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      The complete mitochondrial genome of longlegged spiny lobster Panulirus longipes (A. Milne Edwards, 1868)

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      Author(s): a , b , b
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Panulirus longipes, mitochondrial genome, phylogenetic analysis

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          Abstract

          In this study, we first determined and characterized the complete mitochondrial genome of longlegged spiny lobster Panulirus longipes from South China Sea. The P. longipes mitogenome is 15,739 bp long, and consists of 22 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), and one control region. The nucleotide composition of P. longipes mitogenome is significantly biased (A, G, T, and C was 32.06%, 14.36%, 32.42%, and 21.16%, respectively) with A + T contents of 64.48%. Among 13 PCGs, COX1 gene used an unusual initiation codon CAA, COX1, COX2, ND4 and CYTB genes were ended with an incomplete stop codon T, and ND5 gene with an abnormal stop codon ATT. One microsatellite (C) 10 was identified in P. longipes mitogenome located in the control region. Phylogenetic tree showed that P. longipes was first clustered with Panulirus cygnus, then together with P. japonicus and P. argus.

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          SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

          Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)
          The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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            MISA-web: a web server for microsatellite prediction

            Sebastian Beier, Thomas Thiel, Thomas Münch … (2017)
            Abstract Motivation Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging. Results We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis. Availability and Implementation MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code. Contact scholz@ipk-gatersleben.de
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              Molecular phylogeny of the spiny lobster genus Panulirus (Decapoda: Palinuridae)

              Margaret Ptacek, Shane Sarver, Michael J. Childress … (2001)
              Phylogenetic relationships among all described species and four subspecies (total of 21 taxa) of the spiny lobster genus Panulirus White, 1847, were examined with nucleotide sequence data from portions of two mitochondrial genes, large-subunit ribosomal RNA (16S) and cytochrome oxidase subunit I (COI). Multiple sequence alignments were subjected to maximum-parsimony, neighbour-joining, and maximum-likelihood analysis with Jasus edwardsii as the outgroup. Two major lineages within Panulirus were recovered by all three methods for both the 16S and COI alignments analysed separately and for the combined alignment. The first lineage included all species of Panulirus classified as Groups I and II by previous morphologically based definitions. The second included all species classified as Groups III and IV. Relationships within major lineages were not well resolved; the molecular phylogeny did not support separation of Group I from Group II or of Group III from Group IV. The degree of sequence divergence between different pairs of species was higher in pairwise comparisons between species in Group I/II (16S: 2.8–19.4%; COI: 12.4–31.8%) than in those between species in Group III/IV (16S: 5.3–13.2%; COI: 12.6–19.6%). This pattern suggests that the Group I/II lineage may represent an earlier radiation of species within Panulirus.
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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): 1 March 2021
                Publication date (Electronic, collection): 2021
                Volume: 6
                Issue: 2
                Pages: 660-662
                Affiliations
                [a ]Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education , Sanya, China
                [b ]Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences , Haikou, China
                Author notes
                CONTACT Hongtao Liu xmulht@ 123456gmail.com;
                Liyun Pu puliyun@ 123456163.com Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences , Haikou, China

                Supplemental data for this article can be accessed here .

                Article
                Publisher ID: 1878952
                DOI: 10.1080/23802359.2021.1878952
                PMC ID: 7928049
                SO-VID: 2b3aca01-502c-476b-a36c-7e7d13b0f702
                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 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: 3, Words: 1346
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: panulirus longipes,mitochondrial genome,phylogenetic analysis
                Data availability:
                Keywords: panulirus longipes, mitochondrial genome, phylogenetic analysis

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