Characterization of SNPs associated with the pathogenesis of Heterorhabditis bacteriophora

Heterorhabditis bacteriophora belongs to the Heterorhabditis genera of entomopathogenic nematodes (EPN) that hosts a symbiotic relationship with the entomopathogenic bacteria Photorhabdus (Kenney et al., 2019). The EPNs are capable of independently killing their insect host through a class of bioactive molecules called Excretory or Secreted proteins (ESPs) having proteolytic activities produced at various stages of EPN development (Eliáš et al., 2020). ESPs are known to interfere with the host humoral and cellular immune response. EPNs serve as an important biological control against various insect pests. Many research and industrial bodies have vested interests in understanding the pathogenicity, virulence & longevity of EPNs. H.bacteriophora share similarity in the ESP spectrum with model EPN, Steinernema carpocapsae. With commercial interests in improving the H.bacteriphora as biocontrol agent, ESP identification, description and characterization was extended to relatively less explored H.bacteriophora genome to increase the EPN efficacy. The objective of this work was to locate all of the reported ESP transcripts from H.bacteriophora & S.carpocapsae into IL3 inbred-line genome (commercial line of H.bacteriophora at the e-nema GmbH) and find the linkage of these gene loci with the proximal SNPs; identified previously by GBS. This study identified the target gene sequences of ESPs reported for Phenol-oxidase inhibition in H.bacteriophora and its orthologous ESPs reported in S.carpocapsae. We annotated high homology hits of about 28 ESP transcripts from reported publications (Eliáš et al., 2020; Rougon-Cardoso et al., 2016; Vadnal et al., 2017) into the Hb-IL3 genome with the publicly available archive of TT01 genome (McLean et al., 2018). It was followed by annotating known SNPs with the previous GBS-analyses. The SNPs located in the vicinity and inside the gene clusters were identified gene by gene and those SNPs with the vicinity threshold within 5000bp up- or downstream the gene were considered for further Insilco analyses. The selected SNPs with the different allele versions were translated into proteins with CDS and with whole gene. The different allelic version of translated proteins was aligned to check the difference in protein sequences. These versions of translated proteins were subjected to multiple protein BLAST using NCBI against public protein libraries. Then the obtained protein was researched to establish the correlation between the gene coding those proteins and the virulence of EPNs.