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

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

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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 phylo-genetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages.

Aquatic plantsNymphaeaPhylogenetic analysisPlastid genomicsStructural variation

Weicai Song、Wenbo Shi、Huan Wang、Zirui Zhang、Ruiqing Tao、Jin Liu、Shuo Wang、Michael S.Engel、Chao Shi

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College of Marine Science and Biological Engineering,Qingdao University of Science and Technology,Qingdao 266042,China

Yunnan Institute of Tropical Crops,Xishuangbanna 666100,China

American Museum of Natural History,New York,NY 10024-5192,USA

Natural History Museum,and Department of Ecology &Evolutionary Biology,University of Kansas,Lawrence,KS 66045,USA

Plant Germplasm and Genomics Center,Germplasm Bank of Wild Species in Southwest China,Kunming Institute of Botany,The Chinese Academy of Sciences,Kunming 650204,China

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2024

10.1007/s42995-024-00242-0

海洋生命科学与技术(英文)

海洋生命科学与技术(英文)

ISSN：
年,卷(期)：2024.6(3)