Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

Abstract

BackgroundRecent mitochondrial phylogenomics studies have reported a sister-group relationship of the orders Capsalidea and Dactylogyridea, which is inconsistent with previous morphology- and molecular-based phylogenies. As Dactylogyridea mitochondrial genomes (mitogenomes) are currently represented by only one family, to improve the phylogenetic resolution, we sequenced and characterized two dactylogyridean parasites, Lamellodiscus spari and Lepidotrema longipenis, belonging to a non-represented family Diplectanidae.ResultsThe L. longipenis mitogenome (15,433 bp) contains the standard 36 flatworm mitochondrial genes (atp8 is absent), whereas we failed to detect trnS1, trnC and trnG in L. spari (14,614 bp). Both mitogenomes exhibit unique gene orders (among the Monogenea), with a number of tRNA rearrangements. Both long non-coding regions contain a number of different (partially overlapping) repeat sequences. Intriguingly, these include putative tRNA pseudogenes in a tandem array (17 trnV pseudogenes in L. longipenis, 13 trnY pseudogenes in L. spari). Combined nucleotide diversity, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently showed that nad2, nad5 and nad4 were the most variable PCGs, whereas cox1, cox2 and cytb were the most conserved. Phylogenomic analysis showed that the newly sequenced species of the family Diplectanidae formed a sister-group with the Dactylogyridae + Capsalidae clade. Thus Dactylogyridea (represented by the Diplectanidae and Dactylogyridae) was rendered paraphyletic (with high statistical support) by the nested Capsalidea (represented by the Capsalidae) clade.ConclusionsOur results show that nad2, nad5 and nad4 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in the Diplectanidae. The unique gene order pattern further suggests discontinuous evolution of mitogenomic gene order arrangement in the Class Monogenea. This first report of paraphyly of the Dactylogyridea highlights the need to generate more molecular data for monogenean parasites, in order to be able to clarify their relationships using large datasets, as single-gene markers appear to provide a phylogenetic resolution which is too low for the task.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-3144-6) contains supplementary material, which is available to authorized users.

Molecular phylogenetics and mitogenomics of three avian dicrocoeliids (Digenea: Dicrocoeliidae) and comparison with mammalian dicrocoeliids

“…Thus, our analyses showed the comparatively fast mutation rate of atp6, nad5, nad3 and nad2 while cox1, cytb and nad1 are evolving comparatively slowly in the Dicrocoeliidae. Although cox1, cytb, nad1 and two mt [50,54].…”

The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes

“…The annotated PCGs were then refined using the NCBI Open Reading Frame Finder, and further annotated with BLASTp searches against the NCBI non-redundant protein sequence database (He et al 2018;Wang et al 2018b). The tRNA genes were also predicted using tRNAscan-SE v1.3.1 (Zhang et al 2018). Subsequently, graphical maps of the complete mitogenomes were drawn using OGDraw v1.2 (Wang et al 2018a).…”

Laser capture microdissection in combination with mass spectrometry: Approach to characterization of tissue-specific proteomes of Eudiplozoon nipponicum (Monogenea, Polyopisthocotylea)

“…For this species, as for the whole group of parasitic Monogenea, proteomic but also genomic and transcriptomic data are still scarce. In particular, no comprehensive [32], G. salaris [33], Gyrodactylus thymalli [34], Pseudochauhanea macrorchis [35], Benedenia hoshinai [36], Benedenia humboldti [37], Paratetraonchoides inermis [38], Lamellodiscus spari and Lepidotrema longipenis [39], and Thaparocleidus asoti and T. varicus [40].…”