The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China.
The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China.
复制标题
野木瓜叶绿体全基因组及比对分析揭示中国野木瓜亚科物种的适应性进化
DOI：
10.1186/s12864-021-07484-7
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发表时间：
2021-03-06
期刊：
影响因子：
4.4
通讯作者：
Liao L
中科院分区：
文献类型：
--
作者：
Wen F;Wu X;Li T;Jia M;Liu X;Liao L
背景
野木瓜属于Lardizabaloideae亚科，广泛生长于中国南方。它是一种传统的药用植物，能合成多种具有抗癌、抗炎活性的三萜皂苷。然而，在遗传多样性和进化分析被揭示之前，该物种及其近缘种的野生资源受到过度开发的威胁。因此，对野木瓜叶绿体基因组全序列的测定以及对木通亚科不同种叶绿体基因组的比较分析，对了解野木瓜叶绿体基因组的进化是十分必要的。
结果
对野木瓜（Stauntonia chinensis）及其近缘种叶绿体基因组结构、GC含量、重复序列结构、SSR成分、核苷酸多样性和密码子使用等进行了比较分析。8种木通亚科植物的叶绿体基因组虽然在进化上保守，但比较分析也发现了几个变异热点，被认为是高度变异区域。此外，Ka/Ks分析结果表明，木通亚科植物的叶绿体基因大多数经过了纯化选择，而分支位点模型分析结果表明，该亚科植物中有25个叶绿体蛋白编码基因经过了正选择。贝叶斯和ML的CCG（完整的叶绿体基因组）和CD（编码DNA序列）上的同源性产生了一个很好的解决Lardizabaloideae质体谱系的同源性。
结论
该研究加深了对木通亚科及其近缘种进化的认识。这些遗传资源的获得将为进一步研究拉氏木通亚科的DNA条形码、种间差异、种内和种间变异以及系统发育关系等提供参考。
Background
Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily.
Results
A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages.
Conclusions
This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
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