Transcriptome and DNA methylome provide insights into the molecular regulation of drought stress in sea buckthorn

Zhongrui Lyu; Guoyun Zhang; Yating Song; Songfeng Diao; Caiyun He; Jianguo Zhang

doi:10.1016/j.ygeno.2022.110345

Transcriptome and DNA methylome provide insights into the molecular regulation of drought stress in sea buckthorn

Genomics. 2022 May;114(3):110345. doi: 10.1016/j.ygeno.2022.110345. Epub 2022 Mar 20.

Authors

Zhongrui Lyu¹, Guoyun Zhang¹, Yating Song¹, Songfeng Diao², Caiyun He³, Jianguo Zhang⁴

Affiliations

¹ State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
² Non-timber Forestry Research and Development Center, Chinese Academy of Forestry & Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China.
³ State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China. Electronic address: hecy@caf.ac.cn.
⁴ State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China. Electronic address: zhangjg@caf.ac.cn.

PMID: 35321848
DOI: 10.1016/j.ygeno.2022.110345

Abstract

Sea buckthorn is a typical drought-resistant tree species. However, there is a general lack of understanding of the pattern of DNA methylation linked with sea buckthorn responses to drought, and its relationship with drought tolerance mechanisms. In this study, we performed whole-transcriptome RNA sequencing and methylome sequencing in response to drought stress to explore differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs in sea buckthorn leaves. Based on predicted DE pairs, we constructed a competitive endogenous RNA network, which revealed potential transcriptional regulatory roles in response to drought stress. The results of methylome sequencing revealed that the DNA methylation level was increased in sea buckthorn leaves under drought stress. We identified 13,405 differentially methylated regions between CK and TR. We found one DMR-associated DEG (Vacuolar-sorting receptor 6) involved in the ABA accumulation pathway. In addition, two DNA methyltransferases (HrMET1 and HrDRM1) were closely associated with drought-induced hypermethylation in sea buckthorn. Together, we firstly conducted a comprehensive transcriptomic and epigenetic analysis of sea buckthorn under drought stress, providing a resource for further study of the potential functions of genes, miRNAs, lncRNAs, circRNAs and DNA methyltransferases.

Keywords: Drought stress; Methylome; Sea buckthorn; Whole-transcriptome RNA-seq; circRNAs; lncRNAs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA / metabolism
Droughts
Epigenome
Gene Expression Profiling
Gene Expression Regulation, Plant
Hippophae* / genetics
Hippophae* / metabolism
Methyltransferases / genetics
MicroRNAs* / genetics
MicroRNAs* / metabolism
RNA, Circular / metabolism
RNA, Long Noncoding* / genetics
RNA, Long Noncoding* / metabolism
Stress, Physiological / genetics
Transcriptome

Substances

RNA, Circular
RNA, Long Noncoding
MicroRNAs
Methyltransferases
DNA