College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China.
First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China.
PLoS One. 2022 Aug 5;17(8):e0272563. doi: 10.1371/journal.pone.0272563. eCollection 2022.
Carpesium (Asteraceae) is a genus that contains many plant species with important medicinal values. However, the lack of chloroplast genome research of this genus has greatly hindered the study of its molecular evolution and phylogenetic relationship. This study used the Illumina sequencing platform to sequence three medicinal plants of the Carpesium genus: Carpesium abrotanoides, Carpesium cernuum, and Carpesium faberi, obtaining three complete chloroplast genome sequences after assembly and annotation. It was revealed that the three chloroplast genomes were typical quadripartite structures with lengths of 151,389 bp (C. abrotanoides), 151,278 bp (C. cernuum), and 151,250 bp (C. faberi), respectively. A total of 114 different genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Abundant SSR loci were detected in all three chloroplast genomes, with most composed of A/T. The expansion and contraction of the IR region indicate that the boundary regions of IR/SC are relatively conserved for the three species. Using C. abrotanoides as a reference, most of the non-coding regions of the chloroplast genomes were significantly different among the three species. Five different mutation hot spots (trnC-GCA-petN, psaI, petA-psbJ, ndhF, ycf1) with high nucleotide variability (Pi) can serve as potential DNA barcodes of Carpesium species. Additionally, phylogenetic evolution analysis of the three species suggests that C. cernuum has a closer genetic relationship to C. faberi than C. abrotanoides. Simultaneously, Carpesium is a monophyletic group closely related to the genus Inula. Complete chloroplast genomes of Carpesium species can help study the evolutionary and phylogenetic relationships and are expected to provide genetic marker assistance to identify Carpesium species.
苍耳属（菊科）是一个包含许多具有重要药用价值的植物物种的属。然而，该属的叶绿体基因组研究的缺乏极大地阻碍了其分子进化和系统发育关系的研究。本研究使用 Illumina 测序平台对苍耳属的三种药用植物：苍耳、刺苍耳和白花苍耳进行测序，组装和注释后获得了三个完整的叶绿体基因组序列。结果表明，这三个叶绿体基因组均为典型的四分体结构，长度分别为 151,389 bp（苍耳）、151,278 bp（刺苍耳）和 151,250 bp（白花苍耳）。共注释了 114 个不同的基因，包括 80 个蛋白质编码基因、30 个 tRNA 基因和 4 个 rRNA 基因。在所有三个叶绿体基因组中都检测到丰富的 SSR 位点，大多数由 A/T 组成。IR 区的扩张和收缩表明，IR/SC 的边界区域在这三个物种中相对保守。以苍耳为参照，三个物种的叶绿体基因组中非编码区差异较大。五个不同的突变热点（trnC-GCA-petN、psaI、petA-psbJ、ndhF、ycf1）具有较高的核苷酸变异性（Pi），可作为苍耳属物种的潜在 DNA 条形码。此外，对这三个物种的系统发育进化分析表明，刺苍耳与白花苍耳的遗传关系比苍耳更密切。同时，苍耳属与旋覆花属是一个单系群，亲缘关系较近。苍耳属植物的完整叶绿体基因组有助于研究其进化和系统发育关系，并有望为鉴定苍耳属物种提供遗传标记辅助。
