Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

doi:10.3389/fpls.2023.1265641

KIB OpenIR

	Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution
	Yan,Rongrong; Geng,Yanfei; Jia,Yuhuan; Xiang,Chunlei; Zhou,Xinxin; Hu,Guoxiong
	2023
发表期刊	FRONTIERS IN PLANT SCIENCE
卷号	14 页码:1265641
摘要	Introduction: The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae.Methods: In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses.Results: The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic.Discussion: Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.
关键词	Lindernieae Lindernia Picria Torenia Scrophulariaceae chloroplast genome phylogenomics SEQUENCE PLACEMENT SOFTWARE TORENIA DNA DISINTEGRATION MITOCHONDRIAL ALIGNMENT PLATFORM GENOMES
DOI	10.3389/fpls.2023.1265641
WOS记录号	WOS:001082209900001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74988
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Yan,Rongrong,Geng,Yanfei,Jia,Yuhuan,et al. Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution[J]. FRONTIERS IN PLANT SCIENCE,2023,14:1265641.
APA	Yan,Rongrong,Geng,Yanfei,Jia,Yuhuan,Xiang,Chunlei,Zhou,Xinxin,&Hu,Guoxiong.(2023).Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution.FRONTIERS IN PLANT SCIENCE,14,1265641.
MLA	Yan,Rongrong,et al."Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution".FRONTIERS IN PLANT SCIENCE 14(2023):1265641.

条目包含的文件		下载所有文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
10.3389_fpls.2023.12（5462KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览下载