9
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

      review-article

      Read this article at

      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

          The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost‐effective generation of high‐quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data. Commonly used molecular techniques such as DNA extraction, PCR, and DNA sequencing are within the reach of small laboratories in many countries, with the main obstacles to successful implementation being lack of funding and limited practical experience. Here we describe a successful approach that we developed to obtain DNA sequence data during a small DNA barcoding project in Indonesia.

          Related collections

          Most cited references48

          • Record: found
          • Abstract: found
          • Article: not found

          Consed: a graphical tool for sequence finishing.

          Sequencing of large clones or small genomes is generally done by the shotgun approach (Anderson et al. 1982). This has two phases: (1) a shotgun phase in which a number of reads are generated from random subclones and assembled into contigs, followed by (2) a directed, or finishing phase in which the assembly is inspected for correctness and for various kinds of data anomalies (such as contaminant reads, unremoved vector sequence, and chimeric or deleted reads), additional data are collected to close gaps and resolve low quality regions, and editing is performed to correct assembly or base-calling errors. Finishing is currently a bottleneck in large-scale sequencing efforts, and throughput gains will depend both on reducing the need for human intervention and making it as efficient as possible. We have developed a finishing tool, consed, which attempts to implement these principles. A distinguishing feature relative to other programs is the use of error probabilities from our programs phred and phrap as an objective criterion to guide the entire finishing process. More information is available at http:// www.genome.washington.edu/consed/consed. html.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            A DNA barcode for land plants.

            DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

                Bookmark

                Author and article information

                Contributors
                gill@gilldean.com
                Journal
                Appl Plant Sci
                Appl Plant Sci
                10.1002/(ISSN)2168-0450
                APS3
                Applications in Plant Sciences
                John Wiley and Sons Inc. (Hoboken )
                2168-0450
                13 July 2018
                June 2018
                : 6
                : 7 ( doiID: 10.1002/aps3.2018.6.issue-7 )
                : e01167
                Affiliations
                [ 1 ] Department of Botany University of British Columbia Vancouver V6T1Z4 British Columbia Canada
                [ 2 ] Herbarium Bogoriense Botany Division Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong 16911 Bogor West Java Indonesia
                [ 3 ]Present address: Department of Biology University of Missouri–St. Louis St. Louis Missouri 63121 USA
                [ 4 ]Present address: Zoological Society of London (ZSL) Indonesia Program Bogor 16128 Indonesia
                [ 5 ] Arnold Arboretum of Harvard University Boston Massachusetts 02131 USA
                [ 6 ]Present address: CSIRO Australian National Herbarium Canberra Australian Capital Territory 2601 Australia
                [ 7 ]Present address: University of Alaska Museum of the North Fairbanks Alaska 99775 USA
                Author notes
                [*] [* ]Author for correspondence: gill@ 123456gilldean.com
                Author information
                http://orcid.org/0000-0003-1126-8355
                http://orcid.org/0000-0002-5518-7541
                Article
                APS31167
                10.1002/aps3.1167
                6055555
                57942253-b3cd-4651-990f-c22c08661894
                Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 November 2017
                : 15 May 2018
                Page count
                Figures: 3, Tables: 1, Pages: 12, Words: 11218
                Funding
                Funded by: U.S. National Science Foundation
                Award ID: DEB‐1020868
                Categories
                Review Article
                Review Articles
                Custom metadata
                2.0
                aps31167
                June 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.4.3 mode:remove_FC converted:23.07.2018

                dna barcoding,dna sequence data,limited resources,molecular biology

                Comments

                Comment on this article