Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)
microRNAs (miRNAs) are a recently discovered class of small (~21 nt) endogenous gene regulators that have been shown to play an important role in plant growth and development by aiding in organ maturation, hormone signaling, tissue differentiation, and plant tolerance to environmental stress. Since...
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| Veröffentlicht in: | Planta 2010-11, Vol.232 (6), p.1289-1308 |
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| creator | Frazier, Taylor P Xie, Fuliang Freistaedter, Andrew Burklew, Caitlin E Zhang, Baohong |
| description | microRNAs (miRNAs) are a recently discovered class of small (~21 nt) endogenous gene regulators that have been shown to play an important role in plant growth and development by aiding in organ maturation, hormone signaling, tissue differentiation, and plant tolerance to environmental stress. Since a list of miRNAs has never been generated for tobacco, we employed genome survey sequence analysis to computationally identify 259 potentially conserved tobacco miRNAs, belonging to 65 families, and validated 11 of these miRNAs using qRT-PCR. The 65 miRNA families were dramatically different in size. miRNA precursor (pre-miRNA) sequence analysis showed that tobacco pre-miRNAs greatly varied from 45 to 635 nt in length with an average of 141 ± 108 nt. We were also able to determine the presence of antisense miRNAs as well as miRNA clusters in tobacco. Using previously established protocols, a total of 1,225 potential target genes were predicted for the newly identified tobacco miRNAs. These target genes include transcription factors, DNA replication proteins, metabolic enzymes, as well as other gene targets necessary for proper plant maturation. The results of this study show that conserved miRNAs exist in tobacco and suggest that these miRNAs may play an important role in tobacco growth and development. |
| doi_str_mv | 10.1007/s00425-010-1255-1 |
| format | Article |
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Since a list of miRNAs has never been generated for tobacco, we employed genome survey sequence analysis to computationally identify 259 potentially conserved tobacco miRNAs, belonging to 65 families, and validated 11 of these miRNAs using qRT-PCR. The 65 miRNA families were dramatically different in size. miRNA precursor (pre-miRNA) sequence analysis showed that tobacco pre-miRNAs greatly varied from 45 to 635 nt in length with an average of 141 ± 108 nt. We were also able to determine the presence of antisense miRNAs as well as miRNA clusters in tobacco. Using previously established protocols, a total of 1,225 potential target genes were predicted for the newly identified tobacco miRNAs. These target genes include transcription factors, DNA replication proteins, metabolic enzymes, as well as other gene targets necessary for proper plant maturation. The results of this study show that conserved miRNAs exist in tobacco and suggest that these miRNAs may play an important role in tobacco growth and development.</description><identifier>ISSN: 0032-0935</identifier><identifier>EISSN: 1432-2048</identifier><identifier>DOI: 10.1007/s00425-010-1255-1</identifier><identifier>PMID: 20803216</identifier><identifier>CODEN: PLANAB</identifier><language>eng</language><publisher>Berlin/Heidelberg: Berlin/Heidelberg : Springer-Verlag</publisher><subject>Agriculture ; Antisense ; Base Sequence ; Biological and medical sciences ; Biomedical and Life Sciences ; Comparative genomics ; DNA Primers ; Ecology ; Environmental stress ; Forestry ; Fundamental and applied biological sciences. Psychology ; Gene cluster ; Genes ; Genes, Plant ; Genome survey sequence ; Genomes ; Homolog ; Life Sciences ; Mathematical sequences ; Messenger RNA ; MicroRNA ; MicroRNAs - genetics ; Multigene Family ; Nicotiana ; Nicotiana - genetics ; Nucleotides ; Original Article ; Plant growth ; Plant Sciences ; Plants ; Reverse Transcriptase Polymerase Chain Reaction ; Rice ; Target ; Tobacco ; Transcription factors</subject><ispartof>Planta, 2010-11, Vol.232 (6), p.1289-1308</ispartof><rights>Springer-Verlag Berlin Heidelberg 2010</rights><rights>Springer-Verlag 2010</rights><rights>2015 