DOI: 10.5061/dryad.0cfxpnwfj
title: Comparative genomics of sex-determination-related genes reveals shared evolutionary patterns between bivalves and mammals, but not fruit flies

description: The molecular basis of sex determination (SD), while being extensively
 studied in model organisms, remains poorly understood in many animal
 groups. Bivalves, a diverse class of molluscs with a variety of
 reproductive modes, represent an ideal yet challenging clade for
 investigating SD and the evolution of sexual systems. However, the absence
 of a comprehensive framework has limited progress in this field,
 particularly regarding the study of sex-determination related genes
 (SRGs). In this study, we performed a genome-wide sequence evolutionary
 analysis of the Dmrt, Sox, and Fox gene families in more than 40 bivalve
 species. For the first time, we provide an extensive and
 phylogenetic-aware dataset of these SRGs, and we find support to the
 hypothesis that Dmrt-1L and Sox-H may act as primary sex-determining
 genes, by showing their high levels of sequence diversity within the
 bivalve genomic context. To validate our findings, we studied the same
 gene families in two well-characterized systems, mammals and fruit flies
 (genus Drosophila). In the former, we found that the male sex-determining
 gene Sry exhibits a pattern of amino acid sequence diversity similar to
 that of Dmrt-1L and Sox-H in bivalves, consistent with its role of master
 SD regulator. In contrast, no such pattern was observed among genes of the
 fruit fly SD cascade, which is controlled by a chromosomic mechanism.
 Overall, our findings highlight similarities in the sequence evolution of
 some mammal and bivalve SRGs, possibly driven by a comparable architecture
 of SD cascades. This work underscores once agaithe importance of employing
 a comparative approach when investigating understudied and non-model
 systems.
description: # Comparative genomics of sex-determination-related genes reveals shared
 evolutionary patterns between bivalves and mammals, but not fruit flies
 Dataset DOI: [10.5061/dryad.0cfxpnwfj](10.5061/dryad.0cfxpnwfj) In this
 repository you will find the files of main results generated by the
 analyses in the research paper: **[Nicolini
 F](https://github.com/filonico), Nuzhdin S,** **[Ghiselli
 F](https://github.com/fghiselli),** **[Luchetti
 A](https://github.com/andluche), Milani L**. *Comparative genomics of
 sex-determination-related genes reveals shared evolutionary patterns
 between bivalves and mammals, but not fruit flies.* Visit our research
 group website, **[EVO·COM](https://sites.google.com/view/evo-com-unibo)**!
 ## What you can find here This repository contains three different
 directories, one per each analysed dataset: * in `bivalve_results.tar.gz`
 you can find results for the dataset of bivalve genomes and
 transcriptomes; * in `mammal_results.tar.gz` you can find results for the
 dataset of mammal reference genomes; * in `drosophila_results.tar.gz` you
 can find results for the dataset of fruit fly reference genomes. ##
 Detailed file descriptions ### File: `bivalve_results.tar.gz`
 **Description:** this directory contains result files for the bivalve
 dataset: * `01_FINAL_dataset/` contains the amino acid and nucleotide
 sequences of annotated genes from the bivalve dataset, after their
 processing; * `02_SRG_sequences_phylotree/` contains the sequences and the
 ML phylogenetic trees of annotated Dmrt, Sox, and Fox genes in bivalves; *
 `03_possvm_orthology/` contains the result of the possvm orthology
 inference in Dmrt, Sox, and Fox genes; * `04_OrthoFinder_orthogroups/`
 contains some of the major result files of OrthoFinder; *
 `05_decomposed_orthogroups/` contains the results of the orthogroup
 decomposition (with the list of the obtained decomposed orthogroups and
 their genes), as well as the annotation of Dmrt, Sox, and Fox decomposed
 orthogroups; * `06_SRGs_occurence/` contains the presence/absence matrix
 of Dmrt, Sox, and Fox genes in the analysed species, as well as the
 annotation of possvm orthogroups; * `07_distribution_divergence/` contains
 the median values of the amino acid sequence divergence per decomposed
 orthogroup, as well as the amino acid substitution models and other
 metadata; * `08_additional_trees/` contains additional ML phylogenetic
 trees of Dmrt, Sox, and Fox genes, inferred to better establish the
 identity of certain groups; * `09_GO_enrichment/` contains the
 GO-enrichment results, divided per category (Biological Process, Cellular
 Component, or Molecular Function) and per enrichment method (classic or
 elim, as implemented in `topGO`); * `10_selection_analyses/` contains the
 results of selection analyses for both RELAX and BUSTED; files are in the
 json format, so that they can be uploaded and viewed on [HyPhy
 Vision](http://vision.hyphy.org/). ### File: `mammal_results.tar.gz`
 **Description:** this directory contains result files for the mammal
 dataset: * `01_FINAL_dataset/` contains the amino acid and nucleotide
 sequences of annotated genes from the mammal dataset, after their
 processing; * `02_SRG_sequences_phylotree/` contains the sequences and the
 ML phylogenetic trees of annotated Dmrt, Sox, and Fox genes in mammals; *
 `03_possvm_orthology/` contains the result of the possvm orthology
 inference in Dmrt, Sox, and Fox genes; * `04_OrthoFinder_orthogroups/`
 contains some of the major result files of OrthoFinder; *
 `05_decomposed_orthogroups/` contains the results of the orthogroup
 decomposition (with the list of the obtained decomposed orthogroups and
 their genes), as well as the annotation of Dmrt, Sox, and Fox decomposed
 orthogroups; * `06_SRGs_occurence/` contains the presence/absence matrix
 of Dmrt, Sox, and Fox genes in the analysed species, as well as the
 annotation of possvm orthogroups; * `07_distribution_divergence/` contains
 the median values of the amino acid sequence divergence per decomposed
 orthogroup, as well as the amino acid substitution models and other
 metadata; * `08_GO_enrichment/` contains the GO-enrichment results,
 divided per category (Biological Process, Cellular Component, or Molecular
 Function) and per enrichment method (classic or elim, as implemented in
 `topGO`); ### File: `drosophila_results.tar.gz` **Description:** this
 directory contains result files for the fruit fly dataset: *
 `01_FINAL_dataset/` contains the amino acid and nucleotide sequences of
 annotated genes from the fruit fly dataset, after their processing; *
 `02_SRG_sequences_phylotree/` contains the sequences and the ML
 phylogenetic trees of annotated Dmrt, Sox, and Fox genes in fruit flies; *
 `03_possvm_orthology/` contains the result of the possvm orthology
 inference in Dmrt, Sox, and Fox genes; * `04_OrthoFinder_orthogroups/`
 contains some of the major result files of OrthoFinder; *
 `05_decomposed_orthogroups/` contains the results of the orthogroup
 decomposition (with the list of the obtained decomposed orthogroups and
 their genes), as well as the annotation of Dmrt, Sox, and Fox decomposed
 orthogroups; * `06_SRGs_occurence/` contains the presence/absence matrix
 of Dmrt, Sox, and Fox genes in the analysed species, as well as the
 annotation of possvm orthogroups; * `07_distribution_divergence/` contains
 the median values of the amino acid sequence divergence per decomposed
 orthogroup, as well as the amino acid substitution models and other
 metadata; * `08_GO_enrichment/` contains the GO-enrichment results,
 divided per category (Biological Process, Cellular Component, or Molecular
 Function) and per enrichment method (classic or elim, as implemented in
 `topGO`). ## Code Documented code and data can be accessed in the GitHub
 repository:
 [github.com/filonico/bivalvia_SRGs](https://github.com/filonico/bivalvia_SRGs)