Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage  

作　　者：Xiaoming Song Jingjing Hu Tong Wu Qihang Yang Xuehuan Feng Hao Lin Shuyan Feng Chunlin Cui Ying Yu Rong Zhou Ke Gong Tong Yu Qiaoying Pei Nan Li 

机构地区：[1]College of Life Sciences/Center for Genomics and Bio-computing,North China University of Science and Technology,Tangshan,Hebei,China [2]Food Science and Technology Department,University of Nebraska-Lincoln,Lincoln,NE,USA [3]School of Life Science and Technology and Center for Informational Biology,University of Electronic Science and Technology of China,Chengdu,China [4]Department of Food Science,Aarhus University,Aarhus,Denmark

出　　处：《Horticulture Research》2021年第1期693-713,共21页园艺研究（英文）

基　　金：the National Natural Science Foundation of China(31801856 to X.S.);the Hebei Province Higher Education Youth Talents Program(BJ2018016 to X.S.);the China Postdoctoral Science Foundation(2020M673188 to X.S.);the Natural Science Foundation of Hebei(C2017209103 to X.S.).

摘　　要：Long noncoding RNAs(lncRNAs)are widely present in different species and play critical roles in response to abiotic stresses.However,the functions of lncRNAs in Chinese cabbage under heat stress remain unknown.Here,we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species.The results indicated that lncRNAs were poorly conserved among different species,and only 960 lncRNAs were homologous to 524 miRNA precursors.We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment.In total,18,253 lncRNAs were identified,of which 1229 differentially expressed(DE)lncRNAs were characterized as being heat-responsive.The ceRNA network revealed that 38 lncRNAs,16 miRNAs,and 167 mRNAs were involved in the heat response in Chinese cabbage.Combined analysis of the cis-and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the“protein processing in endoplasmic reticulum”and“plant hormone signal transduction”pathways.Furthermore,the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly.Based on the networks of DE lncRNA-mRNAs,29 and 22 lncRNAs were found to interact with HSP and PYL genes,respectively.Finally,the expression of several critical lncRNAs and their targets was verified by qRT-PCR.Overall,we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage.Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage,and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.

关 键 词：STRESS analysis CHARACTERIZATION 

分 类 号：S634.1[农业科学—蔬菜学]