Comparative Genomics Studies on the dmrt Gene Family in Fish

Abstract

Doublesex and mab-3-related transcription factor (<i>dmrt</i>) 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 <i>dmrt</i> genes based on genomes of 17 fish species. All the examined fish species have <i>dmrt1-5</i> while only five species contained <i>dmrt6.</i> Most fish harbored two <i>dmrt2</i> paralogs (<i>dmrt2a</i> and <i>dmrt2b</i>), with <i>dmrt2b</i> 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 <i>dmrt1-3</i> genes and the <i>dmrt1-3-2(2a)</i> gene cluster. Similar genomic conservation patterns of the <i>dmrt1-dmrt3-dmrt2(2a)</i> 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 <i>dmrt1, dmrt2a, dmrt2b</i>, and <i>dmrt3-5</i> were relatively conserved in fish during the evolutionary process. While <i>dmrt6</i> was lost in most species during evolution. The high conservation of the <i>dmrt1-dmrt3-dmrt2(2a)</i> gene cluster in various fish genomes suggests their crucial biological functions while various <i>dmrt</i> family members and sequences across fish species suggest different biological roles during evolution. This study provides a molecular basis for fish <i>dmrt</i> functional analysis and may serve as a reference for in-depth phylogenomics.