马铃薯‘合作88’自交分离群体叶绿体基因组遗传组成分析

Genetic Analysis of Chloroplast Genome Characteristics of Potato‘Cooperation 88’Selfing Population

为了从基因组水平解析马铃薯品种‘合作88’(Solanum tuberosum‘Cooperation 88’)叶绿体基因组多态性和遗传多样性,了解其自交分离群体叶绿体基因组遗传组成和变异,通过对‘合作88’及其30个自交分离群体材料的叶绿体基因组测序组装,并与其他11个茄科物种、拟南芥和水稻的叶绿体基因组序列进行比较分析。结果表明,‘合作88’叶绿体基因组为典型环状结构,长度为160323 bp,GC含量为38.6%,共注释29个tRNA基因和77个蛋白质编码基因。30个自交后代叶绿体基因组大小在160331~162120 bp之间,注释预测基因数95~106个,GC含量36.7%~38.6%。进一步分析表明,‘合作88’和其30个自交后代叶绿体类型均为W型,未呈现出多态性。‘合作88’和其自交后代均偏好使用以A/U结尾的密码子,子代叶绿体基因组密码子4种碱基使用频率不同,推断其相对同义密码子使用度、有效密码子数和高频密码子数的差异为叶绿体基因组随机突变和翻译自然选择所导致。此外,16个正向重复序列中有12个存在于‘合作88’及所有自交后代中,另有4个为子代中新出现的。UPGMA聚类分析和共线性分析发现重复序列的出现和基因丢失使得自交后代叶绿体基因组遗传多样性增加。

In order to analyze the chloroplast genome polymorphism and genetic diversity of potato‘Cooperation 88’at the genome level and to understand the genetic composition and variation of the chloroplast genome of the selfing population of‘Cooperation 88’,this study assembled the chloroplast genomes of‘Cooperation 88’and 30 selfing progenies and comparatively analyzed them with the chloroplasts genomes of 11 other Solanaceae species,Arabidopsis thaliana and Oryza sativa.The results showed that the assembled chloroplast genome of the‘Cooperation 88’was a typical circular structure with a length of 160323 bp and the GC content of 38.6%,including a total of 29 annotated tRNA genes and 77 protein-coding genes.The size of the chloroplast genome of the 30 selfing progenies ranged from 160331 bp to 162120 bp,the number of genes predicted was 95–106,and the GC content was 36.7%–38.6%.Further analysis showed that the chloroplast types of the parent and 30 selfing progeny were all W-type,showing no polymorphism.Both parent and selfing progenies prefer to use codons ending with A/U,and the progenies chloroplasts genomes codon pairs used different frequencies of the four bases,indicating that the relative synonymous codon usage and effective codons in the chloroplast genome of selfing progenies variations in the number of codons and high-frequency codons were caused by random mutation and translational natural selection in the chloroplast genome.In addition,12 repeats existing in the parent were also present in all progenies but four repeats were new appeared in progeny.UPGMA analysis and collinearity analysis also found that the evolutionary level of the Solanum chloroplast genome was highly conserved,but the appearance of repeats and the loss of genes changed the size of the progeny chloroplast genome and increased their genetic diversity.