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      The complete mitochondrial genome and description of a new cryptic Brazilian species of Metopiellus Raffray (Coleoptera: Staphylinidae: Pselaphinae)

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          Abstract

          Metopiellus Raffray, 1908 is a genus of South American rove beetles typically found in tropical humid forests. Here we describe a new cryptic species from Eastern Amazon, in northern Brazil, Metopiellus crypticus Asenjo sp. nov., and its major morphologic diagnostic features, which were photographed and illustrated. In addition, we bring the complete mitochondrial genome sequence of M. crypticus sp. nov., and its position within the phylogenetic context of the family, including previously available mitogenomes of Staphylinidae species.

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Alexandros Stamatakis (2014)
          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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            MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

            K Katoh (2002)
            A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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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.
              Article 0 comments Cited 1514 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Angélico Asenjo
                Santelmo Vasconcelos
                Journal
                Journal ID (nlm-ta): PeerJ
                Journal ID (iso-abbrev): PeerJ
                Journal ID (publisher-id): peerj
                Title: PeerJ
                Publisher: PeerJ Inc. (San Diego, USA )
                ISSN (Electronic): 2167-8359
                Publication date (Electronic): 27 July 2023
                Publication date Collection: 2023
                Volume: 11
                Electronic Location Identifier: e15697
                Affiliations
                [1 ]Instituto Tecnológico Vale , Belém, Pará, Brazil
                [2 ]BioEspeleo Consultoria Ambiental , Lavras, Minas Gerais, Brazil
                [3 ]Universidade Federal de Minas Gerais , Belo Horizonte, Minas Gerais, Brazil
                Article
                Publisher ID: 15697
                DOI: 10.7717/peerj.15697
                PMC ID: 10387231
                SO-VID: a25e764b-a18d-4cab-b4ef-d280a8a24eb7
                Copyright statement: ©2023 Asenjo et al.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                Date received : 23 March 2023
                Date accepted : 14 June 2023
                Product
                Self URI: https://peerj.com/articles/15697
                Funding
                Funded by: Vale S.A. (Projeto Diversidade Biológica de Cavernas, R100603.CD.0X; Projeto Centro de Triagem de Invertebrados, R100603.CT.0X)
                Funded by: Guilherme Oliveira is a CNPq (Conselho Nacional de Desenvolvimento Científico) fellow
                Award ID: 307479/2016-1
                Funded by: CNPq (Conselho Nacional de Desenvolvimento Científico) fellow
                Award ID: 307479/2016-1
                Funded by: CNPq
                Award ID: 444227/2018-0
                Award ID: 402756/2018-5
                Award ID: 307479/2016-1
                Funded by: CABANA project
                Award ID: RCUK/BB/P027849/1
                This work was funded by Vale S.A. (Projeto Diversidade Biológica de Cavernas, R100603.CD.0X; Projeto Centro de Triagem de Invertebrados, R100603.CT.0X). Guilherme Oliveira is a CNPq (Conselho Nacional de Desenvolvimento Científico) fellow (307479/2016-1) and is funded by CNPq (444227/2018-0, 402756/2018-5, 307479/2016-1) and the CABANA project (RCUK/BB/P027849/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Entomology
                Subject: Genomics
                Subject: Molecular Biology
                Subject: Taxonomy
                Subject: Zoology

                Keywords: amazon basin,beetle,brazil,pselaphinae,taxonomy
                Data availability:
                Keywords: amazon basin, beetle, brazil, pselaphinae, taxonomy

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