Characterization of the complete mitochondrial genome of the Northern Mud Gudgeon,  Ophiocara porocephala  (Perciformes: Eleotridae) with phylogenetic implications

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Abstract

The first mitochondrial genome of Ophiocara porocephala was determined by the combination of next-generation sequencing (NGS) and Sanger sequencing methods. A complete circular mitogenome of O. porocephala (16,529 bp) consisted of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two non-coding regions, including a control region (D-loop) and a light strand origin of replication (O _L). Two start codons (ATG and GTG) and four stop codons (TAG, TAA, TA–, and T–) were used in all the PCGs. Except for ND6 and eight transfer RNAs (tRNAs), all the other genes were encoded in the heavy strand. Based on phylogenetic analysis, O. porocephala formed a clade with three other species in the subfamily Butinae, while the other 10 made a subfamily Eleotrinae clade.

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Most cited references 9

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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

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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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tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

Todd Lowe, Patricia P. Chan (2016)

High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database. Previously, web-server tRNA detection was isolated from knowledge of existing tRNAs and their annotation. In this update of the tRNAscan-SE On-line resource, we tie together improvements in tRNA classification with greatly enhanced biological context via dynamically generated links between web server search results, the most relevant genes in the GtRNAdb and interactive, rich genome context provided by UCSC genome browsers. The tRNAscan-SE On-line web server can be accessed at http://trna.ucsc.edu/tRNAscan-SE/.

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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): 16 March 2021

Publication date (Electronic, collection): 2021

Volume: 6

Issue: 3

Pages: 953-955

Affiliations

[a ]Industry 4.0 Convergence Bionics Engineering, Pukyong National University , Busan, Republic of Korea

[b ]Department of Biology, Faculty of Science and Technology, Advance Tropical Biodiversity, Genomics, and Conservation Research Group, Universitas Airlangga , Surabaya, Indonesia

[c ]Department of Marine, Fisheries and Marine Faculty, Universitas Airlangga C Campus Jl. Mulyorejo Surabaya East Java , Surabaya, Indonesia

[d ]Department of Marine Biology, Pukyong National University , Busan, Republic of Korea

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CONTACT Hyun-Woo Kim kimhw@ 123456pknu.ac.kr Department of Marine Biology, Pukyong National University , Busan48513, Republic of Korea

Author information

Muhammad Hilman Fu’adil Amin https://orcid.org/0000-0001-7385-2536

Bambang Irawan https://orcid.org/0000-0002-1016-4266

Sapto Andriyono https://orcid.org/0000-0002-2566-1636

Hyun-Woo Kim https://orcid.org/0000-0003-1357-5893

Article

Publisher ID: 1889415

DOI: 10.1080/23802359.2021.1889415

PMC ID: 7971195

PubMed ID: 33796696

SO-VID: 19eb6059-a364-47af-abc0-615e06ac0a96

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 of the Northern Mud Gudgeon, Ophiocara porocephala (Perciformes: Eleotridae) with phylogenetic implications

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Most cited references 9

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

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

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

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