(中国农业科学院棉花研究所/棉花生物学国家重点实验室，河南安阳 455000)

摘要：【目的】DNA甲基化是维持和调控基因表达的重要表观遗传方式。DNA甲基化模式和水平取决于DNA甲基转移酶和去甲基化酶的作用,而DNA去甲基化酶在DNA主动去甲基化过程中起关键作用。研究表明植物的DNA去甲基化酶蛋白均含有保守的DNA糖苷酶结构域。本研究鉴定了棉花DNA去甲基化酶家族，并利用生物信息学方法对其进行了分析，为进一步研究棉花去甲基化酶基因功能奠定了基础。【方法】本研究利用棉属二倍体雷蒙德氏棉（JGI）、亚洲棉（CRI）、四倍体陆地棉（JGI）和海岛棉（NAU）基因组信息，以拟南芥中去甲基化酶基因序列为参考序列，进行BLAST分析，共鉴定出25个DNA去甲基化酶基因，其中雷蒙德氏棉中有4个，亚洲棉中有5个，陆地棉中有10个，海岛棉中有6个。运用生物信息学手段进行基因结构和进化分析； 分析了陆地棉中DNA去甲基化酶基因家族成员的表达模式。【结果】根据系统进化分析可知，棉花DNA去甲基化酶基因家族可分为四个亚家族：ROS1，DME，DML2，DML3。 同一物种内的DNA去甲基化酶基因序列相似性较高，亲缘关系较近。基因结构分析表明，四个亚家族的DNA去甲基化酶基因家族成员基因结构差异较大。其中，ROS1和 DME亚家族基因内含子的数目较多，基因结构较为复杂。通过保守结构域分析可知，DNA去甲基化酶家族基因成员都含有一个ENDO3c结构域。【结论】DNA去甲基酶基因家族成员在不同棉种中分布不同，基因结构差异很大。在非生物胁迫条件下、胚珠形成过程中、纤维发育过程中，棉花ROS1亚家族成员高表达。
关键词：DNA去甲基化酶，雷蒙德氏棉，亚洲棉，陆地棉，海岛棉，基因家族

Background
DNA methylation is an important epigenetic factor that maintains and regulates gene expression. The mode and level of DNA methylation depend on the roles of DNA methyltransferase and demethylase, while DNA demethylase plays a key role in the process of DNA demethylation. The results showed that the plant’s DNA demethylase all contained conserved DNA glycosidase domain. This study identified the cotton DNA demethylase gene family and analyzed it using bioinformatics methods to lay the foundation for further study of cotton demethylase gene function.
Results
This study used genomic information from diploid Gossypium raimondii JGI (D), Gossypium arboreum L. CRI (A), Gossypium hirsutum L. JGI (AD1) and Gossypium barbadebse L. NAU (AD2) to Arabidopsis thaliana. Using DNA demethylase genes sequence of Arabidopsis as reference, 25 DNA demethylase genes were identified in cotton by BLAST analysis. There are 4 genes in the genome D, 5 genes in the genome A, 10 genes in the genome AD1, and 6 genes in the genome AD2. The gene structure and evolution were analyzed by bioinformatics, and the expression patterns of DNA demethylase gene family in Gossypium hirsutum L. were analyzed. From the phylogenetic tree analysis, the DNA demethylase gene family of cotton can be divided into four subfamilies: REPRESSOR of SILENCING 1 (ROS1), DEMETER (DME), DEMETER-LIKE 2 (DML2), and DEMETER-LIKE3 (DML3). The sequence similarity of DNA demethylase genes in the same species was higher, and the genetic relationship was also relatively close. Analysis of the gene structure revealed that the DNA demethylase gene family members of the four subfamilies varied greatly. Among them, the number of introns of ROS1 and DME subfamily was larger, and the gene structure was more complex. For the analysis of the conserved domain, it was known that the DNA demethylase family gene member has an endonuclease III (ENDO3c) domain.
Conclusion
The genes of the DNA demethylase family are distributed differently in different cotton species, and the gene structure is very different. High expression of ROS1 genes in cotton were under abiotic stress. The expression levels of ROS1 genes were higher during the formation of cotton ovule. The transcription levels of ROS1 family genes were higher during cotton fiber development.
Titile: Genome-wide identification and expression analysis of DNA demethylase family in cotton
Author: YANG Xiaomin, LU Xuke, CHEN Xiugui, WANG Delong, WANG Junjuan, WANG Shuai, GUO Lixue, CHEN Chao, WANG Xiaoge, WANG Xinlei & YE Wuwei 
Journal of Cotton Research. 2019,2: 16
https://doi.org/10.1186/s42397-019-0033-2
https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0033-2