Song Shiqiang, Zubov Dmitriy, Comes Hans Peter, Li Haiwen, Liu Xuelian, Zhong Xin, Lee Joongku, Yang Zhaoping, Li Pan
College of Life Sciences and Technologies, Tarim University, Alar, China.
Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China.
Front Plant Sci. 2022 Jun 30;13:913011. doi: 10.3389/fpls.2022.913011. eCollection 2022.
Subfamily Nandinoideae Heintze (Berberidaceae), comprising four genera and 19 species, is disjunctively distributed in eastern North America vs. Eurasia (eastern Asia, Central Asia, Middle East, and southeastern Europe), and represents an ideal taxon to explore plastid phylogenomics and plastome evolution in Berberidaceae. Many species of this subfamily have been listed as national or international rare and endangered plants. In this study, we sequenced and assembled 20 complete plastomes, representing three genera and 13 species of Nandinoideae. Together with six plastomes from GenBank, a total of 26 plastomes, representing all four genera and 16 species of Nandinoideae, were used for comparative genomic and phylogenomic analyses. These plastomes showed significant differences in overall size (156,626-161,406 bp), which is mainly due to the expansion in inverted repeat (IR) regions and/or insertion/deletion (indel) events in intergenic spacer (IGS) regions. A 75-bp deletion in the F gene occurred in and when compared with and . We found a severe truncation at the 5' end of 1 in three plastomes, and a premature termination of 1 in . Our phylogenomic results support the topology of {, [, (, )]}. Within the core genus , we identified from northeastern Asia (Clade A) as the earliest diverging species, followed by from eastern China (Clade B), while the rest species clustered into the two sister clades (C and D). Clade C included three species from West Tianshan (, , ). Clade D consisted of from northern Central Asia, plus one species from the Caucasus Mountains () and three from southeastern Europe (, , ). Overall, we identified 21 highly variable plastome regions, including two coding genes (22, 1) and 19 intergenic spacer (IGS) regions, all with nucleotide diversity () values > 0.02. These molecular markers should serve as powerful tools (including DNA barcodes) for future phylogenetic, phylogeographic and conservation genetic studies.
南天竹亚科（小檗科）包含4个属19个物种，间断分布于北美洲东部和欧亚大陆（东亚、中亚、中东和东南欧），是探索小檗科质体系统发育基因组学和质体基因组进化的理想类群。该亚科的许多物种已被列为国家或国际珍稀濒危植物。在本研究中，我们测序并组装了20个完整的质体基因组，代表南天竹亚科的3个属13个物种。连同来自GenBank的6个质体基因组，共26个质体基因组，代表南天竹亚科的所有4个属16个物种，用于比较基因组学和系统发育基因组学分析。这些质体基因组在整体大小（156,626 - 161,406 bp）上显示出显著差异，这主要是由于反向重复（IR）区域的扩展和/或基因间隔区（IGS）中的插入/缺失（indel）事件。与[物种名称]和[物种名称]相比，[物种名称]和[物种名称]的F基因中发生了一个75 bp的缺失。我们在3个[物种名称]的质体基因组中发现1在5'端严重截断，在[物种名称]中1提前终止。我们的系统发育基因组学结果支持{[分支名称1], [分支名称2], (分支名称3), (分支名称4)}的拓扑结构。在核心属[属名]中，我们确定来自东北亚（分支A）的[物种名称]是最早分化的物种，其次是来自中国东部（分支B）的[物种名称]，而其余物种聚为两个姐妹分支（C和D）。分支C包括来自西天山的3个物种（[物种名称1], [物种名称2], [物种名称3]）。分支D由来自中亚北部的[物种名称]，加上来自高加索山脉的1个物种（[物种名称]）和来自东南欧的3个物种（[物种名称1], [物种名称2], [物种名称3]）组成。总体而言，我们确定了21个高度可变的质体基因组区域，包括2个编码基因（22, 1）和19个基因间隔区（IGS）区域，所有这些区域的核苷酸多样性（π）值> 0.02。这些分子标记应作为未来系统发育、系统地理学和保护遗传学研究的有力工具（包括DNA条形码）。
