Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE
We predicted 262 potential MicroRNAs (miRNAs) belonging to 70 miRNA families from the peach (Prunus persica) genome and two specific 5′ and 3′ miRNA rapid amplification of cDNA ends (miR-RACE) PCR reactions and sequence-directed cloning were employed to accurately validate 61 unique P. persica miRNA...
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| Veröffentlicht in: | Journal of plant physiology 2013-01, Vol.170 (1), p.80-92 |
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| creator | Zhang, Yanping Bai, Youhuang Han, Jian Chen, Ming Kayesh, Emrul Jiang, Weibing Fang, Jinggui |
| description | We predicted 262 potential MicroRNAs (miRNAs) belonging to 70 miRNA families from the peach (Prunus persica) genome and two specific 5′ and 3′ miRNA rapid amplification of cDNA ends (miR-RACE) PCR reactions and sequence-directed cloning were employed to accurately validate 61 unique P. persica miRNAs (Ppe-miRNAs) sequences belonging to 61 families comprising 97 Ppe-miRNAs. Validation of the termini nucleotides in particular can define the real sequences of the Ppe-miRNAs on peach genome. Comparison between predicted and validated Ppe-miRNAs through alignment revealed that 43 unique orthologous sequences were identical, while the remaining 18 exhibited some divergences at their termini nucleotides. Quantitative real-time polymerase chain reaction (qRT-PCR) was further employed to analyze the expression of all the 61 miRNAs and 10 putative targets of 8 randomly selected Ppe-miRNAs in peach leaves, flowers and fruits at different stages of development, where both the miRNAs and the putative target genes showed tissue-specific expression. |
| doi_str_mv | 10.1016/j.jplph.2012.08.021 |
| format | Article |
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Validation of the termini nucleotides in particular can define the real sequences of the Ppe-miRNAs on peach genome. Comparison between predicted and validated Ppe-miRNAs through alignment revealed that 43 unique orthologous sequences were identical, while the remaining 18 exhibited some divergences at their termini nucleotides. Quantitative real-time polymerase chain reaction (qRT-PCR) was further employed to analyze the expression of all the 61 miRNAs and 10 putative targets of 8 randomly selected Ppe-miRNAs in peach leaves, flowers and fruits at different stages of development, where both the miRNAs and the putative target genes showed tissue-specific expression.</description><identifier>ISSN: 0176-1617</identifier><identifier>EISSN: 1618-1328</identifier><identifier>DOI: 10.1016/j.jplph.2012.08.021</identifier><identifier>PMID: 23107282</identifier><language>eng</language><publisher>Germany: Elsevier GmbH</publisher><subject>bioinformatics ; Cloning ; complementary DNA ; Computational Biology ; Computational prediction ; developmental stages ; DNA, Complementary - genetics ; flowers ; Flowers - genetics ; Flowers - growth & development ; Fruit - genetics ; Fruit - growth & development ; fruits ; Gene expression ; Gene Expression Regulation, Plant - genetics ; Gene Library ; Gene sequencing ; genes ; Genome, Plant - genetics ; Genomes ; leaves ; microRNA ; microRNAs ; MicroRNAs - genetics ; miR-RACE ; Nucleotides ; Organ Specificity ; Peaches ; Physiology ; Plant Leaves - genetics ; Plant Leaves - growth & development ; prediction ; Prunus ; Prunus - genetics ; Prunus - growth & development ; Prunus persica ; qRT-PCR ; quantitative polymerase chain reaction ; rapid amplification of cDNA ends ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Ribonucleic acids ; RNA, Plant - genetics</subject><ispartof>Journal of plant physiology, 2013-01, Vol.170 (1), p.80-92</ispartof><rights>2012 Elsevier GmbH</rights><rights>Copyright © 2012 Elsevier GmbH. