Characterization of the complete mitochondrial genome of <i>Garra motuoensis</i> (Cypriniformes: Cyprinidae) and its phylogenetic position within genus <i>Garra</i>

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Abstract

Garra motuoensis, an endemic labeonine fish, was reported distributed in the lower Yarlung Tsangpo River drainage with little published biological information. Herein, we sequenced and characterized the complete mitochondrial genome of G. motuoensis, which was 16,806 bp in length, containing 13 PCGs, 22 tRNA genes, two rRNA genes, one light strand replication origin ( O _L ), one control region (D-loop), and one replication region. Phylogenetic analysis based on 13 PCGs sequences revealed that G. motuoensis had a closest relationship with G. qiaojiensis. Then, both species clustered with other species of Garra, and next grouped with other genera of subfamily Labeoninae.

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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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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

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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): 19 April 2022

Publication date (Electronic, collection): 2022

Publication date PMC-release: 19 April 2022

Volume: 7

Issue: 4

Pages: 663-665

Affiliations

[a ]College of Life Sciences, Zaozhuang University , Zaozhuang, China

[b ]The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan, China

[c ]College of Fisheries, Southwest University , Chongqing, China

Author notes

CONTACT Henglun Shen shenhenglun@ 123456126.com College of Life Sciences, Zaozhuang University , Zaozhuang 277160, China

Article

Publisher ID: 2064247

DOI: 10.1080/23802359.2022.2064247

PMC ID: 9037219

PubMed ID: 35478858

SO-VID: 22958cd3-4ce7-4754-9ff5-af98148c43d8

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 Garra motuoensis (Cypriniformes: Cyprinidae) and its phylogenetic position within genus Garra

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Genome Integrity

Most cited references 13

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

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