生物
基因组
系统发育树
单系
硅质
遗传学
系统发育学
进化生物学
基因
克莱德
作者
Rongpeng Liu,Zejing Mu,Xiaolang Du,Guoyue Zhong,Xiaoyun Wang
出处
期刊:Journal of AOAC International
[Oxford University Press]
日期:2023-12-01
标识
DOI:10.1093/jaoacint/qsad129
摘要
Caryophyllaceae is a big family composed of many economic and medicinal species. However, the phylogeny of the family is insufficient and genome data are lacking for many species.Using the next-generation sequencing (NGS) to acquire the chloroplast (cp) genomes of Eremogone acicularis (F.N.Williams) Ikonn., E. brevipetala (Tsui & L.H.Zhou) Sadeghian & Zarre, E. bryophylla (Fernald) Pusalkar & D.K.Singh, E. kansuensis (Maxim.) Dillenb. & Kadereit, Shivparvatia glanduligera (Edgew.) Pusalkar & D.K.Singh, Silene atsaensis (Marq.) Bocquet, S. caespitella Williams and S. lhassana (Williams) Majumdar.Bioinformatic softwares were used to conduct the comparative genome and phylogeny analysis of these cp genomes.The eight cp genomes were 132,188-151,919 bp in length, containing 130-132 genes. A/T was dominant in simple sequence repeats (SSRs). Forward repeats and palindromic repeats were the most frequent in long terminal repeats (LTRs). Compared with the four species of Eremogone Fenzl, the IR boundary of S. caespitella, S. atsaensis, S. lhassana and Sh. glanduligera were significantly expanded. Four and one mutational hotspots were identified in the large single copy (LSC) region and small single copy (SSC) region, respectively. The ratio of nonsynonymous substitution to synonymous substitution (Ka/Ks ratio) showed these cp genomes may have undergone strong purifying selection. In the phylogenetic trees, both Silene L. and Eremogone were monophyletic groups. However, Sh. glanduligera was closely related to Amaranthus hypochondriacus.These results have provided new evidence and useful information for species identification, evolution and genetic research on the Caryophyllaceae.In this study, the eight newly sequenced cp genomes of Caryophyllaceae species were reported for the first time.
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