Comparative analysis of the characteristics of Haplorchis taichui mitochondrial genome with Metagonimus yokogawai and its ribosomal transcription unit with H. pumilio (family Heterophyidae)

Minute intestinal flukes, Haplorchis taichui and H. pumilio, belong to the family Heterophyidae (Trematoda: Platyhelminthes), which have been studied very limited, especially the molecular markers of the mitochondrial genomes (mtDNA) and the ribosome transcription units (rTU or rDNA). We have obtained the complete mitochondrial genome of H. taichui and the coding part of ribosome transcription unit of H. taichui and H. pumilio of Vietnam. Nucleotide and amino acid data were compared between H. taichui and Metagonimus yokogawai for genomic/gene composition, codon usage (skew/skewness), and tandem repeat units (TRU). The complete mtDNA of H. taichui (strain Htai-QT3-VN) with the length of 15,120 bp and M. yokogawai (15,258 bp; Korea; KC330755) contains 36 genes, including 12 protein-coding genes (cox1, cox2, cox3, nad1, nad2, nad3, nad4L, nad4, nad5, nad6, atp6 and cob), 2 ribosomal RNA genes (rRNA); 22 transfer RNA (tRNA or trn) and a noncoding region (NCR) between trnE and trnG, divided into 2 sub-regions containing 5 TRUs (182–183 bp/TRU). H. taichui (Vietnam and Laos) uses A = 19.56%, T = 39.71%, G = 28.34%, C = 12.39% (A + T is 59.27% ​​and G + C is 40.73%) for mtDNA construction, whose skew/skewness value at A+T is negative (–0,340) and G+C is positive (0.392); for 12 protein-coding genes (PCGs) is similar; but for the mito-ribosomal genes (MRGs, of 16S/rrnL and 12S/rrnS) it is less for A+T (57.22%) and more for G+C (42.78%). M. yokogawai had lower A+T (mtDNA/55.68%; PCGs/55.96%; MRGs/54.15%) and higher G+C usage rate than H. taichui. H. taichui of Vietnam and Laos has 10,164 bp encoding for 3,376 amino acids to construct 12 PCGs with the mostly used codons as Phenylalanine (Phe-TTT) and Leucine (Leu-TTG), and the leastly used codonsas Glutamine (Gln-CAA), Arginine (Arg-CGC). Additional condon, Thr-ACA/ACC can be added as the least used in M. yokogawai. The rTU (from 5 '18S to 3' 28S) of H. taichui (7,268 bp) and H. pumilio (7,416 bp) were identified with 5 genomic regions including 18S rDNA, ITS1, 5.8S rDNA, ITS2 and 28S rDNA. The 18S and 5.8S genes of both species were of the same length (1,992 bp for 18S, 160 bp for 5.8S), but different for 28S genes (3,875 bp for H. taichui and 3,870 bp for H. pumilio). ITS1 in H. taichui (797 bp) and ITS2 in H. pumilio (280 bp) do not contain TRUs, whilst ITS1 in H. pumilio (1,106 bp) contains 5 TRUs(136 bp for 3 TRU and 116 bp for 2 TRUs); and ITS2 in H. taichui (444 bp) contain 3 TRUs (83–85 bp/each).

Phylogenetic analyses of ribosomal transcription units from Haplorchis taichui and H. pumilio species of Heterophyidae (Platyhelminthes: Opisthorchiata)

Heterophyidiasis caused by minute intestinal flukes becomes of public concern in many countries worldwide. Haplorchis taichui and H. pumilio, belonging to the family Heterophyidae (Platyhelminthes: Trematoda) are two of many infecting humans and commonly found in Vietnam. Sequence study of these two small intestinal flukes is still very limited, hence we need more prospective markers for taxonomic identification and classification. This study provides complete coding sequence of the ribosomal transcription units (rTU) from H. taichui and H. pumilio (Vietnamese samples) and demonstrates the use of complete 28S rDNA sequences for phylogenetic analysis.The complete coding sequence of the rTU (from 5' 18S to 3' 28S), consisting of complete 18S, ITS-1, 5.8S, ITS2 and complete 28S rRNA genes and spacers, from H. taichui (7,268 bp) and H. pumilio (7,416 bp) from human hosts in Vietnam, were determined and annotated. The 18S and 5.8S genes of both species were of the same length (1,992 bp/18S, 160 bp/5.8S), but 28S genes differed (3,875 bp/H. taichui and 3,870 bp/H. pumilio). ITS-1 in H. taichui (797 bp) and ITS-2 in H. pumilio (280 bp) do not contain tandem repeat units (TRUs), while ITS-1 in H. pumilio (1,106 bp) contains 3 TRUs of 136 bp/each and 2 TRUs of 116 bp/each and ITS-2 in H. taichui (444 bp) contain 3 TRUs (83–85 bp/each). A phylogenetic tree inferred from the alignment of complete 28S rDNA sequences of 32 trematode strains/species, including 2 Vietnamese Haplorchis spp. and 24 species of 8 families in the suborders Xiphidiata (families Nanophyetidae, Paragonimidae, Collyriclidae), Opisthorchiata (Heterophyidae, Opisthorchiidae), and Echinostomata (Echinostomatidae, Fasciolidae). and Schistosoma japonicum of the family Schistosomatidae is used as an outgroup. The topology of the phylogenetic tree clearly confirmed the status of the Vietnamese H. taichui and H. pumilio species. These species gathered in a group (in the family Heterophyidae) clearly identified in the position of "sister” group to those in the family Opisthorchiidae (suborder Opisthorchiata, superfamily Opisthorchioidea).

