The Complete Mitogenome of Toxocara vitulorum: Novel In-Sights into the Phylogenetics in Toxocaridae

Abstract

Toxocara vitulorum (Ascaridida: Nematoda) is one of the most common intestinal nematodes of cattle and buffalos and, therefore, represents a serious threat to their populations worldwide. Despite its significance in veterinary health the epidemiology, population genetics, and molecular ecology of this nematode remain poorly understood. The mitogenome can yield a foundation for studying these areas and assist in the surveillance and control of T. vitulorum. Herein, the first whole mitogenome of T. vitulorum was sequenced utilizing Illumina technology and characterized with bioinformatic pipeline analyses. The entire genome of T. vitulorum was 15,045 bp in length and contained 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The gene arrangement (GA) of T. vitulorum was similar to those of other Toxocara species under GA3. The whole genome showed significant levels of AT and GC skew. Comparative mitogenomics including sequence identities, Ka/Ks, and sliding window analysis, indicated a purifying selection of 12 PCGs with cox1 and nad6 having the lowest and highest evolutionary rate, respectively. Whole amino acid sequence-based phylogenetic analysis supported a novel sister-species relationship of T. vitulorum with the congeneric species Toxocara canis, Toxocara cati, and Toxocara malaysiensis in the family Toxocaridae. Further, 12 (PCGs) single gene-based phylogenies suggested that nad4 and nad6 genes shared same topological trees with that of the whole genome, suggesting that these genes were suitable as novel genetic markers for phylogenetic and evolutionary studies of Ascaridida species. This complete mitogenome of T. vitulorum refined phylogenetic relationships in Toxocaridae and provided the resource of markers for population genetics, systematics, and epidemiology of this bovine nematode.

Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae)

“…The complete mt genome sequences of T. apodemi were the first to be sequenced, with a length of 14303 bp (Accession no. OR241493), which was similar to those of T. canis (14322 bp) and T. malaysiensis (14266 bp), shorter than those of T. vitulorum (15045 bp), and longer than those of T. cati (14029 bp) (Li et al 2008; Xie et al 2022). The complete mt genome of T. apodemi contained 12 PCGs ( cox 1- cox 3, cyt b, atp 6, nad 1- nad 6, and nad 4L), 22 tRNAs, 2 ribosomal RNAs (rRNAs), and 2 non-coding regions (NCRs) (Table 1, Figure 1).…”

“…“T” as the termination codon also appeared in atp 6, nad 5, and nad 4L, which was the same as congeneric species. However, in the nad 2 gene, TAG was the termination codon in T. apodemi , and “TA” or “T” were the termination codons in other species in Toxocara (Li et al 2008; Xie et al 2022). The mt genomes of T. apodemi had relatively compact structures, with fewer spacer regions and short overlaps between some adjacent genes, in which 11 intergenic spacers fluctuated with 1 to 9 bp, and 5 overlaps were 1–2 bp in length (Table 1).…”

“…For example, the RSCU of AGC was 0.27, 0.29, 0.16, and 0.18 in T. cati, T. malaysiensis, T. vitulorum, and T. apodemi, respectively. However, it was 0.06 in T. canis (Li et al 2008;Meng et al 2019;Xie et al 2022).…”

“…Ascaris (Li et al 2008;Zhou et al 2020;Xie et al 2022), and slightly lower than those of Parascaris equorum in Ascaridoidea (70.25%) (Gao et al 2019). The comparison analysis showed that the A+T content of the second coding position of the 12 PCGs was more similar than those of the first and the third coding positions among five Toxocara species (Figure 1).…”

“…Sequences were assembled manually and aligned against the mt genome sequences from Toxocara species using the program Clustal X (v. 1.83) and the MegAlign procedure within the DNAStar (Burland 2000;Larkin et al 2007). The boundaries of 12 protein-coding gene (PCG) sequences, the 16S ribosomal RNA (rrnL) gene, and the 12S ribosomal RNA (rrnS) gene were determined using the mt genome sequences of other Toxocara nematodes available in GenBank using the software MEGA X (Li et al 2008;Kumar et al 2018;Xie et al 2022). A total of 22 transfer RNA (tRNA) genes were identified using the online tool tRNA scan-SE (http://lowelab.ucs c.edu/tRNAscan-SE) or via visual inspection.…”