Mitochondrial genomics in Orthoptera using MOSAS

Sheffield, Nathan C.; Hiatt, Kevin D.; Valentine, Mark C.; Song, Ho‐Jun; Whiting, Michael F.

doi:10.3109/19401736.2010.500812

Cited by 70 publications

(57 citation statements)

References 61 publications

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“…The Acridinae species were split into two clades. Phlaeoba albonema formed one monophyletic clade, while the other two species were grouped together into one clade with species of the Oedipodinae, which was in conflict with the morphological taxonomy and previously reported topologies (Fenn et al 2008, Sheffield et al 2010, Zhao et al 2010. For the Gomphocerinae, both subfamilies Arcypterinae and Gomphocerinae in Xia's (1958) system were consolidated into one group.…”

Section: Phylogenetic Relationships Within the Acrididaecontrasting

confidence: 39%

“…The monophyly of the Caelifera is widely accepted and is supported by morphological and molecular data (Xia 1994, Fenn et al 2008, Eades and Otte 2010, Sheffield et al 2010, Zhao et al 2010. In the present study, five superfamilies of Caelifera lineages were included, and they clustered as a monophyletic clade.…”

Section: Phylogenetic Relationships Within the Ensiferamentioning

confidence: 60%

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The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences

Zhang

Huang

et al. 2013

Zool. Stud.

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Background: The phylogeny of the Orthoptera was analyzed based on 6 datasets from 47 orthopteran mitochondrial genomes (mitogenomes). The phylogenetic signals in the mitogenomes were rigorously examined under analytical regimens of maximum likelihood (ML) and Bayesian inference (BI), along with how gene types and different partitioning schemes influenced the phylogenetic reconstruction within the Orthoptera. The monophyly of the Orthoptera and its two suborders (Caelifera and Ensifera) was consistently recovered in the analyses based on most of the datasets we selected, regardless of the optimality criteria.

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Section: Phylogenetic Relationships Within the Acrididaecontrasting

confidence: 39%

Section: Phylogenetic Relationships Within the Ensiferamentioning

confidence: 60%

The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences

Zhang

Huang

et al. 2013

Zool. Stud.

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“…This gene was detected by aligning other hymenopteran tRNA-Ser(AGN) genes with the P. triangulum mitochondrial genome, and the sequence was manually inspected and the annotation corrected based on the predicted secondary structure. The localization was confirmed by using MOSAS [38]. For annotation of protein-coding genes and rRNAs, the sequence file was imported into DOGMA [39].…”

Section: Methodsmentioning

confidence: 99%

Accelerated Evolution of Mitochondrial but Not Nuclear Genomes of Hymenoptera: New Evidence from Crabronid Wasps

et al. 2012

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Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes.

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“…g ., Celera [13]; SOAPdenovo, [14]; MITObim [15]) and annotating ( e . g ., DOGMA [16]; MOSAS [17]; MITOS [18]) mitogenomes have been developed and used [10, 19–21]. These exciting developments have caused the rate of mitogenome elucidation and deposition to increase tremendously (Fig 1).…”

Section: Introductionmentioning

confidence: 99%

Mitogenome sequence accuracy using different elucidation methods

et al. 2017

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Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform) and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community.

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Mitochondrial genomics in Orthoptera using MOSAS

Cited by 70 publications

References 61 publications

The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences

The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences

Accelerated Evolution of Mitochondrial but Not Nuclear Genomes of Hymenoptera: New Evidence from Crabronid Wasps

Mitogenome sequence accuracy using different elucidation methods

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