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      Characterization of the complete mitochondrial genome of a holothurians species: Holothuria hilla (Holothuroidea: Holothuriidae)

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          Abstract

          Mitochondrial genome sequence is a great potential method to both resolve disputed taxonomic issues and to infer phylogenetic relationships among holothurians. In this study, we present the complete mitochondrial genome of Holothuria hilla which was 15,744 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. The gene content and arrangement were typical for Holothuroidea ground pattern. The overall base composition was 32.43% A, 27.20% T, 24.35% C and 16.02% G, showing a bias toward A + T (59.63%). The maximum-likelihood tree based on the concatenated 13 protein-coding genes revealed the phylogenetic relationships among the Holothuroidea species.

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          MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

          K Tamura, D. Peterson, N. Peterson … (2011)
          Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
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            tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

            Todd Lowe, Sean R. Eddy (1997)
            We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
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              Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata.

              Marleen Perseke, Detlef Bernhard, Guido Fritzsch … (2010)
              The genome architecture and amino acid sequences of six new complete mitochondrial genomes were determined from representatives of Hemichordata (1), Ophiuroidea (3), Echinoidea (1) and Holothuroidea (1) and were analysed together with previously known sequences. Phylogenetic analyses recovered three lineages within echinoderms, Crinoidea, Ophiuroidea and a group comprising Holothuroidea, Echinoidea, and Asteroidea. In contrast to previous analyses of mitochondrial genomes the increased data set recovered the classical echinoderm phylogeny of Eleutherozoa and Echinozoa in Maximum Likelihood and Bayesian analyses using hemichordate out-group representatives. However, an inconsistent ramification appeared with vertebrate out-groups and in Maximum Parsimony and Neighbour Joining reconstructions. The basal (consensus) gene orders of all three lineages could be derived from a hypothetical ancestral crinoid gene order by one single rearrangement in each lineage. The genome architecture was highly conserved in Echinoidea, whereas the highest gene order differences and large amounts of unassigned sequences (UAS) were detected in Ophiuroidea, supporting a higher evolutionary rate than in any other echinoderm lineage. The variability in gene order and UAS regions in ophiuroid genomes suggest dominating rearrangement mechanisms by duplication events. Copyright 2010 Elsevier Inc. All rights reserved.
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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): 3 September 2019
                Publication date (Electronic, collection): 2019
                Volume: 4
                Issue: 2
                Pages: 2847-2848
                Affiliations
                [a ]Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian , Xiamen, China;
                [b ]Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University , Shantou, China
                Author notes
                CONTACT Chen Zhou qhyang1314@ 123456163.com Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian , Xiamen, 361021, China
                Article
                Publisher ID: 1660267
                DOI: 10.1080/23802359.2019.1660267
                PMC ID: 7706501
                SO-VID: a3a0d65a-91a3-4863-a62a-93a393866ef9
                Copyright © © 2019 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 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.

                History
                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 1312
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: holothuria hilla,mitochondrial genome,phylogenetic analysis
                Data availability:
                Keywords: holothuria hilla, mitochondrial genome, phylogenetic analysis

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