Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries
To help develop an understanding of the genes that govern the developmental characteristics of the potato (Solanum tuberosum), as well as the genes associated with responses to specified pathogens and storage conditions, The Canadian Potato Genome Project (CPGP) carried out 5' end sequencing of...
Gespeichert in:
| Veröffentlicht in: | Plant molecular biology 2005-10, Vol.59 (3), p.407-433 |
|---|---|
| Hauptverfasser: | , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 433 |
|---|---|
| container_issue | 3 |
| container_start_page | 407 |
| container_title | Plant molecular biology |
| container_volume | 59 |
| creator | Flinn, B Rothwell, C Griffiths, R Lague, M DeKoeyer, D Sardana, R Audy, P Goyer, C Li, X.Q Wang-Pruski, G |
| description | To help develop an understanding of the genes that govern the developmental characteristics of the potato (Solanum tuberosum), as well as the genes associated with responses to specified pathogens and storage conditions, The Canadian Potato Genome Project (CPGP) carried out 5' end sequencing of regular, normalized and full-length cDNA libraries of the Shepody potato cultivar, generating over 66,600 expressed sequence tags (ESTs). Libraries sequenced represented tuber developmental stages, pathogen-challenged tubers, as well as leaf, floral developmental stages, suspension cultured cells and roots. All libraries analysed to date have contributed unique sequences, with the normalized libraries high on the list. In addition, a low molecular weight library has enhanced the 3' ends of our sequence assemblies. Using the combined assembly dataset, unique tuber developmental, cold storage and pathogen-challenged sequences have been identified. A comparison of the ESTs specific to the pathogen-challenged tuber and foliar libraries revealed minimal overlap between these libraries. Mixed assemblies using over 189,000 potato EST sequences from CPGP and The Institute for Genomics Research (TIGR) has revealed common sequences, as well as CPGP- and TIGR-unique sequences. |
| doi_str_mv | 10.1007/s11103-005-0185-y |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_68697380</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>68697380</sourcerecordid><originalsourceid>FETCH-LOGICAL-c447t-fb989914ecbb5c56e68790711dacdf68701bbf2d1fb453901a2187fa45a47e2f3</originalsourceid><addsrcrecordid>eNqFkcFu1DAQhi0EotvCA3ABiwO3wIwd28mxaqEgVYAEvWI5yXjlKpssnkRi3x6XXQmJCwfLsv39o_F8QrxAeIsA7h0jIugKwFSAjakOj8QGjdOVAdU8FhtA66q6RnUmzpnvAUpK26fiDK3SBqHZiB9f5yUss6Rf-0zMNEimnytNPcklbOWWJsphSfMkwzSUFcYDJ5Yrp2kreSmXIQ9_3tYplaDsrz9fyjF1OeRE_Ew8iWFken7aL8Tdh_ffrz5Wt19uPl1d3lZ9Xbulil3btC3W1Hed6Y0l27gWHOIQ-iGWA2DXRTVg7GqjW8CgsHEx1CbUjlTUF-LNse4-z6ULXvwucU_jGCaaV_a2sa3TDfwXRKfK7Jwu4Ot_wPt5zeX_7J1trTZluAXCI9TnmTlT9PucdiEfPIJ_UOSPinxR5B8U-UPJvDwVXrsdDX8TJycFeHUEYph92ObE_u6bAtRFn1WqYL8BURSVlQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>769635016</pqid></control><display><type>article</type><title>Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries</title><source>MEDLINE</source><source>SpringerLink Journals</source><creator>Flinn, B ; Rothwell, C ; Griffiths, R ; Lague, M ; DeKoeyer, D ; Sardana, R ; Audy, P ; Goyer, C ; Li, X.Q ; Wang-Pruski, G</creator><creatorcontrib>Flinn, B ; Rothwell, C ; Griffiths, R ; Lague, M ; DeKoeyer, D ; Sardana, R ; Audy, P ; Goyer, C ; Li, X.Q ; Wang-Pruski, G</creatorcontrib><description>To help develop an understanding of the genes that govern the developmental characteristics of the potato (Solanum tuberosum), as well as the genes associated with responses to specified pathogens and storage conditions, The Canadian Potato Genome Project (CPGP) carried out 5' end sequencing of regular, normalized and full-length cDNA libraries of the Shepody potato cultivar, generating over 66,600 expressed sequence tags (ESTs). Libraries sequenced represented tuber developmental stages, pathogen-challenged tubers, as well as leaf, floral