Xia Conglong, Wang Manjiong, Guan Yunhui, Li Jian
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, China.
College of Pharmacy, Dali University, Dali, China.
Front Genet. 2022 May 31;13:878182. doi: 10.3389/fgene.2022.878182. eCollection 2022.
is an important medicinal group of the Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. There are about 350 species globally and about 170 species in China. It is challenging to identify the species in morphology, and the lack of molecular biology information hinders the identification and rational utilization of the germplasm of this genus. Therefore, it is necessary to increase the molecular data of species. This paper acquired the complete chloroplast (CP) genome sequence of ten medicinal plants of species from Yunnan by Illumina paired-end (PE) sequencing technology and compared it with other species in the same family and genus. These CP genomes exhibited typical circular quadripartite structure, and their sizes ranged from 155,475 () to 155,921 bp (), including a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRs). Their gene content, order, and GC content (38.1%) were similar. Moreover, their number of genes ranged from 129 () to 132 (. ), including 83 to 85 protein-coding genes (PCGs), 37 tRNA genes (tRNAs), eight rRNA genes (rRNAs), and two pseudogenes. In addition, we performed repeated sequence analysis, genomic structure, and comparative analysis using 42 chloroplast genomes, including ten chloroplast genomes and other sequenced species. A total of 48-79 simple sequence repeats (SSRs) and 17 to 77 long repeat sequences were identified. IR regions showed higher variability than the SSC region and LSC region. Seven mutational hotspots were screened out, including ---, , -, , -, , and ---, respectively. The phylogenetic trees of ten species and other species revealed that the complete CP genome was beneficial in determining the complex phylogenetic relationships among species. This study provides a potential molecular marker and genomic resource for phylogeny and species identification of species and an important reference and basis for Ranunculaceae species identification and phylogeny.
是毛茛科一个重要的药用类群，在中国白族、彝族等民族中被用作传统药物。全球约有350种，中国约有170种。从形态上鉴定该物种具有挑战性，分子生物学信息的缺乏阻碍了该属种质资源的鉴定和合理利用。因此，有必要增加物种的分子数据。本文通过Illumina双末端（PE）测序技术获得了云南10种该属药用植物的完整叶绿体（CP）基因组序列，并与同科同属的其他物种进行了比较。这些CP基因组呈现典型的环状四分体结构，其大小范围为155,475（）至155,921 bp（），包括一个大单拷贝区域（LSC）、一个小单拷贝区域（SSC）和两个反向重复区域（IR）。它们的基因含量、顺序和GC含量（38.1%）相似。此外，它们的基因数量范围为129（）至132（. ），包括83至85个蛋白质编码基因（PCG）、37个tRNA基因（tRNA）、8个rRNA基因（rRNA）和2个假基因。此外，我们使用42个叶绿体基因组进行了重复序列分析、基因组结构和比较分析，其中包括10个该属叶绿体基因组和其他已测序的该属物种。共鉴定出48 - 79个简单序列重复（SSR）和17至77个长重复序列。IR区域显示出比SSC区域和LSC区域更高的变异性。筛选出7个突变热点，分别为---、、-、、-、、和---。10种该属物种和其他该属物种的系统发育树表明，完整的CP基因组有助于确定该属物种间复杂的系统发育关系。本研究为该属物种的系统发育和物种鉴定提供了潜在的分子标记和基因组资源，为毛茛科物种鉴定和系统发育提供了重要参考和依据。
