Table 1.
Primers used for complete mitochondrial genome amplification of Trichuris from baboons (TTB1 and TTB2) and pigs (TSDK and TSUG).
Table 2.
Partial cox1 sequences retrieved from the GenBank database with accession numbers, host, and the country from which the worms were sampled.
All the non-human primates represented in the table were held in captivity.
Table 3.
Mitochondrial genomes of baboon Trichuris (TTB1 and TTB2) and human Trichuris (TTHUG).
Protein coding, transfer RNA (tRNA), and ribosomal DNA (rDNA) genes with lengths in nucleotides (nt) are given. The lengths of TTB1 and TTHUG are identical, and differences are given in parentheses for (TTB2/TTHUG); likewise for the initiation and termination codons.
Table 4.
Mitochondrial genomes of pig Trichuris TSDK and TSUG from Denmark and Uganda, respectively.
Protein-coding, transfer RNA (tRNA), and ribosomal DNA (rDNA) genes are indicated with lengths in nucleotides (nt) for the respective genes. Gene lengths are given for TSDK, and the differences from TSUG are given in parentheses; likewise for the initiation and termination codons.
Table 5.
Overall genetic and protein distances between the Trichuris spp. genomes derived from baboons (TTB1 and TTB2), humans (TTHCH and TTHUG from China and Uganda, respectively), pigs (TSCH, TSUG and TSDK from China, Uganda and Denmark, respectively), and francois' leaf monkey (T.GHL).
The amino acid sequence distances are given above the diagonal and genetic distances below the diagonal.
Fig 1.
Nucleotide diversity (π) for protein coding regions and ribosomal DNA (rrnS and rrnL) measured every 25 bp over 100 bp windows.
The aligned dataset for Trichuris in primates (humans, baboons, francois’ leaf monkey) is given in (A), while that of the pig-derived Trichuris is given in (B).
Fig 2.
Inferred phylogenetic relationship among Trichuris spp. using concatenated amino acid sequences and Maximum Likelihood (ML) and Bayesian Inferences (BI).
The three major groups identified by the phylogenetic tree include primate-, pig- and ruminant- derived Trichuris. Bootstrap frequencies (BF) and posterior probabilities (PP) are indicated on the branches (BF/PP). Scale bar represents the number of substitutions per site.
Fig 3.
Inferred phylogeny among Trichuris spp. recovered from pigs and primates based on partial cox1 sequences and NJ clustering.
Samples for which the full mitochondrial genome is sequenced are indicated by a solid triangle. The phylogeny identified two major clades for Trichuris in pigs, namely ‘T. suis Europe’ and ‘T. suis China’. Five distinct clades for Trichuris spp. recovered from primates (including humans) were identified, namely ‘T. colobae’, ‘Trichuris sp. GHL’, ‘Trichuris Human Uganda’, ‘Trichuris Human China’, and ‘Trichuris sp. non-human primates’. Scale bar indicates number nucleotide substitutions per site. Only bootstrap values > 70 are given.