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      Chloroplast genome structure and phylogenetic position of Ruppia sinensis Shuo Yu & den Hartog

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      Author(s): a , b , c , d
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Ruppia sinensis, Illumina sequencing, chloroplast genome, phylogenetic position

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          Abstract

          Ruppia is widely distributed in marine and inland saline habitats in temperate and tropical regions. In this study, the complete chloroplast genome sequence of R. sinensis was successfully obtained using Illumina sequencing. The full length of the chloroplast genome length was 158,897 bp with a typical quadripartite structure: one large single copy (LSC) region (88,952 bp), one small single copy (SSC) region (19,047 bp), and a pair of inverted repeats (IR) (25,449 bp each). The GC content of this genome was 35.9%. The whole genome contained 136 genes, including 88 protein-coding genes, 40 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that R. sinensis formed a distinct clade, being separated from Zostera marina and Potamogeton perfoliatus.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          Kazutaka Katoh, Daron Standley (2013)
          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
          Article 0 comments Cited 12541 times – based on 0 reviews     Review now
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Alexandros Stamatakis (2014)
            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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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.
              Article 0 comments Cited 7396 times – based on 0 reviews     Review now
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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): 5 September 2019
                Publication date (Electronic, collection): 2019
                Volume: 4
                Issue: 2
                Pages: 2916-2917
                Affiliations
                [a ]Fourth Institute of Oceanography, Ministry of Natural Resources , Beihai, China;
                [b ]Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China;
                [c ]Shanghai Chenshan Botanical Garden , Shanghai, China;
                [d ]School of Ecological and Environmental Sciences, Shanghai Key Lab of Urban Ecological Processes and Eco-Restoration, East China Normal University , Shanghai, China
                Author notes
                CONTACT Kai Jiang jiangkai@ 123456csnbgsh.cn Shanghai Chenshan Botanical Garden , Chenhua Road 3888, Shanghai201602, China
                Article
                Publisher ID: 1662746
                DOI: 10.1080/23802359.2019.1662746
                PMC ID: 7706659
                PubMed ID: 33365790
                SO-VID: 88f6d8a1-81c9-4286-8558-31a5d069118e
                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.

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                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 1000
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: ruppia sinensis,illumina sequencing,chloroplast genome,phylogenetic position
                Data availability:
                Keywords: ruppia sinensis, illumina sequencing, chloroplast genome, phylogenetic position

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