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Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

Brabec J, Kostadinova A, Scholz T, Littlewood DT - Parasit Vectors (2015)

Bottom Line: Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared.Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida.Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and large-scale molecular epidemiology and disease ecology studies based on the most accessible life-cycle stages of eye flukes.

View Article: PubMed Central - PubMed

Affiliation: Institute of Parasitology, Biology Centre of the Czech Academy of Sciences and Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic. brabcak@paru.cas.cz.

ABSTRACT

Background: The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology.

Methods: Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared.

Results: We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida.

Conclusions: Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and large-scale molecular epidemiology and disease ecology studies based on the most accessible life-cycle stages of eye flukes.

No MeSH data available.


Related in: MedlinePlus

Schematic diagram of the mitochondrial gene order of the Trematoda mapped onto the mtDNA amino acid phylogenetic estimate from Fig. 1. Diplostomum spp. gene order highlighted by grey background, altered gene position relative to the Diplostomum spp. indicated in black. Outgroup: Diphyllobothrium spp. and Spirometra erinacei
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Fig3: Schematic diagram of the mitochondrial gene order of the Trematoda mapped onto the mtDNA amino acid phylogenetic estimate from Fig. 1. Diplostomum spp. gene order highlighted by grey background, altered gene position relative to the Diplostomum spp. indicated in black. Outgroup: Diphyllobothrium spp. and Spirometra erinacei

Mentions: Mapping the mt gene arrangement across the phylogenetic tree inferred from mt data revealed that both species of Diplostomum exhibit a closer match to the conserved gene order of the plagiorchiid digeneans with only one or two immediately neighbouring tRNAs positions switched (Fig. 3), rather than to the more extensively rearranged order observed in the mt genomes of the representatives of the Diplostomida (basal schistosomes display at least four single tRNA relocations, derived schistosomes a further two shifts of larger genome chunks involving several protein-coding and tRNA genes). The mt gene order in Diplostomum spp. resembles most closely that of representatives of the flatworm class Cestoda, a sister lineage of the class Trematoda (e.g. [34]) used as an outgroup in our analyses (Fig. 3).Fig. 3


Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

Brabec J, Kostadinova A, Scholz T, Littlewood DT - Parasit Vectors (2015)

Schematic diagram of the mitochondrial gene order of the Trematoda mapped onto the mtDNA amino acid phylogenetic estimate from Fig. 1. Diplostomum spp. gene order highlighted by grey background, altered gene position relative to the Diplostomum spp. indicated in black. Outgroup: Diphyllobothrium spp. and Spirometra erinacei
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4477422&req=5

Fig3: Schematic diagram of the mitochondrial gene order of the Trematoda mapped onto the mtDNA amino acid phylogenetic estimate from Fig. 1. Diplostomum spp. gene order highlighted by grey background, altered gene position relative to the Diplostomum spp. indicated in black. Outgroup: Diphyllobothrium spp. and Spirometra erinacei
Mentions: Mapping the mt gene arrangement across the phylogenetic tree inferred from mt data revealed that both species of Diplostomum exhibit a closer match to the conserved gene order of the plagiorchiid digeneans with only one or two immediately neighbouring tRNAs positions switched (Fig. 3), rather than to the more extensively rearranged order observed in the mt genomes of the representatives of the Diplostomida (basal schistosomes display at least four single tRNA relocations, derived schistosomes a further two shifts of larger genome chunks involving several protein-coding and tRNA genes). The mt gene order in Diplostomum spp. resembles most closely that of representatives of the flatworm class Cestoda, a sister lineage of the class Trematoda (e.g. [34]) used as an outgroup in our analyses (Fig. 3).Fig. 3

Bottom Line: Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared.Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida.Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and large-scale molecular epidemiology and disease ecology studies based on the most accessible life-cycle stages of eye flukes.

View Article: PubMed Central - PubMed

Affiliation: Institute of Parasitology, Biology Centre of the Czech Academy of Sciences and Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic. brabcak@paru.cas.cz.

ABSTRACT

Background: The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology.

Methods: Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared.

Results: We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida.

Conclusions: Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and large-scale molecular epidemiology and disease ecology studies based on the most accessible life-cycle stages of eye flukes.

No MeSH data available.


Related in: MedlinePlus