Wang Liqiang, Zhang Hui, Jiang Mei, Chen Haimei, Huang Linfang, Liu Chang
Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
PeerJ. 2019 Apr 1;7:e6663. doi: 10.7717/peerj.6663. eCollection 2019.
Plastome-based phylogenetic study has largely resolved the phylogeny of Icacinaceae. However, no single complete plastome sequence is available for Icacinaceae species, thereby limiting the further phylogenomics analysis of the members of this family. Here, we obtained the complete plastome sequence of Turcz., which is the first in Icacinaceae, by using the next-generation sequencing technology. The genome was annotated and compared with other closely related plastomes by using mVISTA. The divergence time of six species was analyzed using the BEAST software. The plastome of was 151,994 bp long, with a pair of inverted repeats (IRs, 24,973 bp) separated by a large single-copy (LSC, 84,527 bp) region and a small single-copy (SSC, 17,521 bp) region. The plastome encoded 112 unique genes, including 80 protein-coding, 28 tRNA, and four rRNA genes. Approximately 59 repeat sequences and 188 simple sequence repeats were identified. Four pairs of partially overlapped genes, namely, D/C, F/Ψ1, B/E, and 22/3, were observed. A comparison of the boundaries of the LSC, SSC, and IR regions with four other plastomes from Aquifoliales and Sapindales exhibited a high overall degree of sequence similarity. Four most highly variable regions, namely, H-GUG/A, M/D-GUC, A/J, and 16/Q-UUG, were found. Using the plastome of as reference, we reassembled the plastomes of five species. / ratio analyses revealed that 27 genes and 52 amino acid residue sites from 11 genes had undergone strong positive selection in the branch, with the most abundant proteins being the NDH and ribosomal proteins. Divergence-time analysis indicated that species were first formed 34.40 million years ago. Results revealed that the ancestor of the six species was likely to have split in the late Eocene epoch. In summary, the first complete plastome sequence of provided valuable information regarding the evolutionary processes of species.
基于质体基因组的系统发育研究在很大程度上解决了茶茱萸科的系统发育问题。然而，目前尚无茶茱萸科物种的单个完整质体基因组序列，从而限制了对该科成员的进一步系统基因组学分析。在此，我们利用新一代测序技术获得了Turcz.的完整质体基因组序列，这是茶茱萸科中的首个此类序列。对该基因组进行了注释，并使用mVISTA与其他近缘质体基因组进行了比较。使用BEAST软件分析了六个物种的分歧时间。Turcz.的质体基因组长度为151,994 bp，有一对反向重复序列（IRs，24,973 bp），被一个大单拷贝（LSC，84,527 bp）区域和一个小单拷贝（SSC，17,521 bp）区域隔开。该质体基因组编码112个独特基因，包括80个蛋白质编码基因、28个tRNA基因和4个rRNA基因。鉴定出约59个重复序列和188个简单序列重复。观察到四对部分重叠基因，即D/C、F/Ψ1、B/E和22/3。将LSC、SSC和IR区域的边界与来自冬青目和无患子目其他四个质体基因组进行比较，显示出较高的总体序列相似性。发现了四个高度可变区域，即H-GUG/A、M/D-GUC、A/J和16/Q-UUG。以Turcz.的质体基因组为参考，我们重新组装了五个物种的质体基因组。ω/θ比值分析表明，在该分支中，27个基因和来自11个基因的52个氨基酸残基位点经历了强烈的正选择，其中最丰富的蛋白质是NDH和核糖体蛋白。分歧时间分析表明，该物种最早形成于3440万年前。结果显示，这六个物种的祖先可能在始新世晚期发生了分化。总之，Turcz.的首个完整质体基因组序列为该物种的进化过程提供了有价值的信息。