MORPHOLOGICAL AND MOLECULAR IDENTIFICATION OF ZOONOTIC TREMATODE METACERCARIAE (Haplorchis taitui) IN FRESHWATER FISH IN IRAN

The intestinal trematode, Haplorchis taichui (Nishigori, 1924), is an important in public health that causes infection in humans and animals especially in Asia and in parts of Africa and the Americas. Haplorchis taitui metacercariae were found in the gills of Cyprinion macrostomus (Heckel) and Capoeta barroisi persica (Karaman) collected from the Shapour River. Morphological excysted metacercariae were identified as wet mounts under a stereomicroscope. Then, the samples were subjected to molecular analysis. The result showed that 69% of examined fish (n = 30) were diagnosed infected with encysted metacercariae in gills. The mean intensity was 8.3 ± 16.9 parasites per fish. The morphometrical values agree with the findings of other studies with the small differences and polymerase chain reaction product length and nucleotide sequence analysis of 18S ribosomal deoxyribonucleic acid gene showed a similarity of over 99% between the specimens and the Haplorchis taichui (Nishigori, 1924) recorded in GenBank.

Genetic differences among Haplorchis taichui populations in Indochina revealed by mitochondrial COX1 sequences

Haplorchis taichui is an intestinal heterophyid fluke that is pathogenic to humans. It is widely distributed in Asia, with a particularly high prevalence in Indochina. Previous work revealed that the lack of gene flow between three distinct populations of Vietnamese H. taichui can be attributed to their geographic isolation with no interconnected river basins. To test the hypothesis that interconnected river basins allow gene flow between otherwise isolated populations of H. taichui, as previously demonstrated for another trematode, Opisthorchis viverrini, we compared the genetic structures of seven populations of H. taichui from various localities in the lower Mekong Basin, in Thailand and Laos, with those in Vietnam, using the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene. To determine the gene flow between these H. taichui populations, we calculated their phylogenetic relationships, genetic distances and haplotype diversity. Each population showed very low nucleotide diversity at this locus. However, high levels of genetic differentiation between the populations indicated very little gene flow. A phylogenetic analysis divided the populations into four clusters that correlated with the country of origin. The negligible gene flow between the Thai and Laos populations, despite sharing the Mekong Basin, caused us to reject our hypothesis. Our data suggest that the distribution of H. taichui populations was incidentally associated with national borders.

Genetic characterization of mitochondrial genome of the small intestinal fluke, Haplorchis taichui (Trematoda: Heterophyidae), Vietnamese sample

The small intestinal fluke, Haplorchis taichui Nishigori, 1924, belonging to genus Haplorchis (family Heterophyidae, class Trematoda, phylum Platyhelminthes), is a zoonotic pathogen causing disease in humans and animals. Complete mitochondrial genome (mtDNA) of H. taichui (strain HTAQT, collected from Quang Tri) was obtained and characterized for structural genomics providing valuable data for studies on epidemiology, species identification, diagnosis, classification, molecular phylogenetic relationships and prevention of the disease. The entire nucleotide mtDNA sequence of H. taichui (HTAQT) is 15.119 bp in length, containing 36 genes, including 12 protein-coding genes (cox1, cox2, cox3, nad1, nad2, nad3, nad4L, nad4, nad5, nad6, atp6 and cob); 2 ribosomal RNA genes, rrnL (16S) and rrnS (12S); 22 transfer RNA genes (tRNA or trn), and a non-coding region (NR), divided into two sub-regions of short non-coding (short, SNR) and long non-coding (long, LNR). LNR region, 1.692 bp in length, located between the position of trnG (transfer RNA-Glycine) and trnE (Glutamic acid), contains 6 tandem repeats (TR), arranged as TR1A, TR2A, TR1B, TR2B, TR3A, TR3B, respectively. Each protein coding gene (overall, 12 genes), ribosomal rRNA (2 genes) and tRNA (22 genes) were analyzed, in particular, protein-coding genes were defined in length, start and stop codons, and rRNA and tRNA genes for secondary structure.