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Comparative epigenomics reveals evolution of duplicated genes in potato and tomato
Author(s) -
Wang Lin,
Xie Jiahui,
Hu Jiantuan,
Lan Binyuan,
You Chenjiang,
Li Fenglan,
Wang Zhengjia,
Wang Haifeng
Publication year - 2018
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13790
Subject(s) - biology , dna methylation , gene , methylation , genetics , epigenetics , genome , solanum , epigenomics , ripening , dna , gene expression , botany
Summary The evolution of duplicated genes after polyploidization has been the subject of many evolutionary biology studies. Potato ( Solanum tuberosum ) and tomato ( Solanum lycopersicum ) are the first two sequenced genomes of asterids, and share a common polyploidization event. However, the epigenetic role of DNA methylation on the evolution of duplicated genes derived from polyploidization is not fully understood. Here, we explore the role of the DNA methylation in the evolution of duplicated genes in potato and tomato. The overall levels of DNA methylation are different, although patterns of DNA methylation are similar in potato and tomato. Different types of duplicated genes can display different methylation patterns in potato and tomato. In addition, we found that differences in the methylation levels between duplicated genes were associated with gene expression divergence. In particular, for the majority of duplicated gene pairs, one copy is always hyper‐ or hypo‐methylated compared with the other copy across different tomato fruit ripening stages, and these genes are enriched for specific function related to transcription factor ( TF ) activity. Furthermore, transcription of hundreds of duplicated TF s was shown to be regulated by DNA methylation during fruit ripening stages in tomato, some of which are well‐known fruit ripening TF s. Taken together, our results support the notion that DNA methylation may facilitate divergent evolution of duplicated genes and play roles in important biological processes such as tomato fruit ripening.