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2,878 horizontally transferred genes in rice genome revealed by BLAST homology and phylogenetic tree
Xingyi Guo 1 *,Yu Wang 2 #
1.Institute of Bioinformatics, Zhejiang University
2.Department of Agronomy, Zhejiang University
*Correspondence author
#Submitted by
Subject: Evolutionary Genetics
Funding: 教育部博士点基金(No.20060335115)
Opened online:12 January 2010
Accepted by: none
Citation: Xingyi Guo,Yu Wang.2,878 horizontally transferred genes in rice genome revealed by BLAST homology and phylogenetic tree[OL]. [12 January 2010] http://www.paper.edu.cn/lwzx/en_releasepaper/content/38803
Horizontal gene transfer (HGT) is considered to have an important role to explore new niche, which has been widely described between different species of prokaryotes. The least well-documented form of large-scale HGT deals with the uptake of DNA from prokaryotes into higher eukaryotes. However, the number of genes introgress into rice genome through HGT is still not investigated. Based on large-scale sequences comparisons and phylogenetic analyses, 2, 878, or 6.7% of total 42, 653 genes were isolated from rice genome. More than 55.7% of the transferred genes were identified as duplication genes based sequence similarity. Of the 2,878 genes, total 1515 genes can be divided into 587 neighbour gene groups (2 to 8 members per group) based on their physical positions, which forms 52.6% of the total transferred genes. Meanwhile, many of the groups can be found their syntenic regions in prokaryotes. Among the HGT genes, genes involved in cellular process and metabolism are over-representation, For example, hydrolase, an important enzymes involved in the degradation of carbohydrates from the plant cell wall. There are more HGT genes involved in response to stress and stimulus of biotic and endogenous than non-HGT genes. A high proportion (6.7%) of horizontal transferred genes was observed in rice genome. The rate is the highest one reported for eukaryotes up to now. Many short syntenic regions of HGT genes between rice and prokaryotes suggest that segmental insertion might be a transfer mechanism for HGT in rice. Gene duplication plays an important role in expanding of the horizontally transferred genes in new territory. HGT genes seem tend to target adaptation to an advantage environment.
Keywords:Horizontal gene transfer;gene duplication;rice;prokaryote

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