Mitophylogenomics of the zoonotic fluke Echinostoma malayanum confirms it as a member of the genus Artyfechinostomum Lane, 1915 and illustrates the complexity of Echinostomatidae systematics

• Published in: Parasitology research (1987) Vol. 121; no. 3; pp. 899 - 913
• Main Authors: Pham, Linh Thi Khanh, Saijuntha, Weerachai, Lawton, Scott P., Le, Thanh Hoa
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.03.2022; Springer; Springer Nature B.V
• Subjects: Animals; ATP8 gene; Base composition; Biomedical and Life Sciences; Biomedicine; Codons; Congeners; Echinostoma; Echinostoma - genetics; Echinostomatidae; Echinostomatidae - genetics; Evolution; Genetic distance; Genetics; Genome, Mitochondrial; Genomes; Genomics; Hypoderaeum conoideum; Immunology; Medical Microbiology; Microbiology; Mitochondria; Mitochondrial DNA; Phenylalanine; Phylogeny; Phylogeny - Original Paper; Short tandem repeats; Skewness; Transfer RNA; Trematoda - genetics; Valine; United Kingdom; Vietnam; Thailand; China; India; Tandem repeats; Genetic distance; Echinostomata; Echinostomatidae; Mitophylogenetics; Skewness; Echinostoma/Artyfechinostomum malayanum
• ISSN: 0932-0113; 1432-1955
• DOI: 10.1007/s00436-022-07449-z

The complete mitochondrial genome (mitogenome or mtDNA) of the trematode Echinostoma malayanum Leiper, 1911 was fully determined and annotated. The circular mtDNA molecule comprised 12 protein-coding genes (PCGs) ( cox 1 − 3, cob , nad 1 − 6, nad 4L, atp 6), two mitoribosomal RNAs (MRGs) (16S or rrn L and 12S or rrn S), and 22 transfer RNAs (tRNAs or trn ), and a non-coding region (NCR) rich in long and short tandem repeats (5.5 LRUs/336 bp/each and 7.5 SRUs/207 bp/each). The atp 8 gene is absent and the 3′ end of nad 4L overlaps the 5′ end of nad 4 by 40 bp. Special DHU-arm missing tRNAs for Serine were found for both tRNA Ser1(AGN) and tRNA Ser2(UCN) . Codons of TTT (for phenylalanine), TTG (for leucine), and GTT (for valine) were the most, and CGC (for Arginine) was the least frequently used. A similar usage pattern was seen in base composition, AT and GC skewness for PCGs, MRGs, and mtDNA* (coding cox 3 to nad 5) in E. malayanum and Echinostomatidae. The nucleotide use is characterized by (T > G > A > C) for PCGs/mtDNA*, and by (T > G ≈ A > C) for MRGs. E. malayanum exhibited the lowest genetic distance (0.53%) to Artyfechinostomum sufrartyfex , relatively high to the Echinostoma congeners (13.20–13.99%), higher to  Hypoderaeum conoideum (16.18%), and the highest to interfamilial Echinochasmidae (26.62%); Cyclocoelidae (30.24%); and Himasthlidae (25.36%). Topology indicated the monophyletic position between E. malayanum / A. sufrartyfex and the group of Echinostoma caproni , Echinostoma paraensei , Echinostoma miyagawai , and Echinostoma revolutum , rendering Hypoderaeum conoideum and unidentified Echinostoma species paraphyletic. The strictly closed genomic/taxonomic/phylogenetic features (including base composition, skewness, codon usage/bias, genetic distance, and topo-position) reinforced Echinostoma malayanum to retake its generic validity within the Artyfechinostomum genus.