DOI: 10.5061/dryad.6q573n65z
title: Immune-associated orthologous genes across primates

description: The immune system acts as a bridge between pathogenic microorganisms and
 their hosts. Despite its significance, to date, the evolutionary
 mechanisms of immune system complexity are largely not well understood in
 primates. In this study, we applied a newly developed strategy (TOGA
 pipeline) to generate a robust one-to-one orthologous gene catalog
 including 15,057 protein-coding genes accounting for ~78% of the annotated
 gene set of the human genome (hg38) and representing ~ 28.9 Mbp (coding
 sequence), across 50 primate species and two closest outgroups (Malayan
 flying lemur and Chinese tree shrew). Deeply, to obtain a comprehensive
 immune-associated gene catalog across primates, we investigated six known
 public datasets (GO, KEGG, InnateDB, Immport, HPO and Enard et al., 2016)
 and found that 4,744 of 5,635 immune-associated genes were covered in our
 constructed one-to-one orthologous catalog across 52 species.
description: # Immune-associated orthologous genes across primates
 [https://doi.org/10.5061/dryad.6q573n65z](https://doi.org/10.5061/dryad.6q573n65z) The immune system mediates interactions between pathogens and their hosts, yet the evolution of its complexity in primates remains poorly understood. Here, we used the TOGA pipeline to build a high-confidence one-to-one orthologous gene catalog of 15,057 protein-coding genes (~78% of the human hg38 gene set; ~28.9 Mb coding sequence) across 50 primate species and two close outgroups. By integrating six public immune-gene resources, we further identified 4,744 immune-associated genes represented in this orthologous catalog across 52 species. ## Description of the data and file structure **Primate_codon.fasta**: coding sequences predicted by TOGA software across 52 species. **Orthogroup_primate.txt**: one-to-one orthologous gene catalog including 15,057 protein-coding genes. **Immune_Orthogroup_primate.txt**: one-to-one orthologous gene catalog including 4,744 immune-associated genes. **All_immune_prot_genes.txt**: 5,635 immune-associated genes collected from six known public datasets. **Primate_newick.txt**: primate species tree. **data.zip**: a compressed archive containing data required to run the scripts available in the associated GitHub repository:\ [https://github.com/zhangxp1993/Immune-associated-orthologous-genes-across-primates/.](https://github.com/zhangxp1993/Immune-associated-orthologous-genes-across-primates/) The folder structure for data.zip is as follows: ``` data.zip ├── free_immune ├── hg38_cds.fasta ├── human.longest.transcript.bed ├── mfree_ctl ├── Primate_genome.nwk ├── species_list ├── toga.isoforms.tsv └── TOGA_results ├── Aotus_nancymaae │   ├── codonAlignments.fa │   └── orthologsClassification.tsv ├── Ateles_geoffroyi │   ├── codonAlignments.fa │   └── orthologsClassification.tsv ├── Callithrix_jacchus │   ├── codonAlignments.fa │   └── orthologsClassification.tsv ├── Cebus_albifrons │   ├── codonAlignments.fa │   └── orthologsClassification.tsv └── ... ``` The ellipsis (`...`) indicates additional primate species, each following the same directory and file structure.  ### **File and directory descriptions** * **free_immune/**\ Lists of file paths for each immune-associated orthologous gene used in downstream analyses. * **hg38_cds.fasta**\ Coding DNA sequences (CDS) of human genes based on the hg38 reference genome. * **human.longest.transcript.bed**\ BED-format annotation of the longest transcript for each human gene. * **mfree_ctl**\ Configuration file used to run PAML (`codeml`) analyses. * **Primate_genome.nwk**\ Newick-format phylogenetic tree of the primate species included in this study. * **species_list**\ List of primate species analyzed. * **toga.isoforms.tsv**\ Mapping table linking human genes to their corresponding transcript isoforms used by TOGA. * **TOGA_results/**\ Output directories from TOGA analyses, organized by species. #### TOGA_results species-level directories Each species directory (e.g., `Aotus_nancymaae`, `Ateles_geoffroyi`, `Callithrix_jacchus`, `Cebus_albifrons`, etc.) contains: * **codonAlignments.fa**\ Codon-based sequence alignments corrected for frameshifting insertions and deletions. * **orthologsClassification.tsv**\ Table describing orthology relationships with the following columns: * `t_gene`: Gene name in the reference (human) * `t_transcript`: Transcript identifier in the reference * `q_gene`: Gene identifier in the query species * `q_transcript`: Transcript identifier in the query species * `orthology_class`: Orthology relationship class (e.g., one2one, one2many, many2one, many2many, one2zero) ##