Characterization of the complete mitochondrial genome and phylogenetic analysis of <i>Menochilus sexmaculata</i> (Fabricius, 1781) (Coleoptera: Coccinellidae)

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Abstract

We sequenced the complete mitochondrial genome of Menochilus sexmaculata (Fabricius, 1781) and compared it with that of other insects. The mitogenome of M. sexmaculata is a circular molecule of 16,663 bp with 75.00% AT content, containing 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one non-coding control region. All of the PCGs use the typical ATN as the initiation codon, with the exception of cox1 and nad3 which begin with AAT and TTG, respectively. Cox1, cox2, cox3, nad3, nad4, nad5 and nad6 employ a single T as a termination signal, while others have the typical termination codons (TAA or TAG). All the 22 typical animal tRNA genes are found in M. sexmaculata mitogenome, and most of the tRNAs could be folded into the classic cloverleaf secondary structure. Phylogenetic tree based on 13 PCGs suggested that M. sexmaculata is closely related to Anatis ocellata and Calvia championorum, and clustered within Coccinellidae.

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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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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.

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Animal mitochondrial genomes.

J. L. Boore (1999)

Animal mitochondrial DNA is a small, extrachromosomal genome, typically approximately 16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems-'mitochondrial genomics'-serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.

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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): 18 August 2021

Publication date (Electronic, collection): 2021

Volume: 6

Issue: 9

Pages: 2686-2687

Affiliations

[a ]College of Tropical Crops, Hainan University , Haikou, China

[b ]College of Plant Protection, Hainan University , Haikou, China

[c ]Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences , Haikou, China

Author notes

CONTACT Fengqin Cao caofengqin@ 123456163.com College of Plant Protection, Hainan University , Haikou 570288, China

Article

Publisher ID: 1964401

DOI: 10.1080/23802359.2021.1964401

PMC ID: 8381914

SO-VID: 078c692d-74d0-4363-bc47-9eea3287ebc4

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.

Characterization of the complete mitochondrial genome and phylogenetic analysis of Menochilus sexmaculata (Fabricius, 1781) (Coleoptera: Coccinellidae)

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Most cited references 7

MITOS: improved de novo metazoan mitochondrial genome annotation.

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

Animal mitochondrial genomes.

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