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c482t-2bbe63ceb98e6651f42d3353cbc9e6fa116d8e219d074cadbcd748ca6d000423</citedby><cites>FETCH-LOGICAL-c482t-2bbe63ceb98e6651f42d3353cbc9e6fa116d8e219d074cadbcd748ca6d000423</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jplph.2012.08.021$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,4024,27923,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23107282$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Yanping</creatorcontrib><creatorcontrib>Bai, Youhuang</creatorcontrib><creatorcontrib>Han, Jian</creatorcontrib><creatorcontrib>Chen, Ming</creatorcontrib><creatorcontrib>Kayesh, Emrul</creatorcontrib><creatorcontrib>Jiang, Weibing</creatorcontrib><creatorcontrib>Fang, Jinggui</creatorcontrib><title>Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE</title><title>Journal of plant physiology</title><addtitle>J Plant Physiol</addtitle><description>We predicted 262 potential MicroRNAs (miRNAs) belonging to 70 miRNA families from the peach (Prunus persica) genome and two specific 5′ and 3′ miRNA rapid amplification of cDNA ends (miR-RACE) PCR reactions and sequence-directed cloning were employed to accurately validate 61 unique P. persica miRNAs (Ppe-miRNAs) sequences belonging to 61 families comprising 97 Ppe-miRNAs. Validation of the termini nucleotides in particular can define the real sequences of the Ppe-miRNAs on peach genome. Comparison between predicted and validated Ppe-miRNAs through alignment revealed that 43 unique orthologous sequences were identical, while the remaining 18 exhibited some divergences at their termini nucleotides. Quantitative real-time polymerase chain reaction (qRT-PCR) was further employed to analyze the expression of all the 61 miRNAs and 10 putative targets of 8 randomly selected Ppe-miRNAs in peach leaves, flowers and fruits at different stages of development, where both the miRNAs and the putative target genes showed tissue-specific expression.</description><subject>bioinformatics</subject><subject>Cloning</subject><subject>complementary DNA</subject><subject>Computational Biology</subject><subject>Computational prediction</subject><subject>developmental stages</subject><subject>DNA, Complementary - genetics</subject><subject>flowers</subject><subject>Flowers - genetics</subject><subject>Flowers - growth & development</subject><subject>Fruit - genetics</subject><subject>Fruit - growth & development</subject><subject>fruits</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant - genetics</subject><subject>Gene Library</subject><subject>Gene sequencing</subject><subject>genes</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>leaves</subject><subject>microRNA</subject><subject>microRNAs</subject><subject>MicroRNAs - genetics</subject><subject>miR-RACE</subject><subject>Nucleotides</subject><subject>Organ Specificity</subject><subject>Peaches</subject><subject>Physiology</subject><subject>Plant Leaves - genetics</subject><subject>Plant Leaves - growth & development</subject><subject>prediction</subject><subject>Prunus</subject><subject>Prunus - genetics</subject><subject>Prunus - growth & development</subject><subject>Prunus persica</subject><subject>qRT-PCR</subject><subject>quantitative polymerase chain reaction</subject><subject>rapid amplification of cDNA ends</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>Ribonucleic acids</subject><subject>RNA, Plant - genetics</subject><issn>0176-1617</issn><issn>1618-1328</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU1v1DAQhi0EokvhFyCBj1wS_JE43gOH7ap8SBWgUs6WY0-6s0rixU5a9d_jsC1Hii-WrWfeGc1DyGvOSs64er8v94f-sCsF46JkumSCPyErrrguuBT6KVkx3qgifzQn5EVKe5bftZbPyYmQnDVCixW5PcOAYxfiYCd0iR4ieHQThpGGjg54-XWTKI502gH9HudxzgjEhM7SaxjDAPQWpx29sT16-1CWYYxLlMMENMGvGUYHibZ3S2JxudmevyTPOtsneHV_n5Krj-dX28_FxbdPX7abi8JVWkyFaFtQ0kG71qBUzbtKeClr6Vq3BtVZzpXXIPjas6Zy1rfON5V2VnnGWCXkKXl3jD3EkKdIkxkwOeh7O0KYk-FNVTW80o1-HK3z0oRWij2OCi2VqvK-_wPNR4paLag8oi6GlCJ05hBxsPHOcGYW42Zv_hg3i3HDtMnGc9Wb-wZzO4D_W_OgOANvj0Bng7HXEZP5-SMn1HlDdcPEQnw4EpBF3CBEkxwuxjxmhZPxAf85wm-Bo8ZN</recordid><startdate>20130101</startdate><enddate>20130101</enddate><creator>Zhang, Yanping</creator><creator>Bai, Youhuang</creator><creator>Han, Jian</creator><creator>Chen, Ming</creator><creator>Kayesh, Emrul</creator><creator>Jiang, Weibing</creator><creator>Fang, Jinggui</creator><general>Elsevier