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      Characterization of the complete mitochondrial genome of the Chong’an Moustache Toad, Leptobrachium liui (Pope, 1947) with a phylogenetic analysis of Megophryidae

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          Abstract

          The Chong’an Mustache Toad, Leptobrachium liui (Pope, 1947) is a Chinese endemic species, inhabiting the mountain streams with rich vegetation in southeastern China. The first complete mitochondrial genome (mitogenome) of L. liui was assembled using the data of whole-genome sequencing. The size of the complete mitogenome for L. liui was 17,190 bp, which included 13 PCGs, 23 tRNAs with two concatenated tRNA Met genes, 2 rRNAs, a non-coding region, and a D-loop. The Bayesian tree shows that L. liui was positioned near L. leishanense within the genus Leptobrachium.

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          MITOS: improved de novo metazoan mitochondrial genome annotation.

          Matthias Bernt, Alexander Donath, Frank Jühling … (2013)
          About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.
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            NOVOPlasty: de novo assembly of organelle genomes from whole genome data

            Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits (2016)
            Abstract The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.
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              tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.

              Patricia P. Chan, Todd Lowe (2019)
              Transfer RNAs are the largest, most complex non-coding RNA family, universal to all living organisms. tRNAscan-SE has been the de facto tool for predicting tRNA genes in whole genomes. The newly developed version 2.0 has incorporated advanced methodologies with improved probabilistic search software and a suite of new gene models, enabling better functional classification of predicted genes. This chapter describes the use of the UNIX command-driven and online web versions, illustrating different search modes and options.
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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): 19 March 2021
                Publication date (Electronic, collection): 2021
                Volume: 6
                Issue: 3
                Pages: 1061-1063
                Affiliations
                [a ]Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University , Lishui, China
                [b ]Administration Center of Jiulongshan National Nature Reserve , Suichang, China
                [c ]Development Center of Suichang Ecological Forestry , Suichang, China
                [d ]School of Basic Medical Science, Hubei University of Chinese Medicine , Wuhan, China
                Author notes
                CONTACT Guo-Hua Ding guwoding@ 123456lsu.edu.cn Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University , Lishui 323000, China
                Author information
                https://orcid.org/0000-0002-9295-1684
                https://orcid.org/0000-0002-9571-9864
                Article
                Publisher ID: 1899080
                DOI: 10.1080/23802359.2021.1899080
                PMC ID: 7995853
                SO-VID: 858e8dce-7fce-468c-80ea-6819237eb06c
                Copyright © © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                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.

                History
                Page count
                Figures: 1, Tables: 0, Pages: 3, Words: 1289
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: megophryidae,leptobrachium liui (pope,1947),mitochondrial genome,phylogenetic analysis,whole-genome sequencing
                Data availability:
                Keywords: megophryidae, leptobrachium liui (pope, 1947), mitochondrial genome, phylogenetic analysis, whole-genome sequencing

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