Gou Wei, Jia Sheng-Bin, Price Megan, Guo Xian-Lin, Zhou Song-Dong, He Xing-Jin
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China.
Plants (Basel). 2020 Nov 9;9(11):1523. doi: 10.3390/plants9111523.
Turcz., Hand.-Mazz. and H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of and . Therefore, we aimed to conduct comparative (simple sequence repeat (SSR) structure, codon usage bias, nucleotide diversity (Pi) and inverted repeat (IR) boundaries) and phylogenetic analyses of , and (also compared with and ) to reduce uncertainties in intergeneric and interspecific relationships. We newly assembled eight plastid genomes from , and species, and analyzed them with two plastid genomes from GenBank of . Phylogenetic analyses used these ten genomes and another 22 plastid genome sequences of Apiaceae. We found that the newly assembled eight genomes ranged from 155,435 bp to 157,797 bp in length and all had a typical quadripartite structure. Fifty-five to 75 SSRs were found in , and species, and the most abundant SSR was mononucleotide, which accounted for 58.47% of , 60.21% of and 48.01% of There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. The Pi analysis showed that , and spacer regions had the highest Pi values in the plastid genomes of (0.01889), (0.04333) and (0.01222), respectively. The spacer regions were found in all three genera to have higher diversity values (Pi values: 0.01028-0.2), and thus may provide potential DNA barcodes in phylogenetic analysis. IR boundary analysis showed that the length of and genes entering IRs were usually stable in the same genus. Our phylogenetic tree demonstrated that is sister to ; meanwhile, and are nested together in the East Asia clade, and is nested within individuals of in the clade. This study will enrich the complete plastid genome dataset of the Apiaceae genera and has provided a new insight into phylogeny reconstruction using complete plastid genomes of , and .
Turcz.、Hand.-Mazz. 和H. Wolff是伞形科的三个属，为横断山脉和喜马拉雅山脉所特有，通常生长于海拔超过2000米的地区。这些属之间以及属内的系统发育关系尚不确定，尤其是[具体属名1]和[具体属名2]的位置。因此，我们旨在对[具体属名1]、[具体属名2]和[具体属名3]（也与[其他属名1]和[其他属名2]进行比较）进行比较分析（简单序列重复（SSR）结构、密码子使用偏好、核苷酸多样性（Pi）和反向重复（IR）边界）和系统发育分析，以减少属间和种间关系的不确定性。我们新组装了来自[具体属名1]、[具体属名2]和[具体属名3]物种的8个质体基因组，并与来自GenBank的[其他属名1]的两个质体基因组进行了分析。系统发育分析使用了这10个基因组以及伞形科的另外22个质体基因组序列。我们发现新组装的8个基因组长度在155,435 bp至157,797 bp之间，均具有典型的四分体结构。在[具体属名1]、[具体属名2]和[具体属名3]的物种中发现了55至75个SSR，最丰富的SSR是单核苷酸，分别占[具体属名1]的58.47%、[具体属名2]的60.21%和[具体属名3]的48.01%。这三个属之间的密码子使用频率没有明显差异，密码子数量在21,134至21,254之间。Pi分析表明，[具体属名1]、[具体属名2]和[具体属名3]的间隔区在[具体属名1]、[具体属名2]和[具体属名3]的质体基因组中分别具有最高的Pi值（分别为0.01889、0.04333和0.01222）。在所有三个属中都发现[具体间隔区]具有较高的多样性值（Pi值：0.01028 - 0.2），因此可能在系统发育分析中提供潜在的DNA条形码。IR边界分析表明，[具体基因1]和[具体基因2]进入IRs的长度在同一属中通常是稳定的。我们的系统发育树表明，[具体属名1]是[具体属名2]的姐妹属；同时，[具体属名2]和[具体属名3]在东亚分支中嵌套在一起，而[具体属名3]在[具体属名4]分支中嵌套在[具体属名4]个体内。本研究将丰富伞形科属的完整质体基因组数据集，并为使用[具体属名1]、[具体属名2]和[具体属名3]的完整质体基因组进行系统发育重建提供了新的见解。
