Approaches to variant discovery for conifer transcriptome sequencing

There is a wide diversity of bioinformatic tools available for the assembly of next generation sequence and subsequence variant calling to identify genetic markers at scale. Integration of genomics tools such as genomic selection, association studies, pedigree analysis and analysis of genetic divers...

Full description

Saved in:
Bibliographic Details
Published in:PloS one 2018-11, Vol.13 (11), p.e0205835-e0205835
Main Authors: Telfer, Emily, Graham, Natalie, Macdonald, Lucy, Sturrock, Shane, Wilcox, Phillip, Stanbra, Lisa
Format: Article
Language:English
Subjects:
Bioinformatics
Biology and Life Sciences
Breeding
Computer and Information Sciences
Conifers
Datasets
Deoxyribonucleic acid
DNA
Engineering and Technology
Exons
Gene expression
Gene polymorphism
Gene sequencing
Genetic analysis
Genetic diversity
Genetic markers
Genetics
Genomes
Genomics
Genotypes
Introduced species
Markers
Molecular biology
Pedigree
Pine trees
Polymorphism
Realignment
Research and Analysis Methods
Ribonucleic acid
RNA
Single-nucleotide polymorphism
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c526t-3c9afe4ae17eb8d1cde51f3f3ef09332fd67fc535fdd66c0d518325d75a81ad53
cites cdi_FETCH-LOGICAL-c526t-3c9afe4ae17eb8d1cde51f3f3ef09332fd67fc535fdd66c0d518325d75a81ad53
container_end_page e0205835
container_issue 11
container_start_page e0205835
container_title PloS one
container_volume 13
creator Telfer, Emily
Graham, Natalie
Macdonald, Lucy
Sturrock, Shane
Wilcox, Phillip
Stanbra, Lisa
description There is a wide diversity of bioinformatic tools available for the assembly of next generation sequence and subsequence variant calling to identify genetic markers at scale. Integration of genomics tools such as genomic selection, association studies, pedigree analysis and analysis of genetic diversity, into operational breeding is a goal for New Zealand's most widely planted exotic tree species, Pinus radiata. In the absence of full reference genomes for large megagenomes such as in conifers, RNA sequencing in a range of genotypes and tissue types, offers a rich source of genetic markers for downstream application. We compared nine different assembler and variant calling software combinations in a single transcriptomic library and found that Single Nucleotide Polymorphism (SNPs) discovery could vary by as much as an order of magnitude (8,061 SNPs up to 86,815 SNPs). The assembler with the best realignment of the packages trialled, Trinity, in combination with several variant callers was then applied to a much larger multi-genotype, multi-tissue transcriptome and identified 683,135 in silico SNPs across a predicted 449,951 exons when mapped to the Pinus taeda ver 1.01e reference.
doi_str_mv 10.1371/journal.pone.0205835
format article
fullrecord <record><control><sourceid>proquest_plos_</sourceid><recordid>TN_cdi_plos_journals_2130051991</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><doaj_id>oai_doaj_org_article_ff8cf1259f8248f4a84113413127c9df</doaj_id><sourcerecordid>2130302231</sourcerecordid><originalsourceid>FETCH-LOGICAL-c526t-3c9afe4ae17eb8d1cde51f3f3ef09332fd67fc535fdd66c0d518325d75a81ad53</originalsourceid><addsrcrecordid>eNptUsFu1DAUtBCIloU_QBCJSy-7-PnFjnNBqkqBSpW4wNly7edtVlk72NmV-vfNsmnVIk627HnzZkbD2HvgK8AGPm_SLkfbr4YUacUFlxrlC3YKLYqlEhxfPrmfsDelbDiXqJV6zU6QYysViFP29XwYcrLulko1pmpvc2fjWPmuuLSnfFeFlCuXYhcoV2O2sbjcDWPaUlXoz46i6-L6LXsVbF_o3Xwu2O9vl78ufiyvf36_uji_Xjop1LhE19pAtSVo6EZ7cJ4kBAxIgbeIInjVBCdRBu-VctxL0Cikb6TVYL3EBft45B36VMwcQDECcLIGbQsT4uqI8MluzJC7rc13JtnO_H1IeW1sHjvXkwlBuwBCtkGLWofa6hoAa0AQjWt9mLi-zNt2N1vyjuLkv39G-vwndrdmnfZGCdB8injBzmaCnKaoymi2U6zU9zZS2h11IxcCD7o__QP9v7v6iHI5lZIpPIoBbg6leJgyh1KYuRTT2IenRh6HHlqA90vZtj8</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2130051991</pqid></control><display><type>article</type><title>Approaches to variant discovery for conifer transcriptome sequencing</title><source>Open Access: PubMed Central</source><source>ProQuest - Publicly Available Content Database</source><creator>Telfer, Emily ; Graham, Natalie ; Macdonald, Lucy ; Sturrock, Shane ; Wilcox, Phillip ; Stanbra, Lisa</creator><contributor>Antoniewski, Christophe</contributor><creatorcontrib>Telfer, Emily ; Graham, Natalie ; Macdonald, Lucy ; Sturrock, Shane ; Wilcox, Phillip ; Stanbra, Lisa ; Antoniewski, Christophe</creatorcontrib><description>There is a wide diversity of bioinformatic tools available for the assembly of next generation sequence and subsequence variant calling to identify genetic markers at scale. Integration of genomics tools such as genomic selection, association studies, pedigree analysis and analysis of genetic diversity, into operational breeding is a goal for New Zealand's most widely planted exotic tree species, Pinus radiata. In the absence of full reference genomes for large megagenomes such as in conifers, RNA sequencing in a range of genotypes and tissue types, offers a rich source of genetic markers for downstream application. We compared nine different assembler and variant calling software combinations in a single transcriptomic library and found that Single Nucleotide Polymorphism (SNPs) discovery could vary by as much as an order of magnitude (8,061 SNPs up to 86,815 SNPs). The assembler with the best realignment of the packages trialled, Trinity, in combination with several variant callers was then applied to a much larger multi-genotype, multi-tissue transcriptome and identified 683,135 in silico SNPs across a predicted 449,951 exons when mapped to the Pinus taeda ver 1.01e reference.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0205835</identifier><identifier>PMID: 30395612</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Bioinformatics ; Biology and Life Sciences ; Breeding ; Computer and Information Sciences ; Conifers ; Datasets ; Deoxyribonucleic acid ; DNA ; Engineering and Technology ; Exons ; Gene expression ; Gene polymorphism ; Gene sequencing ; Genetic analysis ; Genetic diversity ; Genetic markers ; Genetics ; Genomes ; Genomics ; Genotypes ; Introduced species ; Markers ; Molecular biology ; Pedigree ; Pine trees ; Polymorphism ; Realignment ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; Single-nucleotide polymorphism</subject><ispartof>PloS one, 2018-11, Vol.13 (11), p.e0205835-e0205835</ispartof><rights>2018 Telfer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2018 Telfer et al 2018 Telfer et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-3c9afe4ae17eb8d1cde51f3f3ef09332fd67fc535fdd66c0d518325d75a81ad53</citedby><cites>FETCH-LOGICAL-c526t-3c9afe4ae17eb8d1cde51f3f3ef09332fd67fc535fdd66c0d518325d75a81ad53</cites><orcidid>0000-0001-5269-6589</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2130051991/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2130051991?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30395612$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Antoniewski, Christophe</contributor><creatorcontrib>Telfer, Emily</creatorcontrib><creatorcontrib>Graham, Natalie</creatorcontrib><creatorcontrib>Macdonald, Lucy</creatorcontrib><creatorcontrib>Sturrock, Shane</creatorcontrib><creatorcontrib>Wilcox, Phillip</creatorcontrib><creatorcontrib>Stanbra, Lisa</creatorcontrib><title>Approaches to variant discovery for conifer transcriptome sequencing</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>There is a wide diversity of bioinformatic tools available for the assembly of next generation sequence and subsequence variant calling to identify genetic markers at scale. Integration of genomics tools such as genomic selection, association studies, pedigree analysis and analysis of genetic diversity, into operational breeding is a goal for New Zealand's most widely planted exotic tree species, Pinus radiata. In the absence of full reference genomes for large megagenomes such as in conifers, RNA sequencing in a range of genotypes and tissue types, offers a rich source of genetic markers for downstream application. We compared nine different assembler and variant calling software combinations in a single transcriptomic library and found that Single Nucleotide Polymorphism (SNPs) discovery could vary by as much as an order of magnitude (8,061 SNPs up to 86,815 SNPs). The assembler with the best realignment of the packages trialled, Trinity, in combination with several variant callers was then applied to a much larger multi-genotype, multi-tissue transcriptome and identified 683,135 in silico SNPs across a predicted 449,951 exons when mapped to the Pinus taeda ver 1.01e reference.