De novo genome assembly and annotation of Gnathostoma spinigerum

Gnathostoma spinigerum is a parasitic nematode implicated in human cases of eosinophilic meningitis. This species is primarily endemic to Thailand and frequently occurs in other regions as imported cases. Although this parasite poses a significant pathogenic risk, its genome has not yet been assembled or annotated. The aim of our study is to generate the first genome assembly of G. spinigerum.

Whole-genome sequence libraries were generated from genomic DNA extracted from a pooled sample of advanced stage 3 larvae. After sequencing, the assembly of the genome was produced using a combination of second- and third-generation sequencing technologies. Multiple draft assemblies were generated and evaluated, and the absence of contamination was determined. Identification and modeling of new G. spinigerum metalloproteinases and tissue inhibitors of metalloproteinases were performed, and molecular dynamics simulations were used to analyze their potential interactions. The final assembly was annotated and made publicly available via the NCBI genome database.

The hybrid assembly approach (using short and long reads) using the SPAdes assembler and with post-assembly polishing (Pilon/Picard) yielded the most complete genome (222-Mb genome size, N50 = 14,149 bp, 69.6% BUSCO assembly). A total of 14,451 protein-coding genes were predicted in the G. spinigerum genome with 62.3% BUSCO annotation completeness. Three-dimensional computational modeling and molecular dynamics of six new metalloproteinases and two new tissue inhibitors of metalloproteinases are presented.

We provide the first sequence assembly and annotation for the nematode G. spinigerum. This draft genome will be an essential resource for future scientific and applied investigations of diseases caused by this parasite.