Identification and characterization of genes related to m^(6)A modification in kiwifruit using RNA-seq and ATAC-seq  

作　　者：Xiaoli Hu Tong Li Changbin Xu Yanna Xu Congjun You Xinyi Li Jinli Gong Xiaolong Li Xuepeng Sun 

机构地区：[1]Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province,Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable,Ministry of Agriculture and Rural Affairs,College of Horticulture Science,Zhejiang A&F University,Hangzhou,Zhejiang 311300,China

出　　处：《Horticultural Plant Journal》2024年第5期1121-1133,共13页园艺学报（英文版）

基　　金：the Natural Science Foundation of Zhejiang province(Grant Nos.LQ23C150003,LR23C150001);the National Natural Science Foundation of China(NSFC)(Grant No.32102318);NSFC Excellent Young Scientists Fund.

摘　　要：N6-methyladenosine(m^(6)A)RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms.Despite its significance,a comprehensive analysis of m^(6)A-related genes in non-model plants,such as kiwifruit,is lacking.Here,we identified 36 m^(6)A-related genes in the kiwifruit genome according to homology and phylogenetic inference.We performed bioinformatics and evolutionary analyses of the writer,eraser,and reader families of m^(6)A modification.Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most m^(6)A-related genes were remarkably expressed under different conditions.Through construction of gene co-expression networks,we found significant correlations between several m^(6)A-related genes and transcription factors(TFs)as well as receptor-like genes during the development and ripening of kiwifruit.Furthermore,we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of m^(6)A-related genes.We identified 10 common open chromatin regions that were present in at least two tissues,and these regions might serve as potential binding sites for MADS protein,C2H2 protein,and other predicted TFs.Our study offers comprehensive insights into the gene family of m^(6)A-related components in kiwifruit,which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit.

关 键 词：KIWIFRUIT N^(6)-methyladenosine Phylogenetic analysis CIS-ELEMENT Co-expression network 

分 类 号：S663.4[农业科学—果树学]