</description><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Breeding</subject><subject>Computer and Information Sciences</subject><subject>Conifers</subject><subject>Datasets</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Engineering and Technology</subject><subject>Exons</subject><subject>Gene expression</subject><subject>Gene polymorphism</subject><subject>Gene sequencing</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Introduced species</subject><subject>Markers</subject><subject>Molecular biology</subject><subject>Pedigree</subject><subject>Pine trees</subject><subject>Polymorphism</subject><subject>Realignment</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Single-nucleotide polymorphism</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptUsFu1DAUtBCIloU_QBCJSy-7-PnFjnNBqkqBSpW4wNly7edtVlk72NmV-vfNsmnVIk627HnzZkbD2HvgK8AGPm_SLkfbr4YUacUFlxrlC3YKLYqlEhxfPrmfsDelbDiXqJV6zU6QYysViFP29XwYcrLulko1pmpvc2fjWPmuuLSnfFeFlCuXYhcoV2O2sbjcDWPaUlXoz46i6-L6LXsVbF_o3Xwu2O9vl78ufiyvf36_uji_Xjop1LhE19pAtSVo6EZ7cJ4kBAxIgbeIInjVBCdRBu-VctxL0Cikb6TVYL3EBft45B36VMwcQDECcLIGbQsT4uqI8MluzJC7rc13JtnO_H1IeW1sHjvXkwlBuwBCtkGLWofa6hoAa0AQjWt9mLi-zNt2N1vyjuLkv39G-vwndrdmnfZGCdB8injBzmaCnKaoymi2U6zU9zZS2h11IxcCD7o__QP9v7v6iHI5lZIpPIoBbg6leJgyh1KYuRTT2IenRh6HHlqA90vZtj8</recordid><startdate>20181105</startdate><enddate>20181105</enddate><creator>Telfer, Emily</creator><creator>Graham, Natalie</creator><creator>Macdonald, Lucy</creator><creator>Sturrock, Shane</creator><creator>Wilcox, Phillip</creator><creator>Stanbra, Lisa</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-5269-6589</orcidid></search><sort><creationdate>20181105</creationdate><title>Approaches to variant discovery for conifer transcriptome sequencing</title><author>Telfer, Emily ; Graham, Natalie ; Macdonald, Lucy ; Sturrock, Shane ; Wilcox, Phillip ; Stanbra, Lisa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-3c9afe4ae17eb8d1cde51f3f3ef09332fd67fc535fdd66c0d518325d75a81ad53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Breeding</topic><topic>Computer and Information Sciences</topic><topic>Conifers</topic><topic>Datasets</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Engineering and Technology</topic><topic>Exons</topic><topic>Gene expression</topic><topic>Gene polymorphism</topic><topic>Gene sequencing</topic><topic>Genetic analysis</topic><topic>Genetic diversity</topic><topic>Genetic markers</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Genotypes</topic><topic>Introduced species</topic><topic>Markers</topic><topic>Molecular biology</topic><topic>Pedigree</topic><topic>Pine trees</topic><topic>Polymorphism</topic><topic>Realignment</topic><topic>Research and Analysis Methods</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Single-nucleotide polymorphism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Telfer, Emily</creatorcontrib><creatorcontrib>Graham, Natalie</creatorcontrib><creatorcontrib>Macdonald, Lucy</creatorcontrib><creatorcontrib>Sturrock, Shane</creatorcontrib><creatorcontrib>Wilcox, Phillip</creatorcontrib><creatorcontrib>Stanbra, Lisa</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing &amp; Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological &amp; Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health &amp; Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science &amp; Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>Advanced Technologies &amp; Aerospace Collection</collection><collection>Agricultural &amp; Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing &amp; Allied Health Database (Alumni