Abstract
Tandem and segmental duplications significantly contribute to gene family expansion and genome evolution. Genome-wide identification of tandem and segmental genes has been analyzed before in several plant genomes. However, comparative studies in functional bias, expression divergence and their roles in species domestication are still lacking. We have carried out a genome-wide identification and comparative analysis of tandem and segmental genes in the rice genome. A total of 3,646 and 3,633 pairs of tandem and segmental genes, respectively, were identified in the genome. They made up around 30% of total annotated rice genes (excluding transposon-coding genes). Both tandem and segmental duplicates showed different physical locations and exhibited a biased subset of functions. These two types of duplicated genes were also under different functional constrains as shown by nonsynonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analysis. They are also differently regulated depending on the tissues and abiotic and biotic stresses based on transcriptomics data. The expression divergence might be related to promoter differentiation and DNA methylation status after tandem or segmental duplications. Both tandem and segmental duplications differ in their contribution to genetic novelty but evidence suggests that they play their role in species domestication and genome evolution.
Highlights
Functional Bias of Genes by Tandem and Segmental Duplication and Functional Complementation In Arabidopsis and rice, tandem gene density was positively corelated with the recombination rate [8,37]
This might be partially due to recombination-mediated processes being involved in tandem duplication [3]
Our analysis showed that no correlation was observed between segmental gene distribution and recombination rate in rice
Summary
In rice, based on our preliminary study, around 6,000 gene families were detected to encode more than two thirds of the total annotated non-transposon proteins. Both tandem and segmental duplications significantly contribute to the origin, expansion and evolution of multigene families. Duplicated genes result from duplications of chromosomal regions ranging from 1 to 400 Kb [5,6]. They arise from the genomic restructure caused by aberrant inter- or intrachromosome recombination [7]
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