Complete mitochondrial genome of  Saiga tatarica  (Ruminantia; Pecora; Bovidae) isolate Wuwei in China

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Abstract

This report described the complete mitochondrial genome of the Saiga antelope, Saiga tatarica, from the Gansu Endangered Animal Research Center (GEARC) in Gansu Province, China. The mitogenome was a circular molecule of 16,376 bps (Genbank accession number: MF497028). It contained 13 protein-coding, 22 tRNA and two rDNA genes. The protein-coding genes had ATA or ATG as the initiation codon, and were terminated by the typical stop codon TAA, except for NAD2 and NAD3. The complete mitogenome sequence would be useful for further understanding origination, evolution and conservation genetics of S. tatarica population in China.

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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Koichiro Tamura, Glen Stecher, Daniel Walter Peterson … (2013)

We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.

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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): 26 September 2017

Publication date (Electronic, collection): 2017

Volume: 2

Issue: 2

Pages: 681-682

Affiliations

[a ]College of Wildlife Resources, Northeast Forestry University , Harbin, China;

[b ]Gansu Endangered Animal Research Center, Wuwei, China ;

[c ]Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry , Beijing, China

Author notes

[*]

These authors contributed equally to this work.

CONTACT Kun Jin jk9551@ 123456sina.com Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry , Beijing, China;

Dong Zheng zhengdong89@ 123456yeah.net College of Wildlife Resources, Northeast Forestry University , Harbin, China

Article

Publisher ID: 1383199

DOI: 10.1080/23802359.2017.1383199

PMC ID: 7800055

SO-VID: e604f61a-3887-499b-bd2b-1ffc2e359379

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.

Complete mitochondrial genome of Saiga tatarica (Ruminantia; Pecora; Bovidae) isolate Wuwei in China

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Genome Integrity

Most cited references 9

The Sequence Alignment/Map format and SAMtools

Fast and accurate short read alignment with Burrows–Wheeler transform

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

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