Genome-wide Identification and Expression Analysis of Dmrt Genes in Bivalves

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2023 Aug 15

PMID 37582778

Authors

Quanchao Wang

Tiangui Cao

Chunde Wang

Affiliations

Soon will be listed here.

Abstract

In recent years, some common themes in the development of sex-specific traits in different animal lineages have started to emerge since the discovery of the Dmrt (doublesex-mab3-related transcription factor gene) genes. Bivalves are characterized by a diversity of sexual systems, including simultaneous hermaphroditism, sequential hermaphroditism, and strict gonochorism. However, to date, no research has focused on the genome-wide characterization and analysis of Dmrt genes in bivalves. In this study, the identification and analysis of Dmrt genes in 15 bivalves were performed using bioinformatics methods. A total of 55 Dmrt genes were retrieved in the studied bivalve genomes. The number of Dmrt genes in different species ranged from 3 to 5. The phylogenetic tree showed that Dmrt genes in bivalves can be subdivided into 5 classes: the Dmrt2-like class, Dmrt3-like class, Dmrt4/5-like class, Dsx-like class, and scallop-specific Dmrt class. The Ka/Ks ratios suggested that all Dmrt classes underwent purifying selection pressure. Furthermore, the spatiotemporal expression of Dmrt genes in four bivalve species suggested that different Dmrt genes may have different functions, and scallop-specific Dmrt genes may play a key role in sex determination/differentiation. In general, this study provides a molecular basis for in-depth examination of the functions of Dmrt genes and phylogenomic analyses in bivalves.

References

Smith C, Roeszler K, Ohnesorg T, Cummins D, Farlie P, Doran T . The avian Z-linked gene DMRT1 is required for male sex determination in the chicken. Nature. 2009; 461(7261):267-71. DOI: 10.1038/nature08298. View

Kopp A . Dmrt genes in the development and evolution of sexual dimorphism. Trends Genet. 2012; 28(4):175-84. PMC: 3350790. DOI: 10.1016/j.tig.2012.02.002. View

Zarkower D . DMRT genes in vertebrate gametogenesis. Curr Top Dev Biol. 2013; 102:327-56. DOI: 10.1016/B978-0-12-416024-8.00012-X. View

Zhang T, Zarkower D . DMRT proteins and coordination of mammalian spermatogenesis. Stem Cell Res. 2017; 24:195-202. PMC: 5634931. DOI: 10.1016/j.scr.2017.07.026. View

Ottolenghi C, Fellous M, Barbieri M, McElreavey K . Novel paralogy relations among human chromosomes support a link between the phylogeny of doublesex-related genes and the evolution of sex determination. Genomics. 2002; 79(3):333-43. DOI: 10.1006/geno.2002.6711. View

Kim S, Kettlewell J, Anderson R, Bardwell V, Zarkower D . Sexually dimorphic expression of multiple doublesex-related genes in the embryonic mouse gonad. Gene Expr Patterns. 2003; 3(1):77-82. DOI: 10.1016/s1567-133x(02)00071-6. View

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

Schultz J, Copley R, Doerks T, Ponting C, Bork P . SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 1999; 28(1):231-4. PMC: 102444. DOI: 10.1093/nar/28.1.231. View

Chen C, Chen H, Zhang Y, Thomas H, Frank M, He Y . TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020; 13(8):1194-1202. DOI: 10.1016/j.molp.2020.06.009. View

10.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

11.

Nguyen L, Schmidt H, von Haeseler A, Minh B . IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2014; 32(1):268-74. PMC: 4271533. DOI: 10.1093/molbev/msu300. View

12.

Letunic I, Bork P . Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019; 47(W1):W256-W259. PMC: 6602468. DOI: 10.1093/nar/gkz239. View

13.

Bailey T, Johnson J, Grant C, Noble W . The MEME Suite. Nucleic Acids Res. 2015; 43(W1):W39-49. PMC: 4489269. DOI: 10.1093/nar/gkv416. View

14.

Doron-Faigenboim A, Stern A, Mayrose I, Bacharach E, Pupko T . Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics. 2005; 21(9):2101-3. DOI: 10.1093/bioinformatics/bti259. View

15.

Patel R, Jain M . NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012; 7(2):e30619. PMC: 3270013. DOI: 10.1371/journal.pone.0030619. View

16.

Kim D, Langmead B, Salzberg S . HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12(4):357-60. PMC: 4655817. DOI: 10.1038/nmeth.3317. View

17.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

18.

Pertea M, Pertea G, Antonescu C, Chang T, Mendell J, Salzberg S . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-5. PMC: 4643835. DOI: 10.1038/nbt.3122. View

19.

Hong C, Park B, Saint-Jeannet J . The function of Dmrt genes in vertebrate development: it is not just about sex. Dev Biol. 2007; 310(1):1-9. DOI: 10.1016/j.ydbio.2007.07.035. View

20.

Picard M, Cosseau C, Mouahid G, Duval D, Grunau C, Toulza E . The roles of Dmrt (Double sex/Male-abnormal-3 Related Transcription factor) genes in sex determination and differentiation mechanisms: Ubiquity and diversity across the animal kingdom. C R Biol. 2015; 338(7):451-62. DOI: 10.1016/j.crvi.2015.04.010. View