Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications

doi:10.1186/s12870-023-04323-7

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	Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications
	Zhao,Yu-Juan; Liu,Jian; Yin,Gen-Shen; Gong,Xun
	2023
发表期刊	BMC PLANT BIOLOGY
卷号	23 期号:1 页码:303
摘要	BackgroundCeratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China. Ceratostigma has been the focal group in several studies, owing to their importance in economic and ecological value and unique breeding styles. Despite this, the genome information is limited and interspecific relationships within the genus Cerotastigma remains unexplored. Here we sequenced, assembled and characterized the 14 plastomes of five species, and conducted phylogenetic analyses of Cerotastigma using plastomes and nuclear ribosomal DNA (nrDNA) data.ResultsFourteen Cerotastigma plastomes possess typical quadripartite structures with lengths from 164,076 to 168,355 bp that consist of a large single copy, a small single copy and a pair of inverted repeats, and contain 127-128 genes, including 82-83 protein coding genes, 37 transfer RNAs and eight ribosomal RNAs. All plastomes are highly conservative and similar in gene order, simple sequence repeats (SSRs), long repeat repeats and codon usage patterns, but some structural variations in the border of single copy and inverted repeats. Mutation hotspots in coding (Pi values > 0.01: matK, ycf3, rps11, rps3, rpl22 and ndhF) and non-coding regions (Pi values > 0.02: trnH-psbA, rps16-trnQ, ndhF-rpl32 and rpl32-trnL) were identified among plastid genomes that could be served as potential molecular markers for species delimitation and genetic variation studies in Cerotastigma. Gene selective pressure analysis showed that most protein-coding genes have been under purifying selection except two genes. Phylogenetic analyses based on whole plastomes and nrDNA strongly support that the five species formed a monophyletic clade. Moreover, interspecific delimitation was well resolved except C. minus, individuals of which clustered into two main clades corresponding to their geographic distributions. The topology inferred from the nrDNA dataset was not congruent with the tree derived from the analyses of the plastid dataset.ConclusionThese findings represent the first important step in elucidating plastome evolution in this widespread distribution genus Cerotastigma in the Qinghai-Tibet Plateau. The detailed information could provide a valuable resource for understanding the molecular dynamics and phylogenetic relationship in the family Plumbaginaceae. Lineage genetic divergence within C. minus was perhaps promoted by geographic barriers in the Himalaya and Hengduan Mountains region, but introgression or hybridization could not be completely excluded.
关键词	Ceratostigma Plastid genome Comparative analysis Interspecific relationship Plumbaginaceae COMPLETE CHLOROPLAST GENOME MEKONG-SALWEEN DIVIDE LIMONIUM-SINENSE INVERTED REPEAT SEQUENCE EVOLUTION DNA PLUMBAGINACEAE CONSEQUENCES DIVERSITY
学科领域	Plant Sciences
DOI	10.1186/s12870-023-04323-7
WOS记录号	WOS:001002198500001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74944
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Zhao,Yu-Juan,Liu,Jian,Yin,Gen-Shen,et al. Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications[J]. BMC PLANT BIOLOGY,2023,23(1):303.
APA	Zhao,Yu-Juan,Liu,Jian,Yin,Gen-Shen,&Gong,Xun.(2023).Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications.BMC PLANT BIOLOGY,23(1),303.
MLA	Zhao,Yu-Juan,et al."Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications".BMC PLANT BIOLOGY 23.1(2023):303.

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