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

doi:10.1186/s12870-023-04271-2

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	Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)
	Weng,Long; Jiang,Yunhui; Wang,Yong; Zhang,Xuemei; Zhou,Ping; Wu,Mei; Li,Hongzhe; Sun,Hang; Chen,Shaotian
	2023
发表期刊	BMC PLANT BIOLOGY
卷号	23 期号:1 页码:284
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.
关键词	Sinodielsia clade Systematics Cp genome Highly variable region Apioideae SUBFAMILY APIOIDEAE SEQUENCE NRDNA ANGIOSPERMS ANGELICA
学科领域	Plant Sciences
DOI	10.1186/s12870-023-04271-2
WOS记录号	WOS:000994914400001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74942
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Weng,Long,Jiang,Yunhui,Wang,Yong,et al. Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)[J]. BMC PLANT BIOLOGY,2023,23(1):284.
APA	Weng,Long.,Jiang,Yunhui.,Wang,Yong.,Zhang,Xuemei.,Zhou,Ping.,...&Chen,Shaotian.(2023).Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae).BMC PLANT BIOLOGY,23(1),284.
MLA	Weng,Long,et al."Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)".BMC PLANT BIOLOGY 23.1(2023):284.

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