Characterization of the Complete Mitochondrial Genomes of Two Sibling Species of Parasitic Roundworms, Haemonchus contortus and Teladorsagia circumcincta

Abstract

Haemonchus contortus and Teladorsagia circumcincta are among the two most pathogenic internal parasitic nematodes infecting small ruminants, such as sheep and goats, and are a global animal health issue. Accurate identification and delineation of Haemonchidae species is essential for development of diagnostic and control strategies with high resolution for Trichostrongyloidea infection in ruminants. Here, we describe in detail and compare the complete mitochondrial (mt) genomes of the New Zealand H. contortus and T. circumcincta field strains to improve our understanding of species- and strain-level evolution in these closely related roundworms. In the present study, we performed extensive comparative bioinformatics analyses on the recently sequenced complete mt genomes of the New Zealand H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP field strains. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP). The AT-rich mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP are 14,001 bp (A+T content of 77.4%) and 14,081 bp (A+T content of 77.3%) in size, respectively. All 36 of the typical nematode mt genes are transcribed in the forward direction in both species and comprise of 12 protein-encoding genes (PCGs), 2 ribosomal RNA (rrn) genes, and 22 transfer RNA (trn) genes. The secondary structures for the 22 trn genes and two rrn genes differ between H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP, however the gene arrangements of both are consistent with other Trichostrongylidea sequenced to date. Comparative analyses of the complete mitochondrial nucleotide sequences, PCGs, A+T rich and non-coding repeat regions of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP further reinforces the high levels of diversity and gene flow observed among Trichostrongylidea, and supports their potential as ideal markers for strain-level identification from different hosts and geographical regions with high resolution for future studies. The complete mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP presented here provide useful novel markers for further studies of the meta-population connectivity and the genetic mechanisms driving evolution in nematode species.

Keywords: Haemonchus contortus; Teladorsagia circumcincta; anthelmintic-susceptible; helminth; mitochondrial genome; parasite.

Figure 1

Mitochondrial genome atlases of H. contortus NZ_Hco_NP (A) and T. circumcincta NZ_Teci_NP (B). Each map is annotated and depicts the 12 protein-coding genes (PCGs, yellow), two ribosomal RNA genes (rrnS and rrnL, red), 22 transfer RNA (trn, blue) genes, and any putative non-coding region if applicable (gray). The innermost circles depict GC (blue) and AT (green) content, respectively, along the genome. Mauve visualization of an alignment of the H. contortus NZ_Hco_NP (top) and T. circumcincta NZ_Teci_NP (bottom) complete mt genomes (C). Mauve alignments of each genome are represented by a horizontal track, with annotated coding regions (white boxes), trn genes (green), and rrn genes (red). Red colored segments represent conserved regions among the two mt genomes.

Figure 2

Gene arrangement and distribution of Haemonchus (A) and Teladorsagia (B) mt genomes. (A) Gene map of the complete mitochondrial genomes for H. contortus Hco_McMaster (light red, EU346694), H. contortus Hco_ISE (light green, LS997568) and H. placei Hpl_MHpl1 (light purple, NC_029736). (B) Gene map of the complete mitochondrial genomes for T. circumcincta AP017699 (light red) and GQ888720 (light green). H. contortus NZ_Hco_NP (A) and T. circumcincta NZ_Teci_NP (B) were used as the reference sequences, respectively. The outermost ring indicates gene arrangement and distribution based on the primary sequence GenBank file. Tandem repeat regions are shown with green blocks (full length) for H. contortus NZ_Hco_NP (circle 2) and light red blocks for all other Haemonchus mt genomes (circle 3). Low complexity repeat regions for H. contortus NZ_Hco_NP are also shown with green blocks (half length) on circle 2. The next two (A) or three (B) rings represent BLAST hits obtained from BLASTX searches performed using a threshold of 1e⁻⁵ for protein sequences of genomes described above, in which the query sequences were translated in reading frames 1 and 2. The inner-most rings indicate the GC content information. The contents of the A+T-rich regions have been shown in more detail in expanded 10× zoomed views. nad1-6, NADH dehydrogenase subunits 1–6; cox1-3, cytochrome c oxidase subunits 1–3; atp6, ATPase subunit 6; cytb, cytochrome b.

Figure 3

Amino acid and codon usage of Trichostrongyloidea complete mt genomes. Heat map analysis was performed based on relative abundances of protein sequence content determined for all mitochondrial genes. The relative inferred codon abundances per mt gene and specific to each mt genome are shown using a heat color scheme (blue to red), indicating low to high relative abundance. Mt genomes are groped based on previous phylogenomic comparison of concatenated PCGs. C. elegans N2 (GenBank accession number JF896456) was also included for comparison. Amino acid families are colored to represent non-polar in black, basic in red, polar in green, and acidic in blue.

Figure 4

Inferred phylogenetic relationship among the nematode superfamily Trichostrongyloidea. Phylogenetic analysis of the complete mitochondrial genomes of different nematode species or conspecific strains is based on the concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) analyses. H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP are in bold, with C. elegans N2 (GenBank accession number JF896456) used as the outgroup. *species with different site of infection to other members of family. The numbers along branches indicate posterior probabilities and bootstrap values resulting from different analyses in the order: BI/ML/MP. Members of different families were shown in colored boxes with the associated main site of infection in parenthesis. GenBank accession numbers are provided (in parentheses) for all reference sequences. Scale bar represents Posterior Probability.