Characterization of the mitochondrial genome of  Arge bella  Wei & Du sp. nov. (Hymenoptera: Argidae)

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Abstract

We describe Arge bella Wei & Du sp. nov., a large and beautiful species of Argidae from south China, and report its mitochondrial genome based on high-throughput sequencing data. We present the gene order, nucleotide composition of protein-coding genes (PCGs), and the secondary structures of RNA genes. The nearly complete mitochondrial genome of A. bella has a length of 15,576 bp and a typical set of 37 genes (22 tRNAs, 13 PCGs, and 2 rRNAs). Three tRNAs are rearranged in the A. bella mitochondrial genome as compared to the ancestral type in insects: trnM and trnQ are shuffled, while trnW is translocated from the trnW- trnC- trnY cluster to a location downstream of trnI. All PCGs are initiated by ATN codons, and terminated with TAA, TA or T as stop codons. All tRNAs have a typical cloverleaf secondary structure, except for trnS1. H821 of rrnS and H976 of rrnL are redundant. A phylogenetic analysis based on mitochondrial genome sequences of A. bella, 21 other symphytan species, two apocritan representatives, and four outgroup taxa supports the placement of Argidae as sister to the Pergidae within the symphytan superfamily Tenthredinoidea.

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Most cited references 54

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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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A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

Fredrik Ronquist, Seraina Klopfstein, Lars Vilhelmsen … (2012)

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.]

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VARNA: Interactive drawing and editing of the RNA secondary structure

Kévin Darty, Alain Denise, Yann Ponty (2009)

Description: VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Features: VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments. Availability: VARNA is a free software, released under the terms of the GPLv3.0 license and available at http://varna.lri.fr Contact: ponty@lri.fr Supplementary information: Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Meicai Wei

Journal

Journal ID (nlm-ta): PeerJ

Journal ID (iso-abbrev): PeerJ

Journal ID (publisher-id): peerj

Journal ID (pmc): peerj

Title: PeerJ

Publisher: PeerJ Inc. (San Diego, USA )

ISSN (Electronic): 2167-8359

Publication date (Electronic): 21 December 2018

Publication date Collection: 2018

Volume: 6

Electronic Location Identifier: e6131

Affiliations

[1 ]Central South University of Forestry and Technology, Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education , Changsha, Hunan, China

[2 ]Jiangxi Normal University, Life Science College , Nanchang, Jiangxi, China

[3 ]Norwegian Institute of Bioeconomy Research, Department of Ecosystems in the Barents Region, Svanhovd Research Station , Svanvik, Norway

Article

Publisher ID: 6131

DOI: 10.7717/peerj.6131

PMC ID: 6305119

PubMed ID: 30595984

SO-VID: 8659fdc1-4fdd-42b9-b9e9-d7107658ba06

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 : 2 October 2018

Date accepted : 17 November 2018

Funding

Funded by: National Natural Science Foundation of China

Award ID: 31501885

Award ID: 31672344

Award ID: 30771741

This work was supported by the National Natural Science Foundation of China (No. 31501885, No.31672344, and No.30771741). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae)

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Abstract

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Hymenoptera

Most cited references 54

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

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

VARNA: Interactive drawing and editing of the RNA secondary structure

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