Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Plant Biol. 2023 May 20;23(1):269. doi: 10.1186/s12870-023-04233-8.
The orchid genus Pholidota Lindl. ex Hook. is economically important as some species has long been used in traditional medicine. However, the systematic status of the genus and intergeneric relationships inferred from previous molecular studies are unclear due to insufficient sampling and lack of informative sites. So far, only limited genomic information has been available. The taxonomy of Pholidota remains unresolved and somewhat controversial. In this study, the complete chloroplast (cp.) genomes of thirteen Pholidota species were sequenced and analyzed to gain insight into the phylogeny of Pholidota and mutation patterns in their cp. genomes.
All examined thirteen Pholidota cp. genomes exhibited typical quadripartite circular structures, with the size ranging from 158,786 to 159,781 bp. The annotation contained a total of 135 genes in each cp. genome, i.e., 89 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The codon usage analysis indicated the preference of A/U-ending codons. Repeat sequence analysis identified 444 tandem repeats, 322 palindromic repeats and 189 dispersed repeats. A total of 525 SSRs, 13,834 SNPs and 8,630 InDels were detected. Six mutational hotspots were identified as potential molecular markers. These molecular markers and highly variable regions are expected to facilitate future genetic and genomic studies. Our phylogenetic analyses confirmed the polyphyletic status of the genus Pholidota, with species grouped into four main clades: Pholidota s.s. was resolved as the sister to a clade containing species of Coelogyne; the other two clades clustered together with species of Bulleyia and Panisea, respectively; species P. ventricosa was placed at the basal position, deviated from all other species.
This is the first study to comprehensively examine the genetic variations and systematically analyze the phylogeny and evolution of Pholidota based on plastid genomic data. These findings contribute to a better understanding of plastid genome evolution of Pholidota and provide new insights into the phylogeny of Pholidota and its closely related genera within the subtribe Coelogyninae. Our research has laid the foundation for future studies on the evolutionary mechanisms and classification of this economically and medicinally important genus.
石豆兰属 Pholidota Lindl. ex Hook. 经济重要，因为一些物种长期以来一直用于传统医学。然而，由于采样不足和缺乏信息位点，之前的分子研究推断出的属的系统地位和属间关系尚不清楚。到目前为止，只有有限的基因组信息可用。石豆兰的分类仍然没有解决，有些争议。在这项研究中，对 13 种石豆兰的完整叶绿体（cp.）基因组进行了测序和分析，以深入了解石豆兰的系统发育和其 cp.基因组中的突变模式。
所有检查的 13 种石豆兰 cp.基因组均表现出典型的四分体圆形结构，大小范围为 158,786 至 159,781 bp。每个 cp.基因组中的注释共包含 135 个基因，即 89 个蛋白质编码基因、38 个 tRNA 基因和 8 个 rRNA 基因。密码子使用分析表明偏爱 A/U 结尾的密码子。重复序列分析鉴定出 444 个串联重复、322 个回文重复和 189 个分散重复。共检测到 525 个 SSRs、13,834 个 SNPs 和 8,630 个 InDels。鉴定出 6 个突变热点作为潜在的分子标记。这些分子标记和高度可变区有望促进未来的遗传和基因组研究。我们的系统发育分析证实了石豆兰属的多系性，物种分为四个主要分支：石豆兰 s.s. 被确定为包含 Coelogyne 物种的分支的姐妹群；另外两个分支分别与 Bulleyia 和 Panisea 的物种聚集在一起；物种 P. ventricosa 位于基部位置，与所有其他物种分开。
这是第一项基于质体基因组数据全面检查石豆兰遗传变异并系统分析其系统发育和进化的研究。这些发现有助于更好地了解石豆兰质体基因组的进化，并为石豆兰及其在 Coelogyninae 亚族中密切相关属的系统发育提供新的见解。我们的研究为未来研究这个经济和药用重要属的进化机制和分类奠定了基础。
