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/.

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)