The complete mitochondrial genome of click beetle  Agrypnus  sp. (Coleoptera: Elateridae) and phylogenetic analysis

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Larvae of click beetles are the most important soil-dwelling agricultural pests and are abundant throughout the world. Agrypnus sp. belongs to the subfamily Agrypninae of Elateridae. Here, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Agrypnus sp., the new representative of the mitogenome of the subfamily. This mitogenome was 16,056 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA unit genes (rRNAs). Gene order was conserved and identical to most other previously sequenced Elateridae. The nucleotide composition biases towards A and T, which together made up 70.8% of the entirety. Phylogenetic analysis based on 13 PCGs sequences showed that Agrypnus sp. got together with the same subfamily species Pyrophorus divergens, Pyrearinus termitilluminans, Ignelater luminosus, and Hapsodrilus ignifer with high support value.

Related collections

Most cited references 9

Record: found
Abstract: found
Article: found

Is Open Access

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

Christoph Hahn, Lutz Bachmann, Bastien Chevreux (2013)

We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.

0 comments Cited 907 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: not found
Article: not found

raxmlGUI: a graphical front-end for RAxML

Daniele Silvestro, Ingo Michalak (2012)

0 comments Cited 350 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

A Comparative Analysis of Mitochondrial Genomes in Coleoptera (Arthropoda: Insecta) and Genome Descriptions of Six New Beetles

N. C. Sheffield, H Song, S. L. Cameron … (2008)

Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

0 comments Cited 85 times – based on 0 reviews      Review now

Bookmark

All references

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): 4 October 2019

Publication date (Electronic, collection): 2019

Volume: 4

Issue: 2

Pages: 3354-3355

Affiliations

[a ]School of Life Sciences, Gannan Normal University , Ganzhou, China;

[b ]National Navel Orange Engineering and Technology Research Center , Ganzhou, China

Author notes

CONTACT Balian Zhong zhongbl008@ 123456163.com School of Life Sciences, Gannan Normal University , Ganzhou, China

Article

Publisher ID: 1673681

DOI: 10.1080/23802359.2019.1673681

PMC ID: 7707258

SO-VID: 6c583e21-8bb9-437f-8c96-2c9bfbc78cb3

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 complete mitochondrial genome of click beetle Agrypnus sp. (Coleoptera: Elateridae) and phylogenetic analysis

Read this article at

Abstract

Related collections

Coleoptera

Most cited references 9

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

raxmlGUI: a graphical front-end for RAxML

A Comparative Analysis of Mitochondrial Genomes in Coleoptera (Arthropoda: Insecta) and Genome Descriptions of Six New Beetles

Author and article information

Journal

Affiliations

Author notes

Article

History

Page count

Categories

Comments

Comment on this article

Similar content 380

Most referenced authors 85