For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
0
views
6
references
 Top references
cited by
0
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      874
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      The complete chloroplast genome sequence of Flacourtia jangomas

      research-article

      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

          In this study, the complete chloroplast genome sequence of Flacourtia jangomas was featured from Illumina pair-end sequencing. In F. jangomas, its length was 156,223 bp, consisting of a large single copy (LSC) region of 84,233 bp, two inverted repeat (IR) copies 27,649 bp and a small single copy (SSC) region of 16,693 bp. The entire GC contents were 37%, and in the LSC, SSC, and IR regions were 35, 31, and 42%, respectively. Flacourtia jangomas has 130 unique genes, including 86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The chloroplast genomes of 12 species of Salicaceae and 1 species of Euphorbiaceae were used to construct the maximum-likelihood phylogenetic tree. It indicated that F. jangomas belongs to Salicaceae and is clustered with Flacourtia indica as sisters.

          Related collections

          Most cited references6

          • 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 10072 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 3826 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

              Christoph Hahn, Lutz Bachmann, Bastien Chevreux (2013)
              We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.
              Article 0 comments Cited 907 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): 24 September 2019
                Publication date (Electronic, collection): 2019
                Volume: 4
                Issue: 2
                Pages: 3232-3233
                Affiliations
                [a ]State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry , Beijing, China;
                [b ]Collaborative Innovation Center of Sustainable, Forestry in Southern China, Nanjing Forestry University , Nanjing, China
                Author notes
                CONTACT Zhaoshan Wang w@ 123456caf.ac.cn State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry , Beijing, China;
                Jianguo Zhang zhangjg@ 123456caf.ac.cn State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry , Beijing, China
                Author information
                https://orcid.org/0000-0002-6411-685X
                Article
                Publisher ID: 1668731
                DOI: 10.1080/23802359.2019.1668731
                PMC ID: 7707272
                SO-VID: 6bf43e02-0200-4086-a244-60fa2e7c67ec
                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: 1115
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: flacourtia jangomas,complete chloroplast genome,phylogenetic analysis
                Data availability:
                Keywords: flacourtia jangomas, complete chloroplast genome, phylogenetic analysis

                Comments

                Comment on this article