Identification of ESTs differentially expressed in green and albino mutant bamboo (Bambusa edulis) by suppressive subtractive hybridization (SSH) and microarray analysis
To gain a better understanding of gene expression in bamboo (Bambusa edulis Murno), we have used a combination of suppressive subtractive hybridization (SSH), microarray hybridization analysis, sequencing, and bioinformatics to identify bamboo genes differentially expressed in a bamboo albino mutant...
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| Veröffentlicht in: | Plant cell, tissue and organ culture tissue and organ culture, 2006-08, Vol.86 (2), p.169-175 |
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| container_title | Plant cell, tissue and organ culture |
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| creator | Lin, C.S Lai, Y.H Sun, C.W Liu, N.T Tsay, H.S Chang, W.C Chen, J.J.W |
| description | To gain a better understanding of gene expression in bamboo (Bambusa edulis Murno), we have used a combination of suppressive subtractive hybridization (SSH), microarray hybridization analysis, sequencing, and bioinformatics to identify bamboo genes differentially expressed in a bamboo albino mutant. Ten expressed sequence tags (ESTs) were found to be differentially expressed; these were isolated and sequenced. RT-PCR analysis of these ESTs supported the results of the microarray analysis. Six ESTs that were nucleus-encoded exhibited differential expression patterns in the green wild-type bamboo relative to the albino mutant. These genes (exception being the Rubisco small subunit) were non-photosynthesis-related genes. The development of a specific SSH cDNA library in which most of the chloroplast-encoded or photosynthesis-related genes had been subtracted proved to be useful for studying the function of non-photosynthesis-related genes in the albino bamboo mutants with aberrant chloroplast genome. The combined use of this SSH library with microarray analysis will provide a powerful analytical tool for future studies of the bamboo genome. |
| doi_str_mv | 10.1007/s11240-006-9105-3 |
| format | Article |
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Ten expressed sequence tags (ESTs) were found to be differentially expressed; these were isolated and sequenced. RT-PCR analysis of these ESTs supported the results of the microarray analysis. Six ESTs that were nucleus-encoded exhibited differential expression patterns in the green wild-type bamboo relative to the albino mutant. These genes (exception being the Rubisco small subunit) were non-photosynthesis-related genes. The development of a specific SSH cDNA library in which most of the chloroplast-encoded or photosynthesis-related genes had been subtracted proved to be useful for studying the function of non-photosynthesis-related genes in the albino bamboo mutants with aberrant chloroplast genome. The combined use of this SSH library with microarray analysis will provide a powerful analytical tool for future studies of the bamboo genome.</description><identifier>ISSN: 0167-6857</identifier><identifier>EISSN: 1573-5044</identifier><identifier>DOI: 10.1007/s11240-006-9105-3</identifier><identifier>CODEN: PTCEDJ</identifier><language>eng</language><publisher>Dordrecht: Springer</publisher><subject>Bambusa ; Biological and medical sciences ; Biotechnology ; chloroplast DNA ; complementary DNA ; Eukaryotic cell cultures ; expressed sequence tags ; Fundamental and applied biological sciences. Psychology ; gene expression ; genetic variation ; hybridization ; Methods. Procedures. Technologies ; microarray technology ; Miscellaneous ; molecular sequence data ; mutants ; nucleotide sequences ; photosynthesis ; Phyllostachys edulis ; plant breeding ; Plant cells and fungal cells</subject><ispartof>Plant cell, tissue and organ culture, 2006-08, Vol.86 (2), p.169-175</ispartof><rights>2006 