Mining salt stress-related genes in Spartina alterniflora via analyzing co-evolution signal across 365 plant species using phylogenetic profiling  

作　　者：Shang Gao Shoukun Chen Maogeng Yang Jinran Wu Shihua Chen Huihui Li 

机构地区：[1]State Key Laboratory of Crop Gene Resources and Breeding,Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China [2]Nanfan Research Institute,Chinese Academy of Agricultural Sciences,Sanya 572024,China [3]Hainan Yazhou Bay Seed Laboratory,Sanya 572024,China [4]Key Laboratory of Plant Molecular&Developmental Biology,College of Life Sciences,Yantai University,Yantai 264005,China [5]The Institute for Learning Sciences and Teacher Education,Australian Catholic University,Brisbane,QLD 4001,Australia

出　　处：《aBIOTECH》2023年第4期291-302,共12页生物技术通报（英文版）

基　　金：supported by the National Key R&D Program of China(2022YFF0711802);the Nanfan special project of the Chinese Academy of Agricultural Sciences(ZDXM2309);the National Natural Science Foundation of China(32022064);the Innovation Program of the Chinese Academy of Agricultural Sciences,the Alibaba Foundation,and the High-performance Computing Platform of YZBSTCACC.

摘　　要：With the increasing number of sequenced species,phylogenetic profiling(PP)has become a powerful method to predict functional genes based on co-evolutionary information.However,its potential in plant genomics has not yet been fully explored.In this context,we combined the power of machine learning and PP to identify salt stress-related genes in a halophytic grass,Spartina alterniflora,using evolutionary information generated from 365 plant species.Our results showed that the genes highly co-evolved with known salt stress-related genes are enriched in biological processes of ion transport,detoxification and metabolic pathways.For ion transport,five identified genes coding two sodium and three potassium transporters were validated to be able to uptake Na?.In addition,we identified two orthologs of trichome-related AtR3-MYB genes,SaCPC1 and SaCPC2,which may be involved in salinity responses.Genes co-evolved with SaCPCs were enriched in functions related to the circadian rhythm and abiotic stress responses.Overall,this work demonstrates the feasibility of mining salt stress-related genes using evolutionary information,highlighting the potential of PP as a valuable tool for plant functional genomics.

关 键 词：Phylogenetic profiling Spartina alterniflora Salt stress-related gene Machine learning Evolutionary information 

分 类 号：Q943.2[生物学—植物学]