The complete mitochondrial genome of the Hainan Island Shrew, <i>Crocidura wuchihensis</i>

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Abstract

The Hainan Island Shrew Crocidura wuchihensis is a small-bodied insectivore species belonging to the Soricidae family. In this study, we determined its the complete mitochondrial genome. The whole mitochondrial genome was found to be 17,253 bp in length and comprises 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a control region. The base composition of the C. wuchihensis total mitogenome as follows: A, 32.8%; G, 13.0%; T, 32.1%; and C, 22.1%, with an A + T content of 64.9%. Notably, a tandem repeat sequence (5′-CAC ACG TGT ACA-3′) was identified in the control region with 24 copy numbers. Additionally, phylogenetic analysis indicated that C. wuchihensis is closely related to Crocidura tanakae and Crocidura dongyangjiangensis based on the concatenated sequences of the 13 protein-coding genes. The characterization of the shrew’s mitogenome will provide the foundation for its use in population genomics and systematic studies of Soricidae.

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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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Tandem repeats finder: a program to analyze DNA sequences.

G. Benson (1999)

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human beta T cellreceptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program.

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Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes

Alexander Donath, Frank Jühling, Marwa Al-Arab … (2019)

Abstract With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.

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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): 8 September 2023

Publication date (Electronic, collection): 2023

Publication date PMC-release: 8 September 2023

Volume: 8

Issue: 9

Pages: 973-976

Affiliations

Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University , Haikou, Hainan Province, China

Author notes

Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2023.2256054.

CONTACT Feiyun Tu tfy@ 123456hainnu.edu.cn Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University , Haikou, China.

Article

Publisher ID: 2256054

DOI: 10.1080/23802359.2023.2256054

PMC ID: 10494728

PubMed ID: 37701526

SO-VID: 1fdea05f-24fc-4bea-b03e-b30269393c3f

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.

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Figures: 3, Tables: 0, Pages: 4, Words: 2173

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