2] Blanc, G., Wolfe, K.H., 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell, 16:1667-1678.
[3] Brown, T.A., 1999. Genomes. BIOS Scientific Publishers Limited, Oxford.
[4] Delcher, A.L., Phillippy, A., Carlton, J., Salzberg, S.L., 2002. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res., 30:2478-2483.
[5] Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al., 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296:92-100.
[6] Karlin, S., Altschul, S.F., 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA, 87(6):2264-2268.
[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.
Open peer comments: Debate/Discuss/Question/Opinion
<1>