Comparative epigenomics reveals evolution of duplicated genes in potato and tomato

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 (菊类植物), 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 TFs was shown to be regulated by DNA methylation during fruit ripening stages in tomato, some of which are well-known fruit ripening TFs. 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.

在多倍化事件之后复制基因的演化是许多进化生物学研究的重点。马铃薯和西红柿是菊类植物中头两个测序的物种，这两个植物共享了一次多倍化事件。然而DNA甲基化的表观遗传对于源自于多倍化事件之后的复制基因演化的作用并没有很系统的研究。本文探索了DNA甲基化在马铃薯和西红柿之间复制基因演化的作用。尽管马铃薯和西红柿DNA甲基化的模式类似，但这两个物种总的DNA甲基化水平是不一样的。另外，作者还发现复制基因之间DNA甲基化水平的差异与基因表达分化相关。尤其在西红柿水果成熟阶段不同时期，对于大多数的复制基因对，其中一个拷贝总是比另外一个拷贝具有更高或者更低的DNA甲基化水平，同时这些基因富集在与转录因子活性相关的功能条目。此外，在西红柿水果成熟阶段，数百个复制转录因子的转录是受DNA甲基化调控的，其中包括一些大家所熟知的水果成熟相关转录因子。综上，本文的结果证明了DNA甲基化可能会促进复制基因不同的演化方向，进而在一些诸如西红柿水果成熟的生物学过程中扮演重要作用。

通讯：王海峰 (http://zbxy.fafu.edu.cn/19/77/c7487a137591/page.htm)

个人简介：男，1985年生；2014年，复旦大学，理学博士；2014.7-2015.7，加州大学洛杉矶分校，博士后；现为福建农林大学特聘教授、硕导。

研究方向：表观遗传和分子进化：1）植物抗生物或非生物胁迫中的表观遗传修饰变化；2）环境基因组学在植物抗病中的作用；3）表观遗传修饰对同源基因功能分化的影响。

2013年，Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms，《Nucleic acids research》（并列一作，通讯戚继）

2014年，Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms，《Frontiers in genetics》（一作，通讯马红）

2014年，The Arabidopsis RAD51 paralogs RAD51B, RAD51D and XRCC2 play partially redundant roles in somatic DNA repair and gene regulation，《New phytologist》（并列一作，通讯马红）

2015年，A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis，《Cell》(二作，通讯Steven E. Jacobsen)

2015年，CG gene body DNA methylation changes and evolution of duplicated genes in cassava，《PNAS》（一作，通讯Israel Ausin）

2016年，METHYLENETETRAHYDROFOLATE DEHYDROGENASE 1 controls DNA methylation in Arabidopsis，《Nature Communications》（共同作者，通讯Steven E. Jacobsen）

2016年，Arabidopsis AtMORC4 and AtMORC7 form Nuclear Bodies and Repress a Large Number of Protein Coding Genes，《PLOS Genetics》（共同作者，通讯Steven E. Jacobsen）

doi: 10.1111/tpj.13790