Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants

doi:10.1007/s42995-024-00242-0

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	Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants
	Song, Weicai; Shi, Wenbo; Wang, Huan; Zhang, Zirui; Tao, Ruiqing; Liu, Jin; Wang, Shuo; Engel, Michael S.; Shi, Chao
	2024
发表期刊	MARINE LIFE SCIENCE & TECHNOLOGY
ISSN	2096-6490
卷号	6 期号:3 页码:425-441
摘要	The aquatic plant Nymphaea, a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae, has been extensively studied. However, the availability of chloroplast genome data for this genus is incomplete, and phylogenetic relationships within the order Nymphaeales remain controversial. In this study, 12 chloroplast genomes of Nymphaea were assembled and analyzed for the first time. These genomes were 158,290-160,042 bp in size and contained 113 non-repeat genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. We also report on codon usage, RNA editing sites, microsatellite structures, and new repetitive sequences in this genus. Comparative genomics revealed that expansion and contraction of IR regions can lead to changes in the gene numbers. Additionally, it was observed that the highly variable regions of the chloroplast genome were mainly located in intergenic regions. Furthermore, the phylogenetic tree showed the order Nymphaeales was divided into three families, and the genus Nymphaea can be divided into five (or three) subgenera, with the subgenus Nymphaea being the oldest. The divergence times of nymphaealean taxa were analyzed, with origins of the order Nymphaeales and family Nymphaeaceae being about 194 and 131 million years, respectively. The results of the phylogenetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages.
DOI	10.1007/s42995-024-00242-0
WOS记录号	WOS:001292094400001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/76114
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Song, Weicai,Shi, Wenbo,Wang, Huan,et al. Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants[J]. MARINE LIFE SCIENCE & TECHNOLOGY,2024,6(3):425-441.
APA	Song, Weicai.,Shi, Wenbo.,Wang, Huan.,Zhang, Zirui.,Tao, Ruiqing.,...&Shi, Chao.(2024).Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants.MARINE LIFE SCIENCE & TECHNOLOGY,6(3),425-441.
MLA	Song, Weicai,et al."Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants".MARINE LIFE SCIENCE & TECHNOLOGY 6.3(2024):425-441.

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