The complete mitochondrial genome of <i>Eremias dzungarica</i> (Reptilia, Squamata, Lacertidae) from the Junggar Basin in Northwest China

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Abstract

The complete mitochondrial genome (mitogenome) of Eremias dzungarica from the Junggar Basin in Northwest China was determined for the first time by next-generation sequencing. The total length is 19,899 bp, containing13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes and one control region. This gene arrangement is similar to the typical mtDNA of vertebrates. The 13 concatenated PCGs were used to perform Bayesian phylogenetic analyses together with several congeners as well as ten representative lacertids with mitogenome data available in GenBank. The resulting phylogenetic tree supports the monophyly of viviparous species in Eremias, with E. dzungarica being more closely related to E. przewalskii than to E. multiocellata. The mitogenome of E. dzungarica will provide fundamental data for the exploration of the mitogenome evolution in lacertids.

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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available 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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Is Open Access

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen, Yanqing Zhou, Yaru Chen … (2018)

Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.

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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): 15 June 2021

Publication date (Electronic, collection): 2021

Volume: 6

Issue: 7

Pages: 2012-2014

Affiliations

[a ]College of Life Sciences and Technology, Inner Mongolia Normal University , Hohhot, China

[b ]Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu, China

Author notes

CONTACT Bin Zhang zhangbinnmg@ 123456hotmail.com College of Life Science and Technology, Inner Mongolia Normal University , Hohhot010022, China

Xianguang Guo guoxg@ 123456cib.ac.cn Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu610041, China

Article

Publisher ID: 1923417

DOI: 10.1080/23802359.2021.1923417

PMC ID: 8208112

PubMed ID: 34189268

SO-VID: 683409c1-4314-41d8-96d4-ac0863ec59af

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 Eremias dzungarica (Reptilia, Squamata, Lacertidae) from the Junggar Basin in Northwest China

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Most cited references 12

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

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

fastp: an ultra-fast all-in-one FASTQ preprocessor

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