Evolutionary Selections On Rice Genome

Charles Darwin proposed that evolution occurs primarily by natural selection,but his view has been argued by neutralism.Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions.This suggestion generated an intense controversy over selectionism and neutralism.In this study, based on investigation of three kinds of DNA sequences in rice genome,our findings indicate that nature selection has been widely existed in rice genome and is one of major driving forces in evolution.Our major findings are followed as:1)miRNA binding sitesMicroRNAs(miRNAs)post-transcriptionally down-regulate gene expression by binding target mRNAs.Analysis of the evolutionary patterns of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets.To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD)event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice(O.sativa)was carried out.Of the 1,331 pairs of duplicate genes from the WGD,105 were computationally predicted to be miRNA targets.Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions.In most(86)of the 105 duplicated gene pairs only one gene is targeted by a miRNA.This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from targeting by miRNA after the WGD(loss of miRNA binding site).The gain/loss rate of miRNA binding sites was estimated to be 5.2×10^-9gain/loss per year.Most(83.8%)of the gains/losses were due to nucleotide mutation.By analysis of cultivated(O.sativa;n=30)and wild(O. rufipogon;n=15)rice populations,no segregating site was observed in the six miRNA binding sites whereas 0.12-0.20 SNPs per 21-nt or 0.00153-0.00180 of the average pairwise nucleotide diversity(π)were found in their flanking regions.Both comparative genomics and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles.Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution.2)Non-coding DNA sequencesA large unexplained structural feature common to rice genome is the presence of vast amount of nonprotein-coding DNA.Thus,understanding the functional significant of intronic noncoding DNA sequences is one of the major challenges in genomcis research at present.Several studies have investigated the relationships between selective constraints in introns and their length,G+C content and location within genes.To date,however,no such investigation has been done in plants.Studies of selective constraints in noncoding DNA have generally involved interspecific comparisons,under the assumption of the same selective pressures acting in each lineage.Such comparisons are limited to cases in which the noncoding sequences are not too strongly diverged so that reliable sequence alignments can be obtained.Here, we investigate selective constraints in a recent segmental duplication that includes 605 paralogous intron pairs that occurred about 7 million years ago in rice(O.sativa). Our principal findings are:(1)intronic divergence is negatively correlated with intron length,a pattern that has previously been described in Drosophila and mammals;(2) there is a signature of strong purifying selection at splice control sites;(3)first introns are significantly longer and have a higher G+C content than other introns;(4)the divergences of first and non-first introns are not significantly different from one another,a pattern that differs from Drosophila and mammals.(5)Short introns are more diverged than fourfold-degenerate sites suggesting that selection reduces divergence at fourfold-degenerate sites.Our observation of stronger selective constraints in long introns suggests that functional elements subject to purifying selection may be concentrated within long introns.Our results are consistent with the presence of strong purifying selection at splicing control sites.Selective constraints are not significantly stronger in first introns of rice,as they are in other species.3)High G+C content genes Two obviously gene classes characterized by high and low G+C content have been found in rice and other cereals,but not dicot genomes.There has been long-standing interest in which evolutionary mechanism can be responsible to explain such G+C content variation in coding genes.Based on substitution at synonymous and non-synonymous sites,and on G+C content along the direction of transcription, mutational bias or natural selection has been proposed to explain the evolutionary divergent pattern of G+C content in rice(O.sativa).Here,we used paralogs with high and low G+C contents in rice and found:(1)a greater increase in G+C content at exonic fourfold-degenerate sites than at flanking introns;(2)with reference to their orthologs in Arabidopsis,most substitution sites between the two kinds of paralogs are found at 2- and 4-degenerate sites with a T→C mode,while A→C and A→G play major roles at 0-degenerate sites;and(3)high G+C genes have greater bias and codon usage is skewed toward codons that are preferred in highly expressed genes.We believe this is strong evidence for selectively driven codon usage in rice.Another cereal,maize,also showed the same trend as in rice.This represents a potential evolutionary process for the origin of genes with a high G+C content in rice and other cereals.