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      The complete mitochondrial genome sequence of the intertidal crab Parasesarma Tripectinis (Arthropoda, Decapoda, Sesarmidae)

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          Abstract

          Parasesarma tripectinis is known as an intertidal crab and inhabits Asian region. This crab has larval release at semilunar rhythm. Here, we report the complete sequence of the mitochondrial genome (mitogenome), which is composed of 15,612 base pair (bp) encoding 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and an A + T rich region. The nucleotide composition of P. tripectinis was G + C: 25.8%, A + T: 74.2%, with a strong AT bias. Phylogenetic analysis using whole mitogenome figured out that P. tripectinis was closely related to Sesarma neglectum which belongs to the same family Sesarmidae.

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          Basic local alignment search tool.

          Stephen F Altschul, Warren Gish, Webb Miller … (1990)
          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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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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              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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                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): 10 February 2018
                Publication date (Electronic, collection): 2018
                Volume: 3
                Issue: 1
                Pages: 193-194
                Affiliations
                [a ]School of Applied Biosciences, Kyungpook National University , Daegu, Republic of Korea;
                [b ]Department of Life Science, Silla University , Busan, Republic of Korea;
                [c ]Department of Biological Sciences Faculty of Science, King Abdulaziz University , Jeddah, Saudi Arabia;
                [d ]Department of Biology, Teachers College & Institute for Phylogenomics and Evolution Kyungpook National University , Daegu, Republic of Korea
                Author notes
                CONTACT Jae-Ho Shin jhshin@ 123456knu.ac.kr Laboratory of Molecular Microbiology, School of Applied Biosciences, Kyungpook National University , Daegu41566, Republic of Korea
                Author information
                https://orcid.org/0000-0001-6450-9787
                Article
                Publisher ID: 1437804
                DOI: 10.1080/23802359.2018.1437804
                PMC ID: 7800240
                SO-VID: b3216ce5-71ea-4b89-af20-baf0f5495fe1
                Copyright © © 2018 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, Pages: 2, Words: 1215
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: parasesarma tripectinis,intertidal crab,sesarmidae
                Data availability:
                Keywords: parasesarma tripectinis, intertidal crab, sesarmidae

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