Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Jianghan University, Wuhan, Hubei, China.
School of Medicine, Jianghan University, Wuhan, Hubei, China.
BMC Genomics. 2024 Jun 5;25(1):561. doi: 10.1186/s12864-024-10455-3.
Artemisia selengensis, classified within the genus Artemisia of the Asteraceae family, is a perennial herb recognized for its dual utility in culinary and medicinal domains. There are few studies on the chloroplast genome of A. selengensis, and the phylogeographic classification is vague, which makes phylogenetic analysis and evolutionary studies very difficult.
The chloroplast genomes of 10 A. selengensis in this study were highly conserved in terms of gene content, gene order, and gene intron number. The genome lengths ranged from 151,148 to 151,257 bp and were typical of a quadripartite structure with a total GC content of approximately 37.5%. The chloroplast genomes of all species encode 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Due to the contraction and expansion of the inverted repeats (IR), the overlap of ycf1 and ndhF genes occurred at the inverted repeats B (IRB) and short single copy sequence (SSC) boundaries. According to a codon use study, the frequent base in the chloroplast genome of A. selengensis' third codon position was A/T. The number of SSR repeats was 42-44, most of which were single nucleotide A/T repeats. Sequence alignment analysis of the chloroplast genome showed that variable regions were mainly distributed in single copy regions, nucleotide diversity values of 0 to 0.009 were calculated by sliding window analysis, 8 mutation hotspot regions were detected, and coding regions were more conserved than non-coding regions. Analysis of non-synonymous substitution (Ka) and synonymous substitution (Ks) revealed that accD, rps12, petB, and atpF genes were affected by positive selection and no genes were affected by neutral selection. Based on the findings of the phylogenetic analysis, Artemisia selengensis was sister to the genus Artemisia Chrysanthemum and formed a monophyletic group with other Artemisia genera.
In this research, the present study systematically compared the chloroplast genomic features of A. selengensis and provided important information for the study of the chloroplast genome of A. selengensis and the evolutionary relationships among Asteraceae species.
菊科蒿属多年生草本植物黄花蒿，兼具食用和药用价值。目前有关黄花蒿叶绿体基因组的研究较少，且其系统发育分类较为模糊，这使得对其进行系统发育分析和进化研究变得非常困难。
本研究对 10 份黄花蒿叶绿体基因组进行了测序，结果表明它们在基因组成、基因顺序和基因内含子数量上高度保守。基因组长度在 151148-151257bp 之间，为典型的四分体结构，总 GC 含量约为 37.5%。所有黄花蒿叶绿体基因组共编码 133 个基因，包括 88 个蛋白编码基因、37 个 tRNA 基因和 8 个 rRNA 基因。由于反向重复（IR）的收缩和扩张，ycf1 和 ndhF 基因在反向重复 B（IRB）和短单拷贝序列（SSC）边界处重叠。根据密码子使用研究，黄花蒿叶绿体基因组第三密码子位置的频繁碱基为 A/T。SSR 重复数为 42-44，大多数为单核苷酸 A/T 重复。叶绿体基因组序列比对分析表明，可变区主要分布在单拷贝区，滑动窗口分析计算得到的核苷酸多样性值为 0-0.009，共检测到 8 个突变热点区，编码区比非编码区更保守。非 synonymous替换（Ka）和同义替换（Ks）分析表明，accD、rps12、petB 和 atpF 基因受到正选择的影响，没有基因受到中性选择的影响。基于系统发育分析的结果，黄花蒿与菊属、 Chrysanthemum 形成单系群，与其他蒿属植物形成一个单系群。
本研究系统比较了黄花蒿叶绿体基因组特征，为黄花蒿叶绿体基因组和菊科植物系统发育关系的研究提供了重要信息。
