The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera)

Carapelli, Antonio; Vannini, Laura; Nardi, Francesco; Boore, Jeffrey L.; Beani, L.; Dallai, Romano; Frati, Francesco

doi:10.1016/j.gene.2006.04.005

Cited by 38 publications

(31 citation statements)

References 58 publications

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“…We observed strong discrepancies among the methodologies used, ML-AA (Figure 2A), BI-DNA (Figure 2B) and BI-AA-CAT (Figure 2C) (see methods for details), confirming the difficulties introduced by such groups. The Strepsiptera species Xenos vesparum [64] appeared within Hymenoptera in the ML-AA tree, being completely trapped by the longest branches of the hymenopterans. The same happened with BI-DNA, although in that case, Xenos appeared in a more basal position within the hymenopterans, apparently slightly reducing the LBA effect.…”

Section: Resultsmentioning

confidence: 99%

What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

Talavera

Vila

2011

BMC Evol Biol

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BackgroundEfforts to solve higher-level evolutionary relationships within the class Insecta by using mitochondrial genomic data are hindered due to fast sequence evolution of several groups, most notably Hymenoptera, Strepsiptera, Phthiraptera, Hemiptera and Thysanoptera. Accelerated rates of substitution on their sequences have been shown to have negative consequences in phylogenetic inference. In this study, we tested several methodological approaches to recover phylogenetic signal from whole mitochondrial genomes. As a model, we used two classical problems in insect phylogenetics: The relationships within Paraneoptera and within Holometabola. Moreover, we assessed the mitochondrial phylogenetic signal limits in the deeper Eumetabola dataset, and we studied the contribution of individual genes.ResultsLong-branch attraction (LBA) artefacts were detected in all the datasets. Methods using Bayesian inference outperformed maximum likelihood approaches, and LBA was avoided in Paraneoptera and Holometabola when using protein sequences and the site-heterogeneous mixture model CAT. The better performance of this method was evidenced by resulting topologies matching generally accepted hypotheses based on nuclear and/or morphological data, and was confirmed by cross-validation and simulation analyses. Using the CAT model, the order Strepsiptera was recovered as sister to Coleoptera for the first time using mitochondrial sequences, in agreement with recent results based on large nuclear and morphological datasets. Also the Hymenoptera-Mecopterida association was obtained, leaving Coleoptera and Strepsiptera as the basal groups of the holometabolan insects, which coincides with one of the two main competing hypotheses. For the Paraneroptera, the currently accepted non-monophyly of Homoptera was documented as a phylogenetic novelty for mitochondrial data. However, results were not satisfactory when exploring the entire Eumetabola, revealing the limits of the phylogenetic signal that can be extracted from Insecta mitogenomes. Based on the combined use of the five best topology-performing genes we obtained comparable results to whole mitogenomes, highlighting the important role of data quality.ConclusionWe show for the first time that mitogenomic data agrees with nuclear and morphological data for several of the most controversial insect evolutionary relationships, adding a new independent source of evidence to study relationships among insect orders. We propose that deeper divergences cannot be inferred with the current available methods due to sequence saturation and compositional bias inconsistencies. Our exploratory analysis indicates that the CAT model is the best dealing with LBA and it could be useful for other groups and datasets with similar phylogenetic difficulties.

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Section: Resultsmentioning

confidence: 99%

What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

Talavera

Vila

2011

BMC Evol Biol

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“…The overall organization of the A. bakeri mt genome is very compact, and the overlaps between ATP8/ATP6 (7 bp) and ND4/ND4L (7 bp) are often been found across the Metazoa 39, 40.…”

Section: Discussionmentioning

confidence: 99%

The Complete Mitochondrial Genome of the Damsel Bug Alloeorhynchus bakeri (Hemiptera: Nabidae)

Liu

Cao³

et al. 2012

Int. J. Biol. Sci.

