Comparative Genomics Studies on the dmrt Gene Family in Fish

Junjian Dong; Jia Li; Jie Hu; Chengfei Sun; Yuanyuan Tian; Wuhui Li; Ningning Yan; Chengxi Sun; Xihui Sheng; Song Yang; Qiong Shi; Xing Ye

doi:10.3389/fgene.2020.563947

Comparative Genomics Studies on the dmrt Gene Family in Fish

Front Genet. 2020 Nov 12:11:563947. doi: 10.3389/fgene.2020.563947. eCollection 2020.

Authors

Junjian Dong¹, Jia Li², Jie Hu¹, Chengfei Sun¹, Yuanyuan Tian¹, Wuhui Li¹, Ningning Yan¹, Chengxi Sun³, Xihui Sheng⁴, Song Yang⁵, Qiong Shi², Xing Ye¹

Affiliations

¹ Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.
² Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI Group, Shenzhen, China.
³ College of Fisheries, Huazhong Agricultural University, Wuhan, China.
⁴ Fisheries College, Guangdong Ocean University, Zhanjiang, China.
⁵ College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.

Abstract

Doublesex and mab-3-related transcription factor (dmrt) genes are widely distributed across various biological groups and play critical roles in sex determination and neural development. Here, we applied bioinformatics methods to exam cross-species changes in the dmrt family members and evolutionary relationships of the dmrt genes based on genomes of 17 fish species. All the examined fish species have dmrt1-5 while only five species contained dmrt6. Most fish harbored two dmrt2 paralogs (dmrt2a and dmrt2b), with dmrt2b being unique to fish. In the phylogenetic tree, 147 DMRT are categorized into eight groups (DMRT1-DMRT8) and then clustered in three main groups. Selective evolutionary pressure analysis indicated purifying selections on dmrt1-3 genes and the dmrt1-3-2(2a) gene cluster. Similar genomic conservation patterns of the dmrt1-dmrt3-dmrt2(2a) gene cluster with 20-kb upstream/downstream regions in fish with various sex-determination systems were observed except for three regions with remarkable diversity. Synteny analysis revealed that dmrt1, dmrt2a, dmrt2b, and dmrt3-5 were relatively conserved in fish during the evolutionary process. While dmrt6 was lost in most species during evolution. The high conservation of the dmrt1-dmrt3-dmrt2(2a) gene cluster in various fish genomes suggests their crucial biological functions while various dmrt family members and sequences across fish species suggest different biological roles during evolution. This study provides a molecular basis for fish dmrt functional analysis and may serve as a reference for in-depth phylogenomics.

Keywords: comparative genomics studies; dmrt genes; fish; phylogenetic evolution; synteny analysis.