Edition)</collection><collection>Meteorological &amp; Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agriculture Science Database</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>ProQuest Biological Science Journals</collection><collection>Engineering Database</collection><collection>Nursing &amp; Allied Health Premium</collection><collection>ProQuest advanced technologies &amp; aerospace journals</collection><collection>ProQuest Advanced Technologies &amp; Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials science collection</collection><collection>ProQuest - Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Telfer, Emily</au><au>Graham, Natalie</au><au>Macdonald, Lucy</au><au>Sturrock, Shane</au><au>Wilcox, Phillip</au><au>Stanbra, Lisa</au><au>Antoniewski, Christophe</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Approaches to variant discovery for conifer transcriptome sequencing</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2018-11-05</date><risdate>2018</risdate><volume>13</volume><issue>11</issue><spage>e0205835</spage><epage>e0205835</epage><pages>e0205835-e0205835</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>There is a wide diversity of bioinformatic tools available for the assembly of next generation sequence and subsequence variant calling to identify genetic markers at scale. Integration of genomics tools such as genomic selection, association studies, pedigree analysis and analysis of genetic diversity, into operational breeding is a goal for New Zealand's most widely planted exotic tree species, Pinus radiata. In the absence of full reference genomes for large megagenomes such as in conifers, RNA sequencing in a range of genotypes and tissue types, offers a rich source of genetic markers for downstream application. We compared nine different assembler and variant calling software combinations in a single transcriptomic library and found that Single Nucleotide Polymorphism (SNPs) discovery could vary by as much as an order of magnitude (8,061 SNPs up to 86,815 SNPs). The assembler with the best realignment of the packages trialled, Trinity, in combination with several variant callers was then applied to a much larger multi-genotype, multi-tissue transcriptome and identified 683,135 in silico SNPs across a predicted 449,951 exons when mapped to the Pinus taeda ver 1.01e reference.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>30395612</pmid><doi>10.1371/journal.pone.0205835</doi><orcidid>https://orcid.org/0000-0001-5269-6589</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1932-6203
ispartof PloS one, 2018-11, Vol.13 (11), p.e0205835-e0205835
issn 1932-6203
1932-6203
language eng
recordid cdi_plos_journals_2130051991
source Open Access: PubMed Central; ProQuest - Publicly Available Content Database
subjects Bioinformatics
Biology and Life Sciences
Breeding
Computer and Information Sciences
Conifers
Datasets
Deoxyribonucleic acid
DNA
Engineering and Technology
Exons
Gene expression
Gene polymorphism
Gene sequencing
Genetic analysis
Genetic diversity
Genetic markers
Genetics
Genomes
Genomics
Genotypes
Introduced species
Markers
Molecular biology
Pedigree
Pine trees
Polymorphism
Realignment
Research and Analysis Methods
Ribonucleic acid
RNA
Single-nucleotide polymorphism
title Approaches to variant discovery for conifer transcriptome sequencing
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-27T12%3A14%3A19IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Approaches%20to%20variant%20discovery%20for%20conifer%20transcriptome%20sequencing&rft.jtitle=PloS%20one&rft.au=Telfer,%20Emily&rft.date=2018-11-05&rft.volume=13&rft.issue=11&rft.spage=e0205835&rft.epage=e0205835&rft.pages=e0205835-e0205835&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0205835&rft_dat=%3Cproquest_plos_%3E2130302231%3C/proquest_plos_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c526t-3c9afe4ae17eb8d1cde51f3f3ef09332fd67fc535fdd66c0d518325d75a81ad53%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2130051991&rft_id=info:pmid/30395612&rfr_iscdi=true