B151977 Cell Biology Research Project (APPENDIX) Supplementary Datasets
This study aimed to ameliorate the limitations posed by the lack of a standardised approach in reporting HES data by providing up-to-date gene annotations for the most recent H. bakeri and H. polygyrus genome assemblies, produced as part of the Darwin Tree of Life Project (The Darwin Tree of Life Project Consortium, 2021; preprint: Stevens et al., 2023). Additionally, this study explored the dynamics underlying the evolution of these complex parasitic genomes. Secreted proteins which have previously been implicated in the immunobiology and infection dynamics of H. bakeri, H. polygyrus and related nematodes were identified in the new H. bakeri and H. polygyrus genome assemblies, highlighting several proteins and domain-types which often differ substantially in copy number between these closely related nematodes. DeepLoc 2.0 was used to predict the subcellular localisation of these proteins, revealing several immunobiologically important proteins which possess signal peptides targeting them for the extracellular space. Orthology inference and phylogenetic analysis of highly represented orthogroups of interest underscored the tumultuous history of gene duplication and loss in the genomes of H. bakeri and H. polygyrus, after millions of years of independent evolution (preprint: Stevens et al., 2023). Supplementary Datasets 1 & 2: Tab separated values; BLAST+ aligments against the H. polygyrus and H. bakeri proteomes, respectively. Supplementary Datasets 3 & 4: Tab separated values; InterPro Scan alignments against the H. polygyrus and H. bakeri proteomes, respectively. Supplementary Datasets 5 & 6: Tab separated values; DeepLoc 2.0 prediction of extracellular H. bakeri and H. polygyrus proteins, respectively.