title: Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish.
abstract: The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes inDanio rerioremains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter methylation of duplicate genes generally decreased with evolutionary time as measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated, while the other was unmethylated across nine different datasets we studied. Moreover, one motif enriched in promoter methylated duplicate genes tended to be bound by the transcription repression factor FOXD3, whereas a motif enriched in the promoter unmethylated sequences interacted with the transcription activator Sp1, indicating a complex interaction between the genomic environment and epigenome. Besides, body-methylated genes showed longer length than body-unmethylated genes. Overall, our results suggest that DNA methylation is highly important in the differential expression and evolution of duplicate genes in zebrafish.
authors.affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, People's Republic of China.|Institute of Hydrobiology, University of Chinese Academy of Sciences, Beijing 100039, People's Republic of China.
authors.forename: Zaixuan
authors.initials: Z
authors.lastname: Zhong
authors.affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, People's Republic of China.|Institute of Hydrobiology, University of Chinese Academy of Sciences, Beijing 100039, People's Republic of China.
authors.forename: Kang
authors.initials: K
authors.lastname: Du
authors.affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, People's Republic of China.|Institute of Hydrobiology, University of Chinese Academy of Sciences, Beijing 100039, People's Republic of China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Yu
authors.affiliation: Institute of Hydrobiology, University of Chinese Academy of Sciences, Beijing 100039, People's Republic of China.|Key Laboratory of the Zoological Systematic and Evolution, Institute of Zoology, Beijing 100000, People's Republic of China.|State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Beijing 100000, People's Republic of China.
authors.forename: Yong E
authors.initials: YE
authors.lastname: Zhang
authors.affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, People's Republic of China clad@ihb.ac.cn.
authors.forename: Shunping
authors.initials: S
authors.lastname: He
keywords: divergence; duplication; methylation; transcriptome; zebrafish