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Comparative Study
. 2015 Mar 16;10(3):e0119239.
doi: 10.1371/journal.pone.0119239. eCollection 2015.

Whole-genome analysis revealed the positively selected genes during the differentiation of indica and temperate japonica rice

Xinli Sun  1 , Qi Jia  1 , Yuchun Guo  1 , Xiujuan Zheng  1 , Kangjing Liang  1
Affiliations
Comparative Study

Whole-genome analysis revealed the positively selected genes during the differentiation of indica and temperate japonica rice

Xinli Sun et al. PLoS One. .

Abstract

To investigate the selective pressures acting on the protein-coding genes during the differentiation of indica and japonica, all of the possible orthologous genes between the Nipponbare and 93-11 genomes were identified and compared with each other. Among these genes, 8,530 pairs had identical sequences, and 27,384 pairs shared more than 90% sequence identity. Only 2,678 pairs of genes displaying a Ka/Ks ratio significantly greater than one were revealed, and most of these genes contained only nonsynonymous sites. The genes without synonymous site were further analyzed with the SNP data of 1529 O. sativa and O. rufipogon accessions, and 1068 genes were identified to be under positive selection during the differentiation of indica and temperate japonica. The positively selected genes (PSGs) are unevenly distributed on 12 chromosomes, and the proteins encoded by the PSGs are dominant with binding, transferase and hydrolase activities, and especially enriched in the plant responses to stimuli, biological regulations, and transport processes. Meanwhile, the most PSGs of the known function and/or expression were involved in the regulation of biotic/abiotic stresses. The evidence of pervasive positive selection suggested that many factors drove the differentiation of indica and japonica, which has already started in wild rice but is much lower than in cultivated rice. Lower differentiation and less PSGs revealed between the Or-It and Or-IIIt wild rice groups implied that artificial selection provides greater contribution on the differentiation than natural selection. In addition, the phylogenetic tree constructed with positively selected sites showed that the japonica varieties exhibited more diversity than indica on differentiation, and Or-III of O. rufipogon exhibited more than Or-I.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. The distribution of the percent identity between the possible orthologs.
The most similar proteins between 93–11 and Nipponbare were selected with BLAST, and 30995 pairs of proteins were obtained; each pair was analyzed via ClustalW 2 to obtain the percent identity.
Fig 2
Fig 2. The distribution of Ka, Ks and Ka/Ks.
(A) Using the gNG method. (B) Using the MYN method. (C) Using the Maximum Likelihood method. Note: Ka/Ks were specified as zero if both Ka and Ks were zero (5247 genes).
Fig 3
Fig 3. The distribution of the numbers of non-synonymous substitutions in NSSGs.
Fig 4
Fig 4. The distribution of the PSGs along rice chromosomes.
(A) The distribution of the PSGs along the chromosomes. ‘+’ indicates the positions of the genes on the chromosomes. (B) The numbers of the PSGs (bars) and the ratios of PSGs (lines) to total genes in each chromosome.
Fig 5
Fig 5. The number of each type of substitutions in the proteins encoded by the PSGs.
See this image and copyright information in PMC

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