Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)

BMC Plant Biology

Research

Ping Zhou¹  Mei Wu²  Long Weng²  Yunhui Jiang²  Shaotian Chen²  Hongzhe Li²  Hang Sun³  Yong Wang⁴  Xuemei Zhang⁵ 

[1] College of Basic Medicine, Yunnan University of Chinese Medicine, 650500, Kunming, China;College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, 650500, Kunming, China;Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China;Yunnan Institute of Forest Inventory and Planning, 650051, Kunming, China;Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, 650500, Kunming, China;

关键词: Sinodielsia;    Systematics;    Cp genome;    Highly variable region;    Apioideae;   

DOI  :  10.1186/s12870-023-04271-2

 received in 2023-01-20, accepted in 2023-05-07,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundThe Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade.ResultsThese 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599–31,486 bp) separated by a large single-copy region (LSC: 82,048–94,046 bp) and a small single-copy region (SSC: 16,343–17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL–accD, ycf4–cemA, petA–psbJ, ycf1–ndhF, ndhF–rpl32 and ycf1, and it was found that ndhF–rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes.ConclusionThe Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF–rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.

【 授权许可】

CC BY   
© The Author(s) 2023

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