Institute of Plant Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
Agricultural Technology Extension Station of Ningxia, Yinchuan, 750001, China.
Sci Rep. 2022 May 18;12(1):8255. doi: 10.1038/s41598-022-11983-2.
Amaranthus is a complex taxon with economic importance as well as harmful weeds. We studied the genetic variation and structure of the chloroplast genomes of 22 samples from 17 species of three subgenera. It was found that the length of the chloroplast genome of Amaranthus varied from 149,949 bp of A. polygonoides to 150,757 bp of A. albus. The frequencies of SNPs and InDels in chloroplast genomes were 1.79% and 2.86%, and the variation mainly occurred in the non-coding regions. The longest InDel was 387 bp, which occurred on ycf2, followed by 384 bp InDel on psbM-trnD. Two InDels in ndhE-I on the SSC make the three subgenera clearly distinguished. In LSC, SSC and IRs regions, there were four 30 bp forward and reverse repeats, and the repeats in SSC and LSC were in nearly opposite positions in circular genome structure, and almost divided the circular genome into symmetrical structures. In the topological tree constructed by chloroplast genome, species in subgen. Amaranthus and subgen. Acnida form monophyletic branches separately and cluster together. A. albus, A. blitoides and A. polygonoides were separated from subgen. Albersia, and the rest of subgen. Albersia were clustered into a monophyletic branch. The rpoC2, ycf1, ndhF-rpl32 were good at distinguishing most amaranths. The trnk-UUU-atpF, trnT-UGU-atpB, psbE-clpP, rpl14-rps19, and ndhF-D can distinguish several similar species. In general, the chloroplast genome is of certain value for the identification of the similar species of Amaranthus, which provides more evidence for clarifying the phylogenetic relationships within the genus.
苋菜是一个复杂的分类群，具有经济重要性和有害杂草。我们研究了来自三个亚属的 17 种 22 个样本的叶绿体基因组的遗传变异和结构。结果发现，苋菜叶绿体基因组的长度从 149949bp 的 A. polygonoides 到 150757bp 的 A. albus。叶绿体基因组中的 SNP 和 InDels 频率分别为 1.79%和 2.86%，变异主要发生在非编码区。最长的 InDel 为 387bp，发生在 ycf2 上，其次是 psbM-trnD 上的 384bp InDel。在 SSC 上的 ndhE-I 中有两个 InDels，使三个亚属明显区分开来。在 LSC、SSC 和 IRs 区域，有四个 30bp 的正向和反向重复，在圆形基因组结构中，SSC 和 LSC 中的重复处于几乎相反的位置，几乎将圆形基因组分为对称结构。在叶绿体基因组构建的拓扑树中，亚属苋菜和亚属 Acnida 的物种分别形成单系分支并聚集在一起。A. albus、A. blitoides 和 A. polygonoides 与亚属 Albersia 分离，其余亚属 Albersia 聚集成一个单系分支。rpoC2、ycf1、ndhF-rpl32 善于区分大多数苋菜。trnk-UUU-atpF、trnT-UGU-atpB、psbE-clpP、rpl14-rps19 和 ndhF-D 可以区分几个相似的物种。一般来说，叶绿体基因组对苋菜相似种的鉴定具有一定的价值，为阐明属内的系统发育关系提供了更多的证据。
