鉴定两个蝴蝶兰属（兰科）物种的完整叶绿体基因组结构并与它们的所属联盟进行比较分析。
Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance.
机构信息
Department of Biological Conservation, Southwest Forestry University, Kunming, Yunnan, 650224, China.
Department of Life Science, Southwest Forestry University, Kunming, Yunnan, 650224, China.
出版信息
BMC Genomics. 2023 Jun 27;24(1):359. doi: 10.1186/s12864-023-09448-5.
BACKGROUND
The taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. The structural characterization of complete chloroplast genomes of P. storbatiana and P. wilsonii were analyzed and compared with those of related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny.
RESULTS
It was shown that chloroplast genomes of Phalaenopsis storbatiana and P. wilsonii had a typical quadripartite structure with conserved genome arrangements and moderate divergence. The chloroplast genomes of P. storbatiana and P. wilsonii were 145,885 bp and 145,445 bp in length, respectively, and shared a similar GC content of 36.8%. Gene annotations of two species revealed 109 single-copy genes consistently. In addition, 20 genes duplicated in the inverted regions, 16 genes each possessed one or more introns, and five ndh (NA (D)H dehydrogenase) genes were observed in both. Comparative analysis of the total cp genomes of P. storbatiana and P. wilsonii with those of other six related Phalaenopsis species confirmed the stable sequence identity for coding and non-coding regions and higher sequence variation in SC regions than IR regions. Most of their protein-coding genes had a high degree of codon preference. Moreover, 45 genes were discovered with significantly positive selection. However, different amplifications in IR regions were observed in these eight species. Phylogenetic analysis based on CDS from 60 species representing main clades in Orchidaceae indicated that Phalaenopsis species including P. stobartiana and P. wilsonii formed a monophyletic clade with high bootstrap nested in tribe Vandeae of Epidendroideae, which was consistent with those from previous studies.
CONCLUSIONS
The results could provide insight into understanding the plastome evolution and phylogenetic relationships of Phalaenopsis.
背景
由于相关物种之间存在一些重叠的形态特征，蝴蝶兰属的分类和种下划分一直存在很大争议，需要进一步的证据来澄清。本研究对石豆兰和华西蝴蝶兰的完整叶绿体基因组结构特征进行了分析，并与相关分类群进行了比较，为了解它们在分类学和系统发育上的基因组信息提供了更好的认识。
结果
结果表明，石豆兰和华西蝴蝶兰的叶绿体基因组具有典型的四部分结构，基因组排列保守，分化适中。石豆兰和华西蝴蝶兰的叶绿体基因组分别长 145885bp 和 145445bp，GC 含量相似，均为 36.8%。两个物种的基因注释都一致显示 109 个单拷贝基因。此外，在反向区域有 20 个基因重复，16 个基因各有一个或多个内含子，在两个物种中都观察到 5 个 ndh（NADH 脱氢酶）基因。石豆兰和华西蝴蝶兰与其他 6 种相关蝴蝶兰属植物的 cp 基因组总比较分析证实了编码和非编码区的稳定序列同一性，以及 SC 区比 IR 区具有更高的序列变异。它们的大多数蛋白质编码基因具有高度的密码子偏好。此外，发现 45 个基因存在显著的正选择。然而，这 8 个物种的 IR 区存在不同的扩增。基于代表 Orchidaceae 主要分支的 60 种植物的 CDS 构建的系统发育分析表明，包括石豆兰和华西蝴蝶兰在内的蝴蝶兰属形成了一个单系分支，在 Epidendroideae 中的 Vandeae 族中具有高的自展值嵌套，与以往的研究一致。
结论
这些结果可以深入了解蝴蝶兰叶绿体基因组的进化和系统发育关系。
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