Complete mitochondrial genomes of four entomopathogenic nematode species of the genus Steinernema

Kikuchi, Taisei; Afrin, Tanzila; Yoshida, M.

doi:10.1186/s13071-016-1730-z

Cited by 10 publications

(7 citation statements)

References 31 publications

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“…To make sure that these duplicated sequences are not artefacts from our own PCR amplification or numt s [ 28 ], we have extracted DNA from an additional C. cotti specimen and amplified, sequenced and assembled its entire genome anew. The sequences were identical, apart from the minor variations expected among individual mitogenomes [ 29 ], thus excluding the possibility of a mistake in the sequencing and assembly process. Unfortunately, these two nematodes were obtained from the same fish specimen, so we cannot directly exclude the possibility of this unique architecture being a lineage-specific phenomenon.…”

Section: Resultsmentioning

confidence: 99%

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

et al. 2017

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BackgroundComplete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes.ResultsThe mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder.ConclusionsWithin the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.Electronic supplementary materialThe online version of this article (doi: 10.1186/s12864-017-4237-x) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

et al. 2017

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“…This phenomenon is also found in the mt genomes of entomopathogenic nematodes and plant-parasitic nematodes. For example, the lengths of the complete mt genomes of the entomopathogenic nematode Steinernema litorale and the plant-parasitic nematode Pratylenchus vulnus are 21,403 bp and 21,656 bp in size, respectively; however, the size of the non-coding regions was extremely long ( S. litorale , 8,137 bp; P. vulnus , 7,748 bp) (Sultana et al, 2013 ; Taisei et al, 2016 ). The total A+T contents of three worms mtDNA of this study were consistent with those of most nematode mt genomes characterized to date, such as T. brevicauda (77.0%) and Wuchereria bancrofti (74.6%) (Ramesh et al, 2012 ; Duan et al, 2015 ), whereas the percentages of A+T content are remarkably higher than those of trematodes and protozoa, such as Echinostoma hortense (63.03%) and Eimeria magna (65.16%) (Tian et al, 2015 ; Liu et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial DNA Evidence Supports the Hypothesis that Triodontophorus Species Belong to Cyathostominae

et al. 2017

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Equine strongyles, the significant nematode pathogens of horses, are characterized by high quantities and species abundance, but classification of this group of parasitic nematodes is debated. Mitochondrial (mt) genome DNA data are often used to address classification controversies. Thus, the objectives of this study were to determine the complete mt genomes of three Cyathostominae nematode species (Cyathostomum catinatum, Cylicostephanus minutus, and Poteriostomum imparidentatum) of horses and reconstruct the phylogenetic relationship of Strongylidae with other nematodes in Strongyloidea to test the hypothesis that Triodontophorus spp. belong to Cyathostominae using the mt genomes. The mt genomes of Cy. catinatum, Cs. minutus, and P. imparidentatum were 13,838, 13,826, and 13,817 bp in length, respectively. Complete mt nucleotide sequence comparison of all Strongylidae nematodes revealed that sequence identity ranged from 77.8 to 91.6%. The mt genome sequences of Triodontophorus species had relatively high identity with Cyathostominae nematodes, rather than Strongylus species of the same subfamily (Strongylinae). Comparative analyses of mt genome organization for Strongyloidea nematodes sequenced to date revealed that members of this superfamily possess identical gene arrangements. Phylogenetic analyses using mtDNA data indicated that the Triodontophorus species clustered with Cyathostominae species instead of Strongylus species. The present study first determined the complete mt genome sequences of Cy. catinatum, Cs. minutus, and P. imparidentatum, which will provide novel genetic markers for further studies of Strongylidae taxonomy, population genetics, and systematics. Importantly, sequence comparison and phylogenetic analyses based on mtDNA sequences supported the hypothesis that Triodontophorus belongs to Cyathostominae.

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“…Shared gene clusters between A. varius and Panagrolaimomorpha species are also very limited: trnT +nad4, trnH +rrnL+nad3, trnP+trnM, nad6 +nad4L+trnW, nad2+trnI and trnN +trnF are shared with Rhabditophanes sp. KR3021 (Hunt et al, 2016), nad4L+trnW, trnH +rrnL+nad3, nad2+trnI, cox3+trnE and trnT +nad4 are shared with Parastrongyloides trichosuri (Hunt et al, 2016), trnH +rrnL+nad3, nad4L+trnW, nad2+trnI and trnT +nad4 are shared with S. carpocapsae (Montiel et al, 2006) and trnH +rrnL+nad3, nad6 +nad4L+trnW, nad2+trnI and trnT +nad4 are shared with S. glaseri, S. litorale, S. kushidai (Kikuchi, Afrin & Yoshida, 2016), H. gingivalis (Kim et al, 2015) and P. redivivus (GenBank accession no. AP017464.1; Clark et al, 2016).…”

Section: Comparison Of Mitochondrial Gene Arrangementmentioning

confidence: 99%

The mitochondrial genome ofAcrobeloides varius(Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)

Kim

Lee

Kil

et al. 2020

PeerJ

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The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.

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Complete mitochondrial genomes of four entomopathogenic nematode species of the genus Steinernema

Cited by 10 publications

References 31 publications

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

Mitochondrial DNA Evidence Supports the Hypothesis that Triodontophorus Species Belong to Cyathostominae

The mitochondrial genome ofAcrobeloides varius(Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)

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