For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
3
views
14
references
 Top references
cited by
3
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      701
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Complete chloroplast genome of Pluchea indica (L.) Less. (Asteraceae) and its phylogenetic analysis

      research-article
      Author(s): , , ,
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Chloroplast genome, illumine sequencing, Pluchea indica (L.) Less, phylogenetic analysis

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          This study presents the chloroplast genome of Pluchea indica(L.) Less, Asteraceae, one wide distributed species of mangrove associates plant in China, which was assembled and analyzed by de novo assembly using whole-genome sequencing data. The accessing NC_015621 was used as a reference sequence in this study. The size of the complete chloroplast genome was found to be 152,298 bp in length, comprising a large single copy region (LSC) of 84,127bp, a small single copy region (SSC) 18,068 bp, and inverted repeat regions (IRS) of 25,051bp. A total of 128 genes, including 84 protein-coding genes, 36 tRNA genes and eight rRNA genes, were predicted from the chloroplast genomes. Among them, 17 genes occur in IRS, containing six protein-coding genes, seven tRNA genes and four rRNA genes. The GC content of P. indica is 37.49%. The phylogenetic analysis with four Asterids species and five other species revealed that P. indica was clusted with Ageratina adenophora.

          Related collections

          Most cited references14

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          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 10162 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            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.
            Article 0 comments Cited 7243 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Matthew Kearse, Richard Moir, Amy Wilson … (2012)
              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
              Article 0 comments Cited 3854 times – based on 0 reviews     Review now
                Bookmark
                All references

                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): 7 December 2017
                Publication date (Electronic, collection): 2017
                Volume: 2
                Issue: 2
                Pages: 918-919
                Affiliations
                Key Laboratory of Tripical Animal and Plant Ecology, Ministry of Education, College of Life Science, Hainan Normal University , Haikou, China
                Author notes
                CONTACT Qiang Liu hnsylq@ 123456163.com Key Laboratory of Tripical Animal and Plant Ecology, Ministry of Education, College of Life Science, Hainan Normal University , Haikou, China
                Article
                Publisher ID: 1413299
                DOI: 10.1080/23802359.2017.1413299
                PMC ID: 7800182
                PubMed ID: 33474035
                SO-VID: 786825ba-c172-449a-b830-2348b5edfee4
                Copyright © © 2017 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: 1342
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: chloroplast genome,illumine sequencing,pluchea indica (l.) less,phylogenetic analysis
                Data availability:
                Keywords: chloroplast genome, illumine sequencing, pluchea indica (l.) less, phylogenetic analysis

                Comments

                Comment on this article

                scite_

                Similar content701

                See all similar

                Cited by3

                See all cited by

                Most referenced authors399

                See all reference authors