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Abstract：
BACKGROUND: Pueraria montana var. lobata (kudzu) is an important food and medicinal crop in Asia. However, the phylogenetic relationships between Pueraria montana var. lobata and the other two varieties (P. montana var. thomsonii and P. montana var. montana) remain debated. Although there is increasing evidence showing that P. montana var. lobata adapts to various environments and is an invasive species in America, few studies have systematically investigated the role of the phylogenetic relationships and evolutionary patterns of plastomes between P. montana var. lobata and its closely related taxa.
RESULTS: 26 newly sequenced chloroplast genomes of Pueraria accessions resulted in assembled plastomes with sizes ranging from 153,360 bp to 153,551 bp. Each chloroplast genome contained 130 genes, including eight rRNA genes, 37 tRNA genes, and 85 protein-coding genes. For 24 newly sequenced accessions of these three varieties of P. montana, we detected three genes and ten noncoding regions with higher nucleotide diversity (π). After incorporated publically available chloroplast genomes of Pueraria and other legumes, 47 chloroplast genomes were used to construct phylogenetic trees, including seven P. montana var. lobata, 14 P. montana var. thomsonii and six P. montana var. montana. Phylogenetic analysis revealed that P. montana var. lobata and P. montana var. thomsonii formed a clade, while all sampled P. montana var. montana formed another cluster based on cp genomes, LSC, SSC and protein-coding genes. Twenty-six amino acid residues were identified under positive selection with the site model. We also detected six genes (accD, ndhB, ndhC, rpl2, rpoC2, and rps2) that account for among-site variation in selective constraint under the clade model between accessions of the Pueraria montana var. lobata clade and the Pueraria montana var. montana clade.
CONCLUSIONS: Our data provide novel comparative plastid genomic insights into conservative gene content and structure of cp genomes pertaining to P. montana var. lobata and the other two varieties, and reveal an important phylogenetic clue and plastid divergence among related taxa of P. montana come from loci that own moderate variation and underwent modest selection.
RESULTS: 26 newly sequenced chloroplast genomes of Pueraria accessions resulted in assembled plastomes with sizes ranging from 153,360 bp to 153,551 bp. Each chloroplast genome contained 130 genes, including eight rRNA genes, 37 tRNA genes, and 85 protein-coding genes. For 24 newly sequenced accessions of these three varieties of P. montana, we detected three genes and ten noncoding regions with higher nucleotide diversity (π). After incorporated publically available chloroplast genomes of Pueraria and other legumes, 47 chloroplast genomes were used to construct phylogenetic trees, including seven P. montana var. lobata, 14 P. montana var. thomsonii and six P. montana var. montana. Phylogenetic analysis revealed that P. montana var. lobata and P. montana var. thomsonii formed a clade, while all sampled P. montana var. montana formed another cluster based on cp genomes, LSC, SSC and protein-coding genes. Twenty-six amino acid residues were identified under positive selection with the site model. We also detected six genes (accD, ndhB, ndhC, rpl2, rpoC2, and rps2) that account for among-site variation in selective constraint under the clade model between accessions of the Pueraria montana var. lobata clade and the Pueraria montana var. montana clade.
CONCLUSIONS: Our data provide novel comparative plastid genomic insights into conservative gene content and structure of cp genomes pertaining to P. montana var. lobata and the other two varieties, and reveal an important phylogenetic clue and plastid divergence among related taxa of P. montana come from loci that own moderate variation and underwent modest selection.
摘要：
背景：蒙大拿州葛根变种。野葛（kudzu）是亚洲重要的食品和药用作物。然而,蒙大拿州葛根之间的系统发育关系。lobata和其他两个品种(P.蒙大拿州var.thomsonii和P.montanavar.蒙大拿州）仍在辩论中。虽然有越来越多的证据表明，蒙大拿州的var。lobata适应各种环境，是美国的入侵物种，很少有研究系统地研究了蒙大拿之间的系统发育关系和质体进化模式的作用。lobata及其密切相关的类群。
结果：26个新测序的葛根叶绿体基因组导致大小从153,360bp到153,551bp的组装体。每个叶绿体基因组包含130个基因，包括八个rRNA基因，37个tRNA基因，和85个蛋白质编码基因。对于这三个蒙大拿州品种的24个新测序种质，我们检测到3个具有较高核苷酸多样性（π）的基因和10个非编码区。在纳入公开可用的葛根和其他豆类的叶绿体基因组后，使用47个叶绿体基因组构建系统发育树，包括七个蒙大拿州的变种。lobata,蒙大拿州第14章。thomsonii和六个P.montanavar。蒙大拿州。系统发育分析表明，蒙大拿州变种。洛巴塔和蒙大拿州的变种。thomsonii形成了一个进化枝,而所有的样本都是P.Montanavar。蒙大拿州基于cp基因组形成了另一个集群，LSC,SSC和蛋白质编码基因。在位点模型的阳性选择下鉴定出26个氨基酸残基。我们还检测到六个基因(accD，ndhB,ndhC,rpl2，rpoC2和rps2），它们解释了蒙大拿州葛根品种之间的进化枝模型下选择性约束的站点间变化。罗巴进化枝和蒙大拿州葛根。蒙大拿州进化枝。
结论：我们的数据提供了新的比较质体基因组对保守基因含量和与蒙大拿相关的cp基因组结构的见解。lobata和其他两个品种，并揭示了蒙大拿州相关分类群之间重要的系统发育线索和质体差异来自具有中等变异并经过适度选择的基因座。
结果：26个新测序的葛根叶绿体基因组导致大小从153,360bp到153,551bp的组装体。每个叶绿体基因组包含130个基因，包括八个rRNA基因，37个tRNA基因，和85个蛋白质编码基因。对于这三个蒙大拿州品种的24个新测序种质，我们检测到3个具有较高核苷酸多样性（π）的基因和10个非编码区。在纳入公开可用的葛根和其他豆类的叶绿体基因组后，使用47个叶绿体基因组构建系统发育树，包括七个蒙大拿州的变种。lobata,蒙大拿州第14章。thomsonii和六个P.montanavar。蒙大拿州。系统发育分析表明，蒙大拿州变种。洛巴塔和蒙大拿州的变种。thomsonii形成了一个进化枝,而所有的样本都是P.Montanavar。蒙大拿州基于cp基因组形成了另一个集群，LSC,SSC和蛋白质编码基因。在位点模型的阳性选择下鉴定出26个氨基酸残基。我们还检测到六个基因(accD，ndhB,ndhC,rpl2，rpoC2和rps2），它们解释了蒙大拿州葛根品种之间的进化枝模型下选择性约束的站点间变化。罗巴进化枝和蒙大拿州葛根。蒙大拿州进化枝。
结论：我们的数据提供了新的比较质体基因组对保守基因含量和与蒙大拿相关的cp基因组结构的见解。lobata和其他两个品种，并揭示了蒙大拿州相关分类群之间重要的系统发育线索和质体差异来自具有中等变异并经过适度选择的基因座。
