Complete chloroplast genomes of four Atalantia (Rutaceae) species: insights into comparative analysis, phylogenetic relationships, and divergence time estimation

doi:10.1007/s00606-023-01868-w

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	Complete chloroplast genomes of four Atalantia (Rutaceae) species: insights into comparative analysis, phylogenetic relationships, and divergence time estimation
	Shi,Wenbo; Song,Weicai; Zhao,Yuqi; Shi,Chao; Wang,Shuo
	2023
发表期刊	PLANT SYSTEMATICS AND EVOLUTION
ISSN	1615-6110
卷号	309 期号:5 页码:31
摘要	Atalantia plants are small trees in the family Rutaceae that have great potential for use in agriculture, medicine, and carving. However, the phylogenetic relationships of Atalantia species have not been systematically studied due to the lack of available molecular resources and highly variable molecular markers. In this study, the complete chloroplast genomes of four Atalantia species were newly sequenced and characterized. The length of the chloroplast genomes in Atalantia species ranged from 159,557 to 160,341 bp, which was more similar to Fortunella and Citrus species in the Rutaceae. The rpl22 genes were pseudogenized at the SSC/IRa boundary. Certain mechanisms have been evolved to compensate for the pseudogenization of the accD and infA genes in Atalantia chloroplast genomes. Some highly divergent intergenic regions (trnH-GUG-psbA, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, atpF-atpI, petN-psbM, psbM-trnD-GUC, ndhC-trnV-UAC, atpB-rbcL, accD-psaI, and ycf4-cemA) and genes (psbM, trnD-GUC, rpl32, ndhF, and ycf1) were detected, which serve as potential phylogenetic markers. The phylogenetic relationships and divergence times of Atalantia species were explored based on the complete chloroplast genome. Based on the phylogenetic trees, Atalantia species were grouped into two sub-branches. Atalantia monophylla and A. buxifolia were found to be more closely related, whereas A. ceylanica and A. roxburghiana exhibited a closer relationship. The divergence time estimation indicated that the common ancestor of the Atalantia species diverged approximately 14.26 million years ago. These findings will help with the identification, categorization, and utilization of Atalantia species.
关键词	Atalantia Chloroplast genome Comparative analysis Divergence times Molecular markers Phylogeny ACETYL-COA CARBOXYLASE CITRUS SEQUENCE AURANTIOIDEAE EVOLUTION DIVERSITY FOSSIL DNA BIOGEOGRAPHY RADIATIONS
DOI	10.1007/s00606-023-01868-w
WOS记录号	WOS:001048628300001
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74804
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Shi,Wenbo,Song,Weicai,Zhao,Yuqi,et al. Complete chloroplast genomes of four Atalantia (Rutaceae) species: insights into comparative analysis, phylogenetic relationships, and divergence time estimation[J]. PLANT SYSTEMATICS AND EVOLUTION,2023,309(5):31.
APA	Shi,Wenbo,Song,Weicai,Zhao,Yuqi,Shi,Chao,&Wang,Shuo.(2023).Complete chloroplast genomes of four Atalantia (Rutaceae) species: insights into comparative analysis, phylogenetic relationships, and divergence time estimation.PLANT SYSTEMATICS AND EVOLUTION,309(5),31.
MLA	Shi,Wenbo,et al."Complete chloroplast genomes of four Atalantia (Rutaceae) species: insights into comparative analysis, phylogenetic relationships, and divergence time estimation".PLANT SYSTEMATICS AND EVOLUTION 309.5(2023):31.

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