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The complete sequence of the mitochondrial DNA (mtDNA) of the damsel bug, Alloeorhynchus bakeri, has been completed and annotated in this study. It represents the first sequenced mitochondrial genome of heteropteran family Nabidae. The circular genome is 15, 851 bp in length with an A+T content of 73.5%, contains the typical 37 genes that are arranged in the same order as that of the putative ancestor of hexapods. Nucleotide composition and codon usage are similar to other known heteropteran mitochondrial genomes. All protein-coding genes (PCGs) use standard initiation codons (methionine and isoleucine), except COI, which started with TTG. Canonical TAA and TAG termination codons are found in eight protein-coding genes, the remaining five (COI, COII, COIII, ND5, ND1) have incomplete termination codons (T or TA). PCGs of two strands present opposite CG skew which is also reflected by the nucleotide composition and codon usage. All tRNAs have the typical clover-leaf structure, except the dihydrouridine (DHU) arm of tRNASer (AGN)which forms a simple loop as known in many other metazoa. Secondary structure models of the ribosomal RNA genes of A. bakeri are presented, similar to those proposed for other insect orders. There are six domains and 45 helices and three domains and 27 helices in the secondary structures of rrnL and rrnS, respectively. The major non-coding region (also called control region) between the small ribosomal subunit and the tRNAIle gene includes two special regions. The first region includes four 133 bp tandem repeat units plus a partial copy of the repeat (28 bp of the beginning), and the second region at the end of control region contains 4 potential stem-loop structures. Finally, PCGs sequences were used to perform a phylogenetic study. Both maximum likelihood and Bayesian inference analyses highly support Nabidae as the sister group to Anthocoridae and Miridae.

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“…They are listed in red in figure 1. For Dermaptera, Embioptera, Thysanoptera, and Strepsiptera, the available data are restricted to single or few mtDNAs that are complete or nearly complete (e.g., Shao and Barker 2003; Carapelli et al 2006; Komoto et al 2012; Wan et al 2012). Thus, a better taxon sampling could reveal the presence of PanGO in these orders.…”

Section: Introductionmentioning

confidence: 99%

Is It an Ant or a Butterfly? Convergent Evolution in the Mitochondrial Gene Order of Hymenoptera and Lepidoptera

Babbucci

Basso

Scupola³

et al. 2014

Genome Biology and Evolution

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Insect mitochondrial genomes (mtDNA) are usually double helical and circular molecules containing 37 genes that are encoded on both strands. The arrangement of the genes is not constant for all species, and produces distinct gene orders (GOs) that have proven to be diagnostic in defining clades at different taxonomic levels. In general, it is believed that distinct taxa have a very low chance of sharing identically arranged GOs. However, examples of identical, homoplastic local rearrangements occurring in distinct taxa do exist. In this study, we sequenced the complete mtDNAs of the ants Formica fusca and Myrmica scabrinodis (Formicidae, Hymenoptera) and compared their GOs with those of other Insecta. The GO of F. fusca was found to be identical to the GO of Dytrisia (the largest clade of Lepidoptera). This finding is the first documented case of an identical GO shared by distinct groups of Insecta, and it is the oldest known event of GO convergent evolution in animals. Both Hymenoptera and Lepidoptera acquired this GO early in their evolution. Using a phylogenetic approach combined with new bioinformatic tools, the chronological order of the evolutionary events that produced the diversity of the hymenopteran GOs was determined. Additionally, new local homoplastic rearrangements shared by distinct groups of insects were identified. Our study showed that local and global homoplasies affecting the insect GOs are more widespread than previously thought. Homoplastic GOs can still be useful for characterizing the various clades, provided that they are appropriately considered in a phylogenetic and taxonomic context.

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The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera)

Cited by 38 publications

References 58 publications

What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

The Complete Mitochondrial Genome of the Damsel Bug Alloeorhynchus bakeri (Hemiptera: Nabidae)

Is It an Ant or a Butterfly? Convergent Evolution in the Mitochondrial Gene Order of Hymenoptera and Lepidoptera

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