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      Genotyping-by-Sequencing of the regional Pacific abalone ( Haliotis discus) genomes reveals population structures and patterns of gene flow

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          Abstract

          Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

              Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: VisualizationRole: Writing – original draft
                Role: Data curationRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: SoftwareRole: Writing – review & editing
                Role: MethodologyRole: Project administration
                Role: Data curationRole: Formal analysisRole: Resources
                Role: ResourcesRole: Writing – review & editing
                Role: MethodologyRole: Writing – review & editing
                Role: InvestigationRole: Methodology
                Role: ConceptualizationRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                7 April 2021
                2021
                : 16
                : 4
                : e0247815
                Affiliations
                [1 ] Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
                [2 ] Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
                [3 ] Genome, Inc, Seoul, Republic of Korea
                University of California, UNITED STATES
                Author notes

                Competing Interests: WK is affiliated with eGnome, a commercial company. This does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products associated with this research to declare.

                ‡ These authors equally contributed and should be regarded as co-first authors.

                Author information
                https://orcid.org/0000-0001-9695-5861
                https://orcid.org/0000-0003-0600-067X
                Article
                PONE-D-20-16611
                10.1371/journal.pone.0247815
                8026068
                33826655
                97ca01fc-3925-47a4-9c7b-16ab20d1f40d
                © 2021 Nam et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 2 June 2020
                : 12 February 2021
                Page count
                Figures: 3, Tables: 3, Pages: 17
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100003566, Ministry of Oceans and Fisheries;
                Award ID: No. 20180430
                Award Recipient :
                Funded by: National Institute of Fisheries Science
                Award ID: No. R2019017
                Award Recipient :
                This research was supported by the National Institute of Fisheries Science (No. R2021041 to BHN) and the Collaborative Genome Program of the Korea Institute of Marine Science and Technology Promotion funded by the Ministry of Oceans and Fisheries (No. 20180430 to BHN), Korea. WK is affiliated with eGnome, a commercial company. eGnome had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Population Genetics
                Biology and Life Sciences
                Population Biology
                Population Genetics
                People and Places
                Geographical Locations
                Asia
                Korea
                People and Places
                Geographical Locations
                Asia
                Japan
                Biology and Life Sciences
                Biochemistry
                Proteins
                Protein Domains
                Biology and Life Sciences
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
                Phylogeography
                Earth Sciences
                Geography
                Biogeography
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                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Genomics
                Biology and Life Sciences
                Conservation Biology
                Conservation Genetics
                Ecology and Environmental Sciences
                Conservation Science
                Conservation Biology
                Conservation Genetics
                Biology and Life Sciences
                Genetics
                Conservation Genetics
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                Custom metadata
                All sequencing data generated and used in this study are available on the NCBI BioProject accession PRJNA665342.

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