Zhong Qiwen, Yang Shipeng, Sun Xuemei, Wang Lihui, Li Yi
Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Xining, Qinghai, China.
Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.
PeerJ. 2019 Aug 30;7:e7596. doi: 10.7717/peerj.7596. eCollection 2019.
Jerusalem artichoke ( L.) is widely cultivated in Northwest China, and it has become an emerging economic crop that is rapidly developing. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (83,981 bp), and a small single-copy region (18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. A total of 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 32 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the Jerusalem artichoke and other species of the composite family revealed that the chloroplast genome sequences of plants of the composite family were highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the gene being the most obvious. A phylogenetic analysis showed that had the closest relationship with Jerusalem artichoke, both members of the genus. Selective locus detection of the gene in eight species of the composite family was performed to explore adaptive evolution traits of the gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the gene has been subject to adaptive evolution. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.
菊芋（Helianthus tuberosus L.）在中国西北地区广泛种植，已成为一种快速发展的新兴经济作物。因其菊糖含量高且抗性强，被广泛应用于功能食品、菊糖加工、饲料及生态治理等领域。本研究利用Illumina测序技术对菊芋完整叶绿体基因组序列进行组装和注释。其全长为151,431 bp，包括四个保守区域：一对反向重复区域（IRa为24,568 bp，IRb为24,603 bp）、一个大单拷贝区域（83,981 bp）和一个小单拷贝区域（18,279 bp）。该基因组共有115个基因，其中19个在IR区域呈反向排列。在编码区和非编码区共鉴定出36个简单序列重复（SSR），其中大部分偏向A/T碱基。共有32个SSR分布在非编码区。对菊芋与菊科其他物种的叶绿体基因组序列进行比较分析发现，菊科植物的叶绿体基因组序列高度保守。在编码区的24个基因位点存在差异，其中 基因的分化程度最为明显。系统发育分析表明， 与菊芋关系最为密切，二者均为 属成员。对菊科八个物种的 基因进行选择性位点检测，以探究菊芋中 基因的适应性进化特征。结果表明，在1239N和1518R位点分别存在显著和极显著的正选择位点，表明 基因经历了适应性进化。我们对菊芋完整叶绿体基因组序列的评估结果将有助于深入研究菊科的进化关系，并为菊芋的遗传改良提供重要的测序信息。