developmental stages, suspension cultured cells and roots. All libraries analysed to date have contributed unique sequences, with the normalized libraries high on the list. In addition, a low molecular weight library has enhanced the 3' ends of our sequence assemblies. Using the combined assembly dataset, unique tuber developmental, cold storage and pathogen-challenged sequences have been identified. A comparison of the ESTs specific to the pathogen-challenged tuber and foliar libraries revealed minimal overlap between these libraries. Mixed assemblies using over 189,000 potato EST sequences from CPGP and The Institute for Genomics Research (TIGR) has revealed common sequences, as well as CPGP- and TIGR-unique sequences.</description><identifier>ISSN: 0167-4412</identifier><identifier>EISSN: 1573-5028</identifier><identifier>DOI: 10.1007/s11103-005-0185-y</identifier><identifier>PMID: 16235108</identifier><language>eng</language><publisher>Netherlands: Springer Nature B.V</publisher><subject>bacterial diseases of plants ; blight ; cDNA libraries ; cold storage ; common scab ; Cultivars ; Developmental stages ; disease resistance ; DNA, Complementary - chemistry ; DNA, Complementary - genetics ; Expressed Sequence Tags ; fungal diseases of plants ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Gene Library ; genomic libraries ; Genomics ; Genomics - methods ; Libraries ; Molecular weight ; Pathogens ; Phytophthora infestans ; plant development ; Potatoes ; Sequence Analysis, DNA ; Solanum tuberosum ; Solanum tuberosum - genetics ; Solanum tuberosum - growth & development ; Streptomyces scabiei ; tuber development ; tubers ; Vegetables</subject><ispartof>Plant molecular biology, 2005-10, Vol.59 (3), p.407-433</ispartof><rights>Springer 2005</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c447t-fb989914ecbb5c56e68790711dacdf68701bbf2d1fb453901a2187fa45a47e2f3</citedby><cites>FETCH-LOGICAL-c447t-fb989914ecbb5c56e68790711dacdf68701bbf2d1fb453901a2187fa45a47e2f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16235108$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Flinn, B</creatorcontrib><creatorcontrib>Rothwell, C</creatorcontrib><creatorcontrib>Griffiths, R</creatorcontrib><creatorcontrib>Lague, M</creatorcontrib><creatorcontrib>DeKoeyer, D</creatorcontrib><creatorcontrib>Sardana, R</creatorcontrib><creatorcontrib>Audy, P</creatorcontrib><creatorcontrib>Goyer, C</creatorcontrib><creatorcontrib>Li, X.Q</creatorcontrib><creatorcontrib>Wang-Pruski, G</creatorcontrib><title>Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries</title><title>Plant molecular biology</title><addtitle>Plant Mol Biol</addtitle><description>To help develop an understanding of the genes that govern the developmental characteristics of the potato (Solanum tuberosum), as well as the genes associated with responses to specified pathogens and storage conditions, The Canadian Potato Genome Project (CPGP) carried out 5' end sequencing of regular, normalized and full-length cDNA libraries of the Shepody potato cultivar, generating over 66,600 expressed sequence tags (ESTs). Libraries sequenced represented tuber developmental stages, pathogen-challenged tubers, as well as leaf, floral developmental stages, suspension cultured cells and roots. All libraries analysed to date have contributed unique sequences, with the normalized libraries high on the list. In addition, a low molecular weight library has enhanced the 3' ends of our sequence assemblies. Using the combined assembly dataset, unique tuber developmental, cold storage and pathogen-challenged sequences have been identified. A comparison of the ESTs specific to the pathogen-challenged tuber and foliar libraries revealed minimal overlap between these libraries. Mixed assemblies using over 189,000 potato EST sequences from CPGP and The Institute for Genomics Research (TIGR) has revealed common sequences, as well as CPGP- and TIGR-unique sequences.