First complete mitochondrial genome of the Alashan ground squirrel ( <i>Spermophilus alashanicus</i>) (Rodentia: Sciuridae) from Ningxia, China

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Abstract

The Alashan ground squirrel ( Spermophilus alashanicus) is primarily distributed in the regions of Inner Mongolia and Ningxia, China. In this study, we present the first complete mitochondrial genome of S. alashanicus. The genome spans 16,464 base pairs and comprises 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a single control region with a marked AT bias. The overall GC content is 35.4%. Phylogenetic analyses indicate that S. alashanicus clusters are closely associated with S. dauricus. This comprehensive characterization of the S. alashanicus mitochondrial genome serves as a foundational resource for future studies on mitochondrial evolution, species identification, population genomics, and phylogenetics.

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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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MEGA11: Molecular Evolutionary Genetics Analysis Version 11

Koichiro Tamura, Glen Stecher, Sudhir Kumar (2021)

The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor , and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net .

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FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

Joseph Brown, Meg Pirrung, Lee McCue (2017)

Abstract Summary FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data. Availability and implementation FQC is implemented in Python 3 and Javascript, and is maintained under an MIT license. Documentation and source code is available at: https://github.com/pnnl/fqc. Contact joseph.brown@pnnl.gov

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Author and article information

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): 24 January 2024

Publication date (Electronic, collection): 2024

Publication date PMC-release: 24 January 2024

Volume: 9

Issue: 1

Pages: 148-152

Affiliations

[a ]College of Wildlife and Protected Area, Northeast Forestry University , Harbin, China

[b ]Ningxia Helan Mountain National Nature Reserve Administration , Yinchuan, China

[c ]Key Laboratory of Conservation Biology, National Forestry and Grassland Administration , Harbin, China

Author notes

Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2305406.

CONTACT Liwei Teng tenglw1975@ 123456163.com

Zhensheng Liu zhenshengliu@ 123456163.com

Yongliang Liang 409617895@ 123456qq.com College of Wildlife and Protected Area, Northeast Forestry University , Harbin 150040, China, Ningxia Helan Mountain National Nature Reserve Administration , Yinchuan 750021, China

Author information

Yao Zhao https://orcid.org/0000-0002-4405-8592

Jun Liang https://orcid.org/0009-0001-0144-9972

Jingyao Li https://orcid.org/0009-0008-3190-173X

Zhirong Zhang https://orcid.org/0000-0002-9916-2338

Yue Sun https://orcid.org/0000-0001-9964-9464

Fubin Liu https://orcid.org/0009-0001-1244-8895

Xu Zhang https://orcid.org/0009-0002-6490-3981

Yongliang Liang https://orcid.org/0000-0002-3773-7298

Liwei Teng https://orcid.org/0000-0001-6886-5201

Zhensheng Liu https://orcid.org/0000-0001-6367-6073

Article

Publisher ID: 2305406

DOI: 10.1080/23802359.2024.2305406

PMC ID: 10810644

PubMed ID: 38274853

SO-VID: 8ef826e8-4f7b-47f2-9463-cab51a6a0e5e

License:

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. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

First complete mitochondrial genome of the Alashan ground squirrel ( Spermophilus alashanicus) (Rodentia: Sciuridae) from Ningxia, China

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Genome Integrity

Most cited references 26

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

MEGA11: Molecular Evolutionary Genetics Analysis Version 11

FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

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