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c446t-562f416756941b6da3164bcda5a4c3d4379fe19646af995d8ea5bbf72500ad083</citedby><cites>FETCH-LOGICAL-c446t-562f416756941b6da3164bcda5a4c3d4379fe19646af995d8ea5bbf72500ad083</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/23391898$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/23391898$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,27901,27902,41464,42533,51294,57992,58225</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23419840$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20803216$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Frazier, Taylor P</creatorcontrib><creatorcontrib>Xie, Fuliang</creatorcontrib><creatorcontrib>Freistaedter, Andrew</creatorcontrib><creatorcontrib>Burklew, Caitlin E</creatorcontrib><creatorcontrib>Zhang, Baohong</creatorcontrib><title>Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)</title><title>Planta</title><addtitle>Planta</addtitle><addtitle>Planta</addtitle><description>microRNAs (miRNAs) are a recently discovered class of small (~21 nt) endogenous gene regulators that have been shown to play an important role in plant growth and development by aiding in organ maturation, hormone signaling, tissue differentiation, and plant tolerance to environmental stress. 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The results of this study show that conserved miRNAs exist in tobacco and suggest that these miRNAs may play an important role in tobacco growth and development.</description><subject>Agriculture</subject><subject>Antisense</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Comparative genomics</subject><subject>DNA Primers</subject><subject>Ecology</subject><subject>Environmental stress</subject><subject>Forestry</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene cluster</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genome survey sequence</subject><subject>Genomes</subject><subject>Homolog</subject><subject>Life Sciences</subject><subject>Mathematical sequences</subject><subject>Messenger RNA</subject><subject>MicroRNA</subject><subject>MicroRNAs - genetics</subject><subject>Multigene Family</subject><subject>Nicotiana</subject><subject>Nicotiana - genetics</subject><subject>Nucleotides</subject><subject>Original Article</subject><subject>Plant growth</subject><subject>Plant Sciences</subject><subject>Plants</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>Rice</subject><subject>Target</subject><subject>Tobacco</subject><subject>Transcription factors</subject><issn>0032-0935</issn><issn>1432-2048</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kU1v1DAQhi0EosvCD-AAREgIOARmHDuxj1XFR6WqSEDP0cSxt17txsV2DvDr8ZKFIg6cbM_7zDszHsYeI7xBgO5tAhBc1oBQI5eyxjtshaLhNQeh7rIVQLmDbuQJe5DSFqCIXXefnXBQRcJ2xdz5aKfsnTeUfZgqmsbKXFMkk230P5ZgcNXemxg-X56mX0S-tj5WmeLG5mpjJ5sqP1U5DGRMqF5dehOyp4kKUkLz_vVDds_RLtlHx3PNrt6_-3r2sb749OH87PSiNkK0uZYtdwLbTrZa4NCO1GArBjOSJGGasXSvnUXdipac1nJUluQwuI5LABpBNWv2cvG9ieHbbFPu9z4Zu9vRZMOc-k5qyQUv_7Bmz_8ht2GOU2muVyCV4sgPdrhAZfiUonX9TfR7it97hP6wgn5ZQQ-Hd1lBjyXn6dF4HvZ2_JPx-88L8OIIUDK0c5Em49Mt1wjUSkDh-MKlIk0bG287_F_1J0vSNuUQ_zJtNCp9mOjZojsKPW1iKXz1hQM2gBo4omp-AsyUr7k</recordid><startdate>20101101</startdate><enddate>20101101</enddate><creator>Frazier, Taylor P</creator><creator>Xie, Fuliang</creator><creator>Freistaedter, Andrew</creator><creator>Burklew, Caitlin E</creator><creator>Zhang, Baohong</creator><general>Berlin/Heidelberg : Springer-Verlag</general><general>Springer-Verlag</general><general>Springer</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>IQODW</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>7QP</scope><scope>7QR</scope><scope>7TM</scope><scope>7X2</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>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</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>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PHGZM</scope><scope>PHGZT</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20101101</creationdate><title>Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)</title><author>Frazier, Taylor P ; Xie, Fuliang ; Freistaedter, Andrew ; Burklew, Caitlin E ; Zhang, Baohong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c446t-562f416756941b6da3164bcda5a4c3d4379fe19646af995d8ea5bbf72500ad083</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Agriculture</topic><topic>Antisense</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Comparative genomics</topic><topic>DNA Primers</topic><topic>Ecology</topic><topic>Environmental stress</topic><topic>Forestry</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene