The mitogenome of the true bug <i>Nysius cymoides</i> (Insecta, Heteroptera) and the phylogeny of Lygaeoidea

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Abstract

The complete mitochondrial genome of the true bug (Homoptera) Nysius cymoides (Spinola, 1837) is herein described and used for phylogenetic comparison with other species of Lygaeoidea. The mtDNA has a gene order and other molecular features typically observed in hexapods, and a long A + T-rich region, due to the occurrence of several repeat units. The phylogenetic analyses support the monophyly of all families except Rhyparochromidae.

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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

Dinghua Li, Chi-Man Liu, Ruibang Luo … (2015)

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a fourfold improvement. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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MITOS: improved de novo metazoan mitochondrial genome annotation.

Matthias Bernt, Alexander Donath, Frank Jühling … (2013)

About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.

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Journal

Journal ID (nlm-ta): Mitochondrial DNA B Resour

Journal ID (iso-abbrev): Mitochondrial DNA B Resour

Title: Mitochondrial DNA. Part B, Resources

Publisher: Taylor & Francis

ISSN (Electronic): 2380-2359

Publication date (Electronic, pub): 15 July 2021

Publication date (Electronic, collection): 2021

Volume: 6

Issue: 8

Pages: 2366-2368

Affiliations

[a ]Department of Life Sciences, University of Siena , Siena, Italy

[b ]Faculty of Sciences of Bizerte, Carthage University , Tunis, Tunisia

[c ]LR11INRAT06 Laboratory of Biotechnology Applied to Agriculture, National Agricultural Research Institute of Tunisia (INRAT), Carthage University , Tunis, Tunisia

[d ]AgroBioSciences (AgBS), Mohammed VI Polytechnic University (UM6P) , Ben Guerir, Morocco

Author notes

CONTACT Antonio Carapelli antonio.carapelli@ 123456unisi.it Department of Life Sciences, University of Siena , Siena, Italy

Author information

Antonio Carapelli https://orcid.org/0000-0002-3165-9620

Claudia Brunetti https://orcid.org/0000-0002-5260-5840

Claudio Cucini https://orcid.org/0000-0003-1918-0702

Elena Cardaioli https://orcid.org/0000-0003-2850-6698

Abir Soltani https://orcid.org/0000-0002-8886-6567

Moez Amri https://orcid.org/0000-0002-4707-0618

Jouda Mediouni Ben Jemâa https://orcid.org/0000-0003-0916-9243

Pietro Paolo Fanciulli https://orcid.org/0000-0003-2999-6203

Francesco Nardi https://orcid.org/0000-0003-0271-9855

Article

Publisher ID: 1951139

DOI: 10.1080/23802359.2021.1951139

PMC ID: 8284137

PubMed ID: 34345698

SO-VID: cb7f6e7b-8d34-4aa9-a06d-0341200c0067

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The mitogenome of the true bug Nysius cymoides (Insecta, Heteroptera) and the phylogeny of Lygaeoidea

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Coleoptera

Most cited references 10

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

MITOS: improved de novo metazoan mitochondrial genome annotation.

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