The complete mitochondrial genome and description of a new cryptic species of Benedenia Diesing, 1858 (Monogenea: Capsalidae), a major pathogen infecting the yellowtail kingfish Seriola lalandi Valenciennes in the South-East Pacific

Abstract

Background: The monogenean Benedenia seriolae parasitizes fishes belonging to the genus Seriola, represents a species complex, and causes substantial impact on fish welfare in aquaculture systems worldwide. This study reports, for the first time, the complete mitochondrial genome of B. humboldti n. sp., a new cryptic species from the South-East Pacific (SEP).

Methods: The mitogenome of B. humboldti n. sp. was assembled from short Illumina 150 bp pair-end reads. The phylogenetic position of B. humboldti n. sp. among other closely related congeneric and confamiliar capsalids was examined using mitochondrial protein-coding genes (PCGs). Morphology of B. humboldti n. sp. was examined based on fixed and stained specimens.

Results: The AT-rich mitochondrial genome of B. humboldti is 13,455 bp in length and comprises 12 PCGs (atp8 was absent as in other monogenean genomes), 2 ribosomal RNA genes, and 22 transfer RNA genes. All protein-coding, ribosomal RNA, and transfer RNA genes are encoded on the H-strand. The gene order observed in the mitochondrial genome of B. humboldti n. sp. was identical to that of B. seriolae from Japan but different from that of B. seriolae from Australia. The genetic distance between B. humboldti n. sp. and B. seriolae from Japan was high. Minor but reliable differences in the shape of the penis were observed between Benedenia humboldti n. sp. and congeneric species.

Conclusions: Phylogenetic analyses based on PCGs in association with differences in the shape of the penis permitted us to conclude that the material from the South-East Pacific represents a new species of Benedenia infecting S. lalandi off the coast of Chile. The discovery of this parasite represents the first step to improving our understanding of infestation dynamics and to develop control strategies for this pathogen infecting the farmed yellowtail kingfish, Seriola lalandi, in the South-East Pacific.

Keywords: Disease; Flatworm; Fluke; Marine; Purifying selection; Vector.

Fig. 1

Circular genome map of Benedenia humboldti n. sp. mitochondrial DNA. The map is annotated and depicts 12 protein-coding genes (PCGs), 2 ribosomal RNA genes [rrnS (12S ribosomal RNA) and rrnL (16S ribosomal RNA)] and 22 transfer RNA (tRNA) genes. The inner circle depicts GC content along the genome. The putative non-coding region likely involved in the initiation of the mitogenome replication is not annotated

Fig. 2

Mitochondrial gene order of Benedenia humboldti n. sp. and closely related congeneric species

Fig. 3

a Selective pressure analysis in protein-coding genes present in the mitochondrial genome of Benedenia humboldti n. sp. K_A, K_S and K_A/K_S values were calculated using the γ-MYN model. b Selective pressure analysis in the cox1 gene of Benedenia humboldti n. sp. K_A, K_S and K_A/K_S values were calculated using the γ-MYN model and adopting a sliding window of length = 57 and step length = 12. See “Methods” and “Results and discussion” for further details

Fig. 4

Secondary structure of tRNAs in the mitochondrial genome of Benedenia humboldti n. sp. predicted by MITFI and tRNAscan-SE v.2.0

Fig. 5

Phylogenetic analysis of Benedenia humboldti n. sp. and related species. ‛Total evidenceʼ phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the protein-coding genes present in the mitochondrial genome of representatives of the subclass Monopisthocotylea. In the analysis, three species of the subclass Polyopisthocotylea were used as the outgroup. Numbers at the branches represent bootstrap values. The optimal molecular evolution model estimated with ProtTest as implemented in NOVOPlasty was the mtZOA+F+I+G4 model; this model was also found to be optimal and applied to two different partitions (partition 1: atp6 + nad1 + nad3 + nad4l + nad2, partition 2: cob + cox1 + cox2)

Fig. 6

Benedenia humboldti n. sp. Entire worm, ventral view (composite drawing mostly from type-specimens). Abbreviations: aa, anterior attachment organ; ah, anterior hamulus; as, accessory sclerite; cgp, common genital pore; e, eye-spots; eg, egg; g, germarium; gc, gut caeca; h, haptor; ifc, internal fertilization chamber; mv, marginal valve; p, pharynx; pe, penis; ph, posterior hamulus; prh, prohaptor; t, testis; te, tendons; u, uterus; vd, vas deferens; vf, vitelline follicle; vr, vitelline reservoir

Fig. 7

Benedenia humboldti n. sp. Haptoral sclerites and egg shape. a Accessory sclerite. b Anterior hamulus. c Posterior hamulus. d Egg

Fig. 8

Benedenia humboldti n. sp. Reproductive system, ventral view, with vitellarium omitted. Abbreviations: ar, accessory gland reservoir; cgp, common genital pore; ifc, internal fertilization chamber; cv, constricted region of vagina; eg, egg; g, germarium; o, oötype; ov, ovovitelline duct; pe, penis; pv, proximal storage region of vagina; s, columnar structure; sv, seminal vesicle; t, testis; u, uterus; vd, vas deferens; vp, vaginal pore; vr, vitelline reservoir

Fig. 9

Benedenia humboldti n. sp. Penis shape of Benedenia humboldti n. sp. from Seriola lalandi off Chile (a) and B. seriolae from S. quinqueradiata off Japan (b). Specimens of B. seriolae were kindly donated by Dr Shirakashi. Abbreviations: cgp, common genital pore; lo, lobe; pe, penis; vp, vaginal pore. Scale-bars: 500 µm