Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China.
Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Hua Zhong Agricultural University, Wuhan, China.
PLoS One. 2018 May 24;13(5):e0197393. doi: 10.1371/journal.pone.0197393. eCollection 2018.
Actinidia arguta is the most basal species in a phylogenetically and economically important genus in the family Actinidiaceae. To better understand the molecular basis of the Actinidia arguta chloroplast (cp), we sequenced the complete cp genome from A. arguta using Illumina and PacBio RS II sequencing technologies. The cp genome from A. arguta was 157,611 bp in length and composed of a pair of 24,232 bp inverted repeats (IRs) separated by a 20,463 bp small single copy region (SSC) and an 88,684 bp large single copy region (LSC). Overall, the cp genome contained 113 unique genes. The cp genomes from A. arguta and three other Actinidia species from GenBank were subjected to a comparative analysis. Indel mutation events and high frequencies of base substitution were identified, and the accD and ycf2 genes showed a high degree of variation within Actinidia. Forty-seven simple sequence repeats (SSRs) and 155 repetitive structures were identified, further demonstrating the rapid evolution in Actinidia. The cp genome analysis and the identification of variable loci provide vital information for understanding the evolution and function of the chloroplast and for characterizing Actinidia population genetics.
软枣猕猴桃是猕猴桃科中进化上和经济上都很重要的属中最原始的物种。为了更好地了解软枣猕猴桃叶绿体（cp）的分子基础，我们使用 Illumina 和 PacBio RS II 测序技术对 A. arguta 的完整 cp 基因组进行了测序。A. arguta 的 cp 基因组长 157611bp，由一对 24232bp 的反向重复（IRs）组成，它们被 20463bp 的小单拷贝区（SSC）和 88684bp 的大单拷贝区（LSC）隔开。总的来说，cp 基因组包含 113 个独特的基因。对 A. arguta 的 cp 基因组和来自 GenBank 的另外三种猕猴桃属物种的 cp 基因组进行了比较分析。鉴定出了插入缺失突变事件和碱基替换的高频发生，并且 accD 和 ycf2 基因在猕猴桃属内表现出高度的变异。鉴定出了 47 个简单序列重复（SSR）和 155 个重复结构，进一步证明了猕猴桃属的快速进化。cp 基因组分析和可变基因座的鉴定为理解叶绿体的进化和功能以及表征猕猴桃种群遗传学提供了重要信息。