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c330t-e5350e5b68b4b418f00e42ab3a21ff41bb6ca8514b3e351fd11f5c3e4582ec223</citedby><cites>FETCH-LOGICAL-c330t-e5350e5b68b4b418f00e42ab3a21ff41bb6ca8514b3e351fd11f5c3e4582ec223</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27923,27924</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18059784$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><creatorcontrib>Lin, C.S</creatorcontrib><creatorcontrib>Lai, Y.H</creatorcontrib><creatorcontrib>Sun, C.W</creatorcontrib><creatorcontrib>Liu, N.T</creatorcontrib><creatorcontrib>Tsay, H.S</creatorcontrib><creatorcontrib>Chang, W.C</creatorcontrib><creatorcontrib>Chen, J.J.W</creatorcontrib><title>Identification of ESTs differentially expressed in green and albino mutant bamboo (Bambusa edulis) by suppressive subtractive hybridization (SSH) and microarray analysis</title><title>Plant cell, tissue and organ culture</title><description>To gain a better understanding of gene expression in bamboo (Bambusa edulis Murno), we have used a combination of suppressive subtractive hybridization (SSH), microarray hybridization analysis, sequencing, and bioinformatics to identify bamboo genes differentially expressed in a bamboo albino mutant. Ten expressed sequence tags (ESTs) were found to be differentially expressed; these were isolated and sequenced. RT-PCR analysis of these ESTs supported the results of the microarray analysis. Six ESTs that were nucleus-encoded exhibited differential expression patterns in the green wild-type bamboo relative to the albino mutant. These genes (exception being the Rubisco small subunit) were non-photosynthesis-related genes. The development of a specific SSH cDNA library in which most of the chloroplast-encoded or photosynthesis-related genes had been subtracted proved to be useful for studying the function of non-photosynthesis-related genes in the albino bamboo mutants with aberrant chloroplast genome. The combined use of this SSH library with microarray analysis will provide a powerful analytical tool for future studies of the bamboo genome.</description><subject>Bambusa</subject><subject>Biological and medical sciences</subject><subject>Biotechnology</subject><subject>chloroplast DNA</subject><subject>complementary DNA</subject><subject>Eukaryotic cell cultures</subject><subject>expressed sequence tags</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>gene expression</subject><subject>genetic variation</subject><subject>hybridization</subject><subject>Methods. Procedures. Technologies</subject><subject>microarray technology</subject><subject>Miscellaneous</subject><subject>molecular sequence data</subject><subject>mutants</subject><subject>nucleotide sequences</subject><subject>photosynthesis</subject><subject>Phyllostachys edulis</subject><subject>plant breeding</subject><subject>Plant cells and fungal cells</subject><issn>0167-6857</issn><issn>1573-5044</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><recordid>eNpFkc-O1DAMxisEEsPCA3AiF9DuoWA3Sds5wmr_SStxmN1z5KTOEtRph6RdUd6ItySzXYmTbfnnz5a_oniP8BkBmi8JsVJQAtTlFkGX8kWxQd3IUoNSL4sNYN2Udaub18WblH5CBqXCTfH3puNhCj44msI4iNGLi91dEl3wnuOxRX2_CP59iJwSdyIM4iEyD4KGTlBvwzCK_TzRMAlLezuO4vRbjnMiwd3ch3Qm7CLSfHgSCI-ccztFctMx_7HYGLrwZ11-uttdnz0J74OLI8VISy6pX1JIb4tXnvrE757jSXF_eXF3fl3efr-6Of96WzopYSpZSw2sbd1aZRW2HoBVRVZShd4rtLZ21GpUVrLU6DtEr51kpduKXVXJk-LTqnuI46-Z02T2ITnuexp4nJPBra6wwiaDuIL51JQie3OIYU9xMQjmaIpZTTH51-ZoipF55uOzOCVHvY80uJD-D7agt02rMvdh5TyNhh5iZu53FaAEhAxIKf8BFVqZYw</recordid><startdate>20060801</startdate><enddate>20060801</enddate><creator>Lin, C.S</creator><creator>Lai, Y.H</creator><creator>Sun, C.W</creator><creator>Liu, N.T</creator><creator>Tsay, H.S</creator><creator>Chang, W.C</creator><creator>Chen, J.J.W</creator><general>Springer</general><scope>FBQ</scope><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope></search><sort><creationdate>20060801</creationdate><title>Identification of ESTs differentially expressed in green and albino mutant bamboo (Bambusa edulis) by suppressive subtractive hybridization (SSH) and microarray analysis</title><author>Lin, C.S ; Lai, Y.H ; Sun, C.W ; Liu, N.T ; Tsay, H.S ; Chang, W.C ; Chen, J.J.W</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c330t-e5350e5b68b4b418f00e42ab3a21ff41bb6ca8514b3e351fd11f5c3e4582ec223</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Bambusa</topic><topic>Biological and medical sciences</topic><topic>Biotechnology</topic><topic>chloroplast DNA</topic><topic>complementary DNA</topic><topic>Eukaryotic cell cultures</topic><topic>expressed sequence tags</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>gene expression</topic><topic>genetic variation</topic><topic>hybridization</topic><topic>Methods. Procedures. Technologies</topic><topic>microarray technology</topic><topic>Miscellaneous</topic><topic>molecular sequence data</topic><topic>mutants</topic><topic>nucleotide sequences</topic><topic>photosynthesis</topic><topic>Phyllostachys edulis</topic><topic>plant breeding</topic><topic>Plant cells and fungal cells</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lin, C.S</creatorcontrib><creatorcontrib>Lai, Y.H</creatorcontrib><creatorcontrib>Sun, C.W</creatorcontrib><creatorcontrib>Liu, N.T</creatorcontrib><creatorcontrib>Tsay, H.S</creatorcontrib><creatorcontrib>Chang, W.C</creatorcontrib><creatorcontrib>Chen, J.J.W</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><jtitle>Plant cell, tissue and organ culture</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lin, C.S</au><au>Lai, Y.H</au><au>Sun, C.W</au><au>Liu, N.T</au><au>Tsay, H.S</au><au>Chang, W.C</au><au>Chen, J.J.W</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of ESTs differentially expressed in green and albino mutant bamboo (Bambusa edulis) by suppressive subtractive hybridization (SSH) and microarray analysis</atitle><jtitle>Plant cell, tissue and organ culture</jtitle><date>2006-08-01</date><risdate>2006</risdate><volume>86</volume><issue>2</issue><spage>169</spage><epage>175</epage><pages>169-175</pages><issn>0167-6857</issn><eissn>1573-5044</eissn><coden>PTCEDJ</coden><abstract>To gain a better understanding of gene expression in bamboo (Bambusa edulis Murno), we have used a combination of suppressive subtractive hybridization (SSH), microarray hybridization analysis, sequencing, and bioinformatics to identify bamboo genes differentially expressed in a bamboo albino mutant. Ten expressed sequence tags (ESTs) were found to be differentially expressed; these were isolated and sequenced. RT-PCR analysis of these ESTs supported the results of the microarray analysis. Six ESTs that were nucleus-encoded exhibited differential expression patterns in the green wild-type bamboo relative to the albino mutant. These genes (exception being the Rubisco small subunit) were non-photosynthesis-related genes. The development of a specific SSH cDNA library in which most of the chloroplast-encoded or photosynthesis-related genes had been subtracted proved to be useful for studying the function of non-photosynthesis-related genes in the albino bamboo mutants with aberrant chloroplast genome. The combined use of this SSH library with microarray analysis will provide a powerful analytical tool for future studies of the bamboo genome.</abstract><cop>Dordrecht</cop><pub>Springer</pub><doi>10.1007/s11240-006-9105-3</doi><tpages>7</tpages></addata></record> |
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| subjects | Bambusa Biological and medical sciences Biotechnology chloroplast DNA complementary DNA Eukaryotic cell cultures expressed sequence tags Fundamental and applied biological sciences. Psychology gene expression genetic variation hybridization Methods. Procedures. Technologies microarray technology Miscellaneous molecular sequence data mutants nucleotide sequences photosynthesis Phyllostachys edulis plant breeding Plant cells and fungal cells |
| title | Identification of ESTs differentially expressed in green and albino mutant bamboo (Bambusa edulis) by suppressive subtractive hybridization (SSH) and microarray analysis |
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