四种禾本科作物叶绿体基因组碱基替换的侧翼序列特征

Patterns of nucleotide substitutional flanking sequences in chloroplast genomes of four Poaceae species

对于核苷酸替换对相邻位点依赖性及侧翼序列特征的研究有助于厘清不同物种之间的进化关系,可以作为基因编辑和基因修饰技术的基础。早期研究表明, CpG甲基化效应广泛存在于哺乳动物和细菌基因组中,而叶绿体某些基因中的颠换相邻位点表现出一定的碱基组成偏好。本研究将4种禾本科作物小麦(Triticum aestivum)、水稻(Oryza sativa)、玉米(Zea mays)和高粱(Sorghum bicolor)的叶绿体基因组序列分为两组比对,查找替换位点并统计侧翼序列各位点碱基组成。通过相对熵(KL散度)作图,发现小麦和水稻的叶绿体基因组中相邻序列的碱基组成受到替换的影响随着距离的增大而减小,而玉米和高粱叶绿体基因组缺少相应规律。对于相对熵较高的替换相邻位点,通过不同核苷酸相对熵贡献的研究,发现4种禾本科作物的叶绿体基因组均表现出CpG甲基化效应以及颠换相邻位点的特殊组成规律。本研究为相对熵在植物基因组分子进化领域的应用提供参考。

The study on the neighboring sites and flanking sequences of nucleotide substitutions not only contributes to exploring the phylogeny of different species,but also lays a basis of the gene editing and modification technique.As suggested by previous studies,CpG methylation effect exists in the mammalian and bacterial genomes,while the base composition of neighboring sites is highly correlated with transversional neighboring sites in the chloroplast genome.Herein,according to the alignment of chloroplast genomes,wheat(Triticum aestivum),rice(Oryza sativa),maize(Zea mays)and sorghum(Sorghum bicolor)were divided into two groups.On this basis,substitution sites were found and the base composition of substitutional flanking sites were counted to calculate the relative entropy.Relative entropy mapping shows that the impact on the base composition of flanking sequences decreases with the distance to the substitution sites in wheat and rice chloroplast genomes,while this rule is not found in chloroplast genomes of maize and sorghum.Based on the nucleotide contribution of neighboring sites with higher relative entropy,CpG methylation effect and the special nucleotide composition of transversional neighboring sites were observed in the chloroplast genomes of four Poaceae species.This paper provides a reference for the application of relative entropy into the molecular evolution study of the plant genome.