A Genome-wide Survey Of Copy Number Variations Reveals An Asymmetric Evolution Of Duplicated Genes In Rice

As a common type of genomic variation,copy number variation(CNV)is an important driving force of gene evolution and can also affect gene expression abundance.Many CNVs have been reported to be associated with important agronomic traits,suggesting that research on CNV may be a new direction in crop breeding area.At present,however,the systematic descriptions of the effects of CNV on gene expression and its evolution law are rare in plants.Here,we developed a comprehensive pipeline and strict standards to call highly accurate CNVs using the next-generation sequencing data of 93 O.sativa accessions,which provided reliable methodology and CNV data for rice functional genomics research.Based on transcriptome data of each accession,the correlation analyses between expression level and copy number of genes were performed.Then,further analysis of the identified duplicated genes revealed the difference on the evolutionary fates and expression levels of different copies,providing new evidence for asymmetric evolution of duplicated genes.Our results are mainly as follows:1.Compared with the Nipponbare,the CNV number of each accession varied from 2,000 to 8,000,with the accuracy of nearly 95% randomly verified by q PCR,and 1,308 to 3,446 non-transposon genes were affected.The distribution of CNVs on different chromosomes and different regions was not evenly and their length showed a typical L-shaped distribution.2.In rice root,most(82.32%,2,175)of genes didn't show significant correlations between copy number and expression level and only nearly 13.17%(348)of genes were significantly positively correlated.Surprisingly,4.50%(119)of genes were significantly negatively correlated.3.Even for positively correlated genes,the gene dosage effect is not exponential or linear.For each additional copy,the rate of the increase in expression decreased as the copy number increased.The effect of tandem duplications on expression was generally stronger than that of non-tandem ones.4.Among the 8,163 duplicate pairs identified in 93 accessions,the proportion of pseudogenization and undifferentiation pairs were 36.46%(2,976)and 58.15%(4,747),respectively,suggesting that maintaining the function of ancestral gene and pseudogenization are two main evolutionary fates of duplicated genes.And only 5.39% of duplicate pairs had experienced function divergence.5.During the divergence of the Oryza genera,after gene duplication,with the extension of time,more and more duplicate pairs underwent functional differentiation,and the proportion of neofunctionalization pairs in functional differentiation tended to be higher.The selection constraints of the subfunctionalizated pairs were significantly stronger than those of the neofunctionalizated pairs,so the sequences of subfunctionalizated pairs were more conservative.6.In terms of evolutionary fate,the offspring copy tended to be pseudogenized,while the parent copy tended to maintain the original function.At the expression level,the offspring copy was often higher than the parent copy.So,the evolution of duplicated genes is asymmetric in terms of fate and expression.