cluster</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genome survey sequence</topic><topic>Genomes</topic><topic>Homolog</topic><topic>Life Sciences</topic><topic>Mathematical sequences</topic><topic>Messenger RNA</topic><topic>MicroRNA</topic><topic>MicroRNAs - genetics</topic><topic>Multigene Family</topic><topic>Nicotiana</topic><topic>Nicotiana - genetics</topic><topic>Nucleotides</topic><topic>Original Article</topic><topic>Plant growth</topic><topic>Plant Sciences</topic><topic>Plants</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>Rice</topic><topic>Target</topic><topic>Tobacco</topic><topic>Transcription factors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Frazier, Taylor P</creatorcontrib><creatorcontrib>Xie, Fuliang</creatorcontrib><creatorcontrib>Freistaedter, Andrew</creatorcontrib><creatorcontrib>Burklew, Caitlin E</creatorcontrib><creatorcontrib>Zhang, Baohong</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</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>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Agricultural Science Collection</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>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</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>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest Central (New)</collection><collection>ProQuest One Academic (New)</collection><collection>ProQuest Health & Medical Research Collection</collection><collection>ProQuest One Academic Middle East (New)</collection><collection>ProQuest One Health & Nursing</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Applied & Life Sciences</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Planta</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Frazier, Taylor P</au><au>Xie, Fuliang</au><au>Freistaedter, Andrew</au><au>Burklew, Caitlin E</au><au>Zhang, Baohong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)</atitle><jtitle>Planta</jtitle><stitle>Planta</stitle><addtitle>Planta</addtitle><date>2010-11-01</date><risdate>2010</risdate><volume>232</volume><issue>6</issue><spage>1289</spage><epage>1308</epage><pages>1289-1308</pages><issn>0032-0935</issn><eissn>1432-2048</eissn><coden>PLANAB</coden><abstract>microRNAs (miRNAs) are a recently discovered class of small (~21 nt) endogenous gene regulators that have been shown to play an important role in plant growth and development by aiding in organ maturation, hormone signaling, tissue differentiation, and plant tolerance to environmental stress. Since a list of miRNAs has never been generated for tobacco, we employed genome survey sequence analysis to computationally identify 259 potentially conserved tobacco miRNAs, belonging to 65 families, and validated 11 of these miRNAs using qRT-PCR. The 65 miRNA families were dramatically different in size. miRNA precursor (pre-miRNA) sequence analysis showed that tobacco pre-miRNAs greatly varied from 45 to 635 nt in length with an average of 141 ± 108 nt. We were also able to determine the presence of antisense miRNAs as well as miRNA clusters in tobacco. Using previously established protocols, a total of 1,225 potential target genes were predicted for the newly identified tobacco miRNAs. These target genes include transcription factors, DNA replication proteins, metabolic enzymes, as well as other gene targets necessary for proper plant maturation. The results of this study show that conserved miRNAs exist in tobacco and suggest that these miRNAs may play an important role in tobacco growth and development.</abstract><cop>Berlin/Heidelberg</cop><pub>Berlin/Heidelberg : Springer-Verlag</pub><pmid>20803216</pmid><doi>10.1007/s00425-010-1255-1</doi><tpages>20</tpages></addata></record> |
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| subjects | Agriculture Antisense Base Sequence Biological and medical sciences Biomedical and Life Sciences Comparative genomics DNA Primers Ecology Environmental stress Forestry Fundamental and applied biological sciences. Psychology Gene cluster Genes Genes, Plant Genome survey sequence Genomes Homolog Life Sciences Mathematical sequences Messenger RNA MicroRNA MicroRNAs - genetics Multigene Family Nicotiana Nicotiana - genetics Nucleotides Original Article Plant growth Plant Sciences Plants Reverse Transcriptase Polymerase Chain Reaction Rice Target Tobacco Transcription factors |
| title | Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum) |
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