Characteristic and phylogenetic analyses of mitochondrial genome for <i>Rhinogobius filamentosus</i> (Teleostei: Gobiidae: Gobionellinae), an endemic species in China

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Abstract

This study sequenced and annotated the complete mitochondrial genome sequence of Rhinogobius filamentosus, an endemic species in China. The complete mitochondrial genome was 16,510 base pairs long and contained 13 protein-coding genes (PCGs, 11,414 bp), 22 tRNA genes (1,555 bp), two rRNA genes (2,615 bp), two non-coding regions (D-loop: control region displacement loop, 478 bp; OL: origin of L-strand replication, 30 bp). The overall base composition of the genome was estimated to be T (25.4%), C (30.2%), A (27.6%) and G (16.7%), showing an AT bias (53%). Phylogenetic analyses revealed that the genus Rhinogobius included two clades. For one clade, R. filamentosus clustered with R. duospilus, and they formed a sister-group relationship with other ten Rhinogobius species. This work would be essential in revealing the evolutionary relationships in Gobionellinae.

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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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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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metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov … (2017)

While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.

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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): 27 September 2022

Publication date (Electronic, collection): 2022

Publication date PMC-release: 27 September 2022

Volume: 7

Issue: 9

Pages: 1752-1755

Affiliations

[a ]College of Fisheries Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College , Taizhou City, Jiangsu Province, P.R. China

[b ]College of Fisheries and Life Science, Dalian Ocean University , Dalian City, Liaoning Province, P.R. China

Author notes

CONTACT Xiao Jiang Chen 2007020030@ 123456jsahvc.edu.cn Jiangsu Agri-animal Husbandry Vocational College , Taizhou, 225300, China

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Xiao Jiang Chen https://orcid.org/0000-0002-0934-0330

Article

Publisher ID: 2126735

DOI: 10.1080/23802359.2022.2126735

PMC ID: 9518265

PubMed ID: 36188662

SO-VID: 2883cc69-cf79-4947-9b02-6be1c6febddb

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This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Characteristic and phylogenetic analyses of mitochondrial genome for Rhinogobius filamentosus (Teleostei: Gobiidae: Gobionellinae), an endemic species in China

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Genome Integrity

Most cited references 19

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

MITOS: improved de novo metazoan mitochondrial genome annotation.

metaSPAdes: a new versatile metagenomic assembler

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