The genome of C. bovis

The following files are key data files used in the manuscript:

caenorhabditis_35species_1167orthos.supermatrix.fa: supermatrix consisting of the concatenated alignments of 1,167 single-copy orthologues which was used to infer the species tree. 

caenorhabditis_35species_1167orthos.treefile: Caenorhabditis species tree in newick format from IQ-TREE

CBOVI.caenorhabditis_bovis_LS_v1.annotations.gff3: GFF3 (annotation) file for the C. bovis reference genome from BRAKER

CBOVI.caenorhabditis_bovis_LS_v1.cds.fna: predicted coding sequences (CDS) for the C. bovis reference genome from BRAKER

CBOVI.caenorhabditis_bovis_LS_v1.proteins.faa: predicted protein/amino acid sequences for the C. bovis reference genome from BRAKER

CBOVI.caenorhabditis_bovis_LS_v1.scaffolds.fna: genome fasta for the C. bovis reference genome (Note: contains contigs, file named scaffold.fna to match filenames of other Caenorhabditis species)

Orthogroups.txt: orthology clustering file of protein sequences from C. bovis, 32 other Caenorhabditis species and two Diploscapter outgroup taxa from OrthoFinder

The following files are tables that were included in the supplementary information in a previous version of the manuscript:

TableS3_gene_families.tsv: table with a line for each orthogroup showing counts in C. bovis, averages in other species, and functional annotation generated using Pfam. 

TableS6_software_params.xlsx: versions of software used and relevant parameters. 

TableS7_phylogenomics_accessions.xlsx: accessions for all data using in orthology clustering and phylogenomic analyses.