Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence

Abstract

Neospora caninum is an apicomplexan parasite responsible for neosporosis, a disease causing hind limb paralysis in dogs and abortion in cattle, resulting in substantial economic losses to beef and dairy industries. Marked differences in pathogenicity exist between N. caninum strains suggesting that intrinsic genetic differences exist between them. These differences likely exist in genes expressed during the tachyzoite lifecycle stage which is responsible for the pathogenesis of neosporosis. An improved understanding of these genetic differences is essential to understanding N. caninum virulence, though such knowledge is scarce. Using a variant detection workflow we compared the tachyzoite transcriptomes of two N. caninum strains with different virulence properties: NC-Liverpool (virulent) and NC-Nowra (avirulent). This workflow identified 3130 SNPs and 6123 indels between the strains, and nine markers capturing 30 variants were Sanger sequenced for both strains. Sequencing of these loci was extended to an additional eight strains and subsequent phylogenetic analysis supported a genetic population structure comprised of two major clades with no geographical segregation. Sequence polymorphisms within coding regions of tachyzoite-associated genes were concentrated on chromosomes XI and XII, with 19 distinct tachyzoite-associated SNP hotspot regions identified within coding regions of the N. caninum nuclear genome. The variants were predominantly located in loci associated with protein binding, protein–protein interactions, transcription, and translation. Furthermore, 468 nonsynonymous SNPs identified within protein-coding genes were associated with protein kinase activity, protein binding, protein phosphorylation, and proteolysis. This work may implicate these processes and the specific proteins involved as novel effectors of N. caninum tachyzoite virulence.

An Integrative Phenotype–Genotype Approach Using Phenotypic Characteristics from the UAE National Diabetes Study Identifies HSD17B12 as a Candidate Gene for Obesity and Type 2 Diabetes

“…Random genetic variants are unlikely to occur in the same genomic position unless there is a positive selection for that mutation, which might represent a fitness advantage [17]. However, genetic variants in terms of single nucleotide polymorphism (SNP) can cluster in particular chromosomal regions [18]. Those regions might represent an increased vulnerability to mutation as a result of their unique sequence, structural, and functional features [19].…”

Annotating the ‘hypothetical’ in hypothetical proteins: In-silico analysis of uncharacterised proteins for the Apicomplexan parasite, Neospora caninum

“…Genes, further cementing their functional significance within the N. caninum proteome. The annotation of SUB2 in this study, as well as the previous identification of the SUB2 gene as a SNP hotspot (Calarco et al, 2018), suggests that this protein could represent a potential virulence factor of N. caninum that warrants future investigation.…”

“…To obtain experimental evidence supporting the expression of the proteins in the final callset, the de novo transcriptome assembled using RNA-seq data generated from NC-Liverpool tachyzoites as per a previous study (Calarco et al, 2018) was exploited. Each protein sequence was subjected to a BLAST analysis against the NC-Liverpool transcriptome, using the command-line NCBI BLAST tool (version 2.7.1), where the most confident transcriptome contig hits (low e-value and high bit score) for each protein were retained.…”

“…All but three of the final 32 proteins (F0VIG7, F0VEH5, and F0VK21) had high confidence BLAST hits to contigs in the NC-Liverpool transcriptome published in Calarco et al (2018), with percentage identities (PID) > 80%. Additionally, some of the proteins had BLAST hits to the same NC-Liverpool transcriptome contig, indicating that they may be paralogous genes within N. caninum.…”

Functional characterization of acyl-CoA binding protein in Neospora caninum

“…Neospora caninum is an apicomplexan parasite responsible for neosporosis, a disease characterized by abortions and stillbirths (mainly among cattle) and by neuromuscular diseases in dogs [1,2], that results in substantial economic losses to the beef and dairy industries worldwide [3].…”