The complete mitochondrial genome of the cowpea weevil,  Callosobruchus maculates  (Coleoptera: Chrysomelidae: Bruchinae) and a related phylogenetic analysis of Chrysomelidae

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Abstract

In this study, the complete 17,809 bp mitochondrial genome of Callosobruchus maculates (F.) (Coleoptera: Chrysomelidae: Bruchinae) was sequenced using Illumina’s HiSeq2000 platform. The mitogenome is a double-stranded circular molecule of 17,809 bp in length with 21 transfer RNA genes, 13 protein-coding genes, and two ribosomal RNA genes as in other insects. Specially, there is a 2008 bp-inserted segment between ND2 and tRNA-Trp from 1180 to 3187, which cannot be aligned to any known gene of mitogenomes. To estimate the taxonomic status of Bruchinae, total 17 species from eight subfamilies of Chrysomelidae were selected as ingroups and three species of Lamiinae as outgroups for phylogenetic analysis based on mitogenome. The results showed that three major lineages were formed, including a basal ‘Eumolpine’ clade (Cassidinae, Eumolpinae, Cryptocephalinae, Clytrinae), ‘'Criocerine’ clade (Criocerinae, Bruchinae) and ‘Chrysomeline’ clade (Chrysomelinae, Galerucinae s. l.). Bruchinae showed more closed relationship with Criocerinae than other subfamilies. More thorough taxon sampling will be needed to well understand the relationship in Chrysomelidae.

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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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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Matthew Kearse, Richard Moir, Amy Wilson … (2012)

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com

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SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

Gaurav Vaidya, David Lohman, Rudolf Meier (2011)

We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.

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Author and article information

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): 26 May 2018

Publication date (Electronic, collection): 2018

Volume: 3

Issue: 2

Pages: 645-647

Affiliations

[a ]Inspection and Quarantine Technical Center, Beijing Inspection and Quarantine Testing Bureau , Beijing, China;

[b ]Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing, China;

[c ]Jilin Entry-Exit Inspection and Quarantine Bureau , Changchun, China

Author notes

CONTACT Xing-Ke Yang yangxk@ 123456ioz.ac.cn ;

Rui-E Nie niere@ 123456ioz.ac.cn Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , 1 Beichen West Road, Chaoyang District, Beijing 100101, China

Article

Publisher ID: 1413308

DOI: 10.1080/23802359.2017.1413308

PMC ID: 7799975

SO-VID: f0bf8ac0-ea40-4371-b0dd-727545f5d73d

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.

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The complete mitochondrial genome of the cowpea weevil, Callosobruchus maculates (Coleoptera: Chrysomelidae: Bruchinae) and a related phylogenetic analysis of Chrysomelidae

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Coleoptera

Most cited references 30

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

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

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