</description><subject>bacterial diseases of plants</subject><subject>blight</subject><subject>cDNA libraries</subject><subject>cold storage</subject><subject>common scab</subject><subject>Cultivars</subject><subject>Developmental stages</subject><subject>disease resistance</subject><subject>DNA, Complementary - chemistry</subject><subject>DNA, Complementary - genetics</subject><subject>Expressed Sequence Tags</subject><subject>fungal diseases of plants</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene Library</subject><subject>genomic libraries</subject><subject>Genomics</subject><subject>Genomics - methods</subject><subject>Libraries</subject><subject>Molecular weight</subject><subject>Pathogens</subject><subject>Phytophthora infestans</subject><subject>plant development</subject><subject>Potatoes</subject><subject>Sequence Analysis, DNA</subject><subject>Solanum tuberosum</subject><subject>Solanum tuberosum - genetics</subject><subject>Solanum tuberosum - growth & development</subject><subject>Streptomyces scabiei</subject><subject>tuber development</subject><subject>tubers</subject><subject>Vegetables</subject><issn>0167-4412</issn><issn>1573-5028</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqFkcFu1DAQhi0EotvCA3ABiwO3wIwd28mxaqEgVYAEvWI5yXjlKpssnkRi3x6XXQmJCwfLsv39o_F8QrxAeIsA7h0jIugKwFSAjakOj8QGjdOVAdU8FhtA66q6RnUmzpnvAUpK26fiDK3SBqHZiB9f5yUss6Rf-0zMNEimnytNPcklbOWWJsphSfMkwzSUFcYDJ5Yrp2kreSmXIQ9_3tYplaDsrz9fyjF1OeRE_Ew8iWFken7aL8Tdh_ffrz5Wt19uPl1d3lZ9Xbulil3btC3W1Hed6Y0l27gWHOIQ-iGWA2DXRTVg7GqjW8CgsHEx1CbUjlTUF-LNse4-z6ULXvwucU_jGCaaV_a2sa3TDfwXRKfK7Jwu4Ot_wPt5zeX_7J1trTZluAXCI9TnmTlT9PucdiEfPIJ_UOSPinxR5B8U-UPJvDwVXrsdDX8TJycFeHUEYph92ObE_u6bAtRFn1WqYL8BURSVlQ</recordid><startdate>20051001</startdate><enddate>20051001</enddate><creator>Flinn, B</creator><creator>Rothwell, C</creator><creator>Griffiths, R</creator><creator>Lague, M</creator><creator>DeKoeyer, D</creator><creator>Sardana, R</creator><creator>Audy, P</creator><creator>Goyer, C</creator><creator>Li, X.Q</creator><creator>Wang-Pruski, G</creator><general>Springer Nature B.V</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><scope>7QO</scope><scope>7X8</scope></search><sort><creationdate>20051001</creationdate><title>Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries</title><author>Flinn, B ; Rothwell, C ; Griffiths, R ; Lague, M ; DeKoeyer, D ; Sardana, R ; Audy, P ; Goyer, C ; Li, X.Q ; Wang-Pruski, G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c447t-fb989914ecbb5c56e68790711dacdf68701bbf2d1fb453901a2187fa45a47e2f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>bacterial diseases of plants</topic><topic>blight</topic><topic>cDNA libraries</topic><topic>cold storage</topic><topic>common scab</topic><topic>Cultivars</topic><topic>Developmental stages</topic><topic>disease resistance</topic><topic>DNA, Complementary - chemistry</topic><topic>DNA, Complementary - genetics</topic><topic>Expressed Sequence Tags</topic><topic>fungal diseases of plants</topic><topic>Gene Expression Regulation, Developmental</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene Library</topic><topic>genomic libraries</topic><topic>Genomics</topic><topic>Genomics - methods</topic><topic>Libraries</topic><topic>Molecular weight</topic><topic>Pathogens</topic><topic>Phytophthora infestans</topic><topic>plant development</topic><topic>Potatoes</topic><topic>Sequence Analysis, DNA</topic><topic>Solanum tuberosum</topic><topic>Solanum tuberosum - genetics</topic><topic>Solanum tuberosum - growth & development</topic><topic>Streptomyces scabiei</topic><topic>tuber development</topic><topic>tubers</topic><topic>Vegetables</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Flinn, B</creatorcontrib><creatorcontrib>Rothwell, C</creatorcontrib><creatorcontrib>Griffiths, R</creatorcontrib><creatorcontrib>Lague, M</creatorcontrib><creatorcontrib>DeKoeyer, D</creatorcontrib><creatorcontrib>Sardana, R</creatorcontrib><creatorcontrib>Audy, P</creatorcontrib><creatorcontrib>Goyer, C</creatorcontrib><creatorcontrib>Li, X.Q</creatorcontrib><creatorcontrib>Wang-Pruski, G</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech 