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

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

机构地区：[1]College of Marine Science and Biological Engineering,Qingdao University of Science and Technology,Qingdao 266042,China [2]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 [3]Yunnan Institute of Tropical Crops,Xishuangbanna 666100,China [4]American Museum of Natural History,New York,NY 10024-5192,USA [5]Natural History Museum,and Department of Ecology&Evolutionary Biology,University of Kansas,Lawrence,KS 66045,USA

出　　处：《Marine Life Science & Technology》2024年第3期425-441,共17页海洋生命科学与技术（英文）

基　　金：supported by the National Natural Science Foundation of China(No.32370244);the Taishan Scholar Project(No.tsqn202306214);the Shandong Province Natural Science Foundation of China(No.ZR2023MC157);the State Key Laboratory of Pal-aeobiology and Stratigraphy(No.223123).

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

关 键 词：Aquatic plants NYMPHAEA Phylogenetic analysis Plastid genomics Structural variation 

分 类 号：Q942[生物学—植物学]