DNA methylation role in subgenome expression dominance of Juglans regia and its wild relative J. mandshurica
Author:
Li Mengdi1ORCID,
Ou Mengwei1,
He Xiaozhou1,
Ye Hang1,
Ma Jiayu1,
Liu Hengzhao1,
Yang Huijuan1ORCID,
Zhao Peng1ORCID
Affiliation:
1. Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi’an, Shaanxi 710069 , China
Abstract
Abstract
Subgenome expression dominance plays a crucial role in the environmental adaptation of polyploids. However, the epigenetic molecular mechanism underlying this process has not been thoroughly investigated, particularly in perennial woody plants. Persian walnut (Juglans regia) and its wild relative, Manchurian walnut (Juglans mandshurica), are woody plants of great economic importance and are both paleopolyploids that have undergone whole-genome duplication events. In this study, we explored the characteristics of subgenome expression dominance in these 2 Juglans species and examined its epigenetic basis. We divided their genomes into dominant subgenome (DS) and submissive subgenome (SS) and found that the DS-specific genes might play critical roles in biotic stress response or pathogen defense. We comprehensively elucidated the characteristics of biased gene expression, asymmetric DNA methylation, transposable elements (TEs), and alternative splicing (AS) events of homoeologous gene pairs between subgenomes. The results showed that biased expression genes (BEGs) in 2 Juglans species were mainly related to external stimuli response, while non-BEGs were related to complexes that might be involved in signal transduction. DS genes had higher expression and more AS events while having less DNA methylation and TEs than homoeologous genes from the SS in the 2 Juglans species. Further studies showed that DNA methylation might contribute to the biased expression of gene pairs by modifying LTR/TIR/nonTIR TEs and improving the AS efficiency of corresponding precursor mRNAs in a particular context. Our study contributes to understanding the epigenetic basis of subgenome expression dominance and the environmental adaptation of perennial woody plants.
Funder
National Natural Science Foundation of China
China Postdoctoral Science Foundation
Science Foundation for Distinguished Young Scholars of Shaanxi Province
Shaanxi Academy of Fundamental Science
Natural Science Foundation of Shaanxi Province of China
Key Laboratory of Resource Biology and Biotechnology in Western China
Publisher
Oxford University Press (OUP)
Subject
Plant Science,Genetics,Physiology
Cited by
1 articles.
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