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>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</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>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</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 Basic</collection><collection>Genetics Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Plant molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Flinn, B</au><au>Rothwell, C</au><au>Griffiths, R</au><au>Lague, M</au><au>DeKoeyer, D</au><au>Sardana, R</au><au>Audy, P</au><au>Goyer, C</au><au>Li, X.Q</au><au>Wang-Pruski, G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries</atitle><jtitle>Plant molecular biology</jtitle><addtitle>Plant Mol Biol</addtitle><date>2005-10-01</date><risdate>2005</risdate><volume>59</volume><issue>3</issue><spage>407</spage><epage>433</epage><pages>407-433</pages><issn>0167-4412</issn><eissn>1573-5028</eissn><abstract>To help develop an understanding of the genes that govern the developmental characteristics of the potato (Solanum tuberosum), as well as the genes associated with responses to specified pathogens and storage conditions, The Canadian Potato Genome Project (CPGP) carried out 5' end sequencing of regular, normalized and full-length cDNA libraries of the Shepody potato cultivar, generating over 66,600 expressed sequence tags (ESTs). Libraries sequenced represented tuber developmental stages, pathogen-challenged tubers, as well as leaf, floral developmental stages, suspension cultured cells and roots. All libraries analysed to date have contributed unique sequences, with the normalized libraries high on the list. In addition, a low molecular weight library has enhanced the 3' ends of our sequence assemblies. Using the combined assembly dataset, unique tuber developmental, cold storage and pathogen-challenged sequences have been identified. A comparison of the ESTs specific to the pathogen-challenged tuber and foliar libraries revealed minimal overlap between these libraries. Mixed assemblies using over 189,000 potato EST sequences from CPGP and The Institute for Genomics Research (TIGR) has revealed common sequences, as well as CPGP- and TIGR-unique sequences.</abstract><cop>Netherlands</cop><pub>Springer Nature B.V</pub><pmid>16235108</pmid><doi>10.1007/s11103-005-0185-y</doi><tpages>27</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0167-4412 |
| ispartof | Plant molecular biology, 2005-10, Vol.59 (3), p.407-433 |
| issn | 0167-4412 1573-5028 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_68697380 |
| source | MEDLINE; SpringerLink Journals |
| subjects | bacterial diseases of plants blight cDNA libraries cold storage common scab Cultivars Developmental stages disease resistance DNA, Complementary - chemistry DNA, Complementary - genetics Expressed Sequence Tags fungal diseases of plants Gene Expression Regulation, Developmental Gene Expression Regulation, Plant Gene Library genomic libraries Genomics Genomics - methods Libraries Molecular weight Pathogens Phytophthora infestans plant development Potatoes Sequence Analysis, DNA Solanum tuberosum Solanum tuberosum - genetics Solanum tuberosum - growth & development Streptomyces scabiei tuber development tubers Vegetables |
| title | Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-09T04%3A32%3A14IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Potato%20expressed%20sequence%20tag%20generation%20and%20analysis%20using%20standard%20and%20unique%20cDNA%20libraries&rft.jtitle=Plant%20molecular%20biology&rft.au=Flinn,%20B&rft.date=2005-10-01&rft.volume=59&rft.issue=3&rft.spage=407&rft.epage=433&rft.pages=407-433&rft.issn=0167-4412&rft.eissn=1573-5028&rft_id=info:doi/10.1007/s11103-005-0185-y&rft_dat=%3Cproquest_cross%3E68697380%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=769635016&rft_id=info:pmid/16235108&rfr_iscdi=true |