Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution  

作　　者：Weihong Wu Xiao Feng Nan Wang Shao Shao Min Liu Fa Si Linhao Chen Chuanfeng Jin Shaohua Xu Zixiao Guo Cairong Zhong Suhua Shi Ziwen He 

机构地区：[1]State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources,School of Life Sciences,Sun Yat-sen University,Guangzhou 510275,China [2]Greater Bay Area Institute of Precision Medicine,School of Life Sciences,Fudan University,Guangzhou 511462,China [3]Hainan Academy of Forestry(Hainan Academy of Mangrove),Haikou 571100,China

出　　处：《Journal of Integrative Plant Biology》2024年第4期824-843,共20页植物学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(32170230,31971540,31830005,42276159);the Guangdong Basic and Applied Basic Research Foundation(2023B1515020083);the Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(311021006)。

摘　　要：Nypa fruticans(Wurmb),a mangrove palm species with origins dating back to the Late Cretaceous period,is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms.Here,we present a chromosome-level genome sequence and assembly for N.fruticans.We integrated the genomes of N.fruticans and other palm family members for a comparative genomic analysis,which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago,shaping the distinctive characteristics observed in this clade.We also inferred a low mutation rate for the N.fruticans genome,which underwent strong purifying selection and evolved slowly,thus contributing to its stability over a long evolutionary period.Moreover,ancient duplicates were preferentially retained,with critical genes having experienced positive selection,enhancing waterlogging tolerance in N.fruticans.Furthermore,we discovered that the pseudogenization of Early Methionine-labelled 1(EM1)and EM6 in N.fruticans underly its crypto-vivipary characteristics,reflecting its intertidal adaptation.Our study provides valuable genomic insights into the evolutionary history,genome stability,and adaptive evolution of the mangrove palm.Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

关 键 词：crypto-vivipary genome stability long-term adaptation mangrove Nypa fruticans PALM 

分 类 号：Q943.2[生物学—植物学]