Supplementary Files

Supplementary file 1: Scaffolds and contigs removed from the Heterorhabditis bacteriophora assembly because of low coverage in the new whole genome sequencing dataset. Text file.
Supplementary File 2: BRAKER1/soft-masked annotations of Heterorhabditis bacteriophora. A zipped archive (14.1 Mb) of the BRAKER1/soft-masked annotations of Heterorhabditis bacteriophora. The archive contains three text files: the GFF format file, the GTF format file and the amino acid sequences of the protein predictions in FASTA format.
Supplementary File 3: BRAKER1/hard-masked annotations of Heterorhabditis bacteriophora. A zipped archive (13.4 Mb) of the BRAKER1/hard-masked annotations of Heterorhabditis bacteriophora. The archive contains three text files: the GFF format file, the GTF format file and the amino acid sequences of the protein predictions in FASTA format.
Supplementary File 4: Comparison of the BRAKER1/soft-masked and BRAKER1/hard-masked gene predictions from Heterorhabditis bacteriophora. Tab-delimited text file.
Supplementary File 5: OrthoFinder analyses of Heterorhabditis bacteriophora predicted proteomes. A zipped archive (278.8 Mb) of the OrthoFinder analyses of Heterorhabditis bacteriophora predicted proteomes with 23 other nematode species. The archive contains the following files:
	SF5.1 A list of the proteomes included in the OrthoFinder analyses (text format file)
	SF5.2 List of Heterorhabditis bacteriophora proteins of length <30 amino acids excluded from the OrthoFinder analyses (text format file)
	SF5.3 The OrthoFinder output files. A zipped archive of the three OrthoFinder clustering result files (published H. bacteriophora + 23 species; BRAKER1/soft-masked + 23 species: published + soft-masked + 23 species).
	SF5.4 Table with count of orthogroups at each contribution ratio from the BRAKER1/soft-masked and published proteomes after clustering with 23 other Clade V nematodes. Empty cells denote contribution combinations with no orthogroups.
Supplementary File 6: KinFin analyses of Heterorhabditis bacteriophora predicted proteomes. A zipped archive (27.8 Mb) of the KinFin analyses from the OrthoFinder analyses of Heterorhabditis bacteriophora predicted proteomes.
Supplementary File 7: Phylogenetic analyses of Heterorhabditis bacteriophora predicted proteomes. A zipped archive (11.2 Mb) of the supermatrix alignment and the phylogenetic trees produced for the the analyses of the Heterorhabditis bacteriophora proteomes. The archive contains the following files:
	SF7.1 Alignments of orthogroups used to build the supermatrix (directory of aligned sequences in fasta format).
	SF7.2 Supermatrix of aligned sequences (FASTA .fas format file).
	SF7.3 Phylogenetic analysis output files (NEWICK format text file).
Supplementary File 8: Secretome analyses of Heterorhabditis bacteriophora predicted proteomes. Secretome analyses of Heterorhabditis bacteriophora and other rhabditine nematodes. The zipped archive (8 kb) contains the following text format files.
	SF8.1 Secretome predictions from the published Bai et al. (2013) protein predictions.
	SF8.2 Secretome predictions from the BRAKER1/soft-masked predictions.
Supplementary File 9: BRAKER1 and JIGSAW annotation pipelines. Figure illustrating the differences between the BRAKER1 and the Bai et al 2013 JIGSAW prediction methods used for Heterorhabditis bacteriophora. PDF file.