GmbH</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>7X8</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7SC</scope><scope>7U5</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope></search><sort><creationdate>20130101</creationdate><title>Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE</title><author>Zhang, Yanping ; Bai, Youhuang ; Han, Jian ; Chen, Ming ; Kayesh, Emrul ; Jiang, Weibing ; Fang, Jinggui</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c482t-2bbe63ceb98e6651f42d3353cbc9e6fa116d8e219d074cadbcd748ca6d000423</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>bioinformatics</topic><topic>Cloning</topic><topic>complementary DNA</topic><topic>Computational Biology</topic><topic>Computational prediction</topic><topic>developmental stages</topic><topic>DNA, Complementary - genetics</topic><topic>flowers</topic><topic>Flowers - genetics</topic><topic>Flowers - growth & development</topic><topic>Fruit - genetics</topic><topic>Fruit - growth & development</topic><topic>fruits</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Plant - genetics</topic><topic>Gene Library</topic><topic>Gene sequencing</topic><topic>genes</topic><topic>Genome, Plant - genetics</topic><topic>Genomes</topic><topic>leaves</topic><topic>microRNA</topic><topic>microRNAs</topic><topic>MicroRNAs - genetics</topic><topic>miR-RACE</topic><topic>Nucleotides</topic><topic>Organ Specificity</topic><topic>Peaches</topic><topic>Physiology</topic><topic>Plant Leaves - genetics</topic><topic>Plant Leaves - growth & development</topic><topic>prediction</topic><topic>Prunus</topic><topic>Prunus - genetics</topic><topic>Prunus - growth & development</topic><topic>Prunus persica</topic><topic>qRT-PCR</topic><topic>quantitative polymerase chain reaction</topic><topic>rapid amplification of cDNA ends</topic><topic>Real-Time Polymerase Chain Reaction</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>Ribonucleic acids</topic><topic>RNA, Plant - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Yanping</creatorcontrib><creatorcontrib>Bai, Youhuang</creatorcontrib><creatorcontrib>Han, Jian</creatorcontrib><creatorcontrib>Chen, Ming</creatorcontrib><creatorcontrib>Kayesh, Emrul</creatorcontrib><creatorcontrib>Jiang, Weibing</creatorcontrib><creatorcontrib>Fang, Jinggui</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>MEDLINE - Academic</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><jtitle>Journal of plant physiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Yanping</au><au>Bai, Youhuang</au><au>Han, Jian</au><au>Chen, Ming</au><au>Kayesh, Emrul</au><au>Jiang, Weibing</au><au>Fang, Jinggui</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE</atitle><jtitle>Journal of plant physiology</jtitle><addtitle>J Plant Physiol</addtitle><date>2013-01-01</date><risdate>2013</risdate><volume>170</volume><issue>1</issue><spage>80</spage><epage>92</epage><pages>80-92</pages><issn>0176-1617</issn><eissn>1618-1328</eissn><abstract>We predicted 262 potential MicroRNAs (miRNAs) belonging to 70 miRNA families from the peach (Prunus persica) genome and two specific 5′ and 3′ miRNA rapid amplification of cDNA ends (miR-RACE) PCR reactions and sequence-directed cloning were employed to accurately validate 61 unique P. persica miRNAs (Ppe-miRNAs) sequences belonging to 61 families comprising 97 Ppe-miRNAs. Validation of the termini nucleotides in particular can define the real sequences of the Ppe-miRNAs on peach genome. Comparison between predicted and validated Ppe-miRNAs through alignment revealed that 43 unique orthologous sequences were identical, while the remaining 18 exhibited some divergences at their termini nucleotides. Quantitative real-time polymerase chain reaction (qRT-PCR) was further employed to analyze the expression of all the 61 miRNAs and 10 putative targets of 8 randomly selected Ppe-miRNAs in peach leaves, flowers and fruits at different stages of development, where both the miRNAs and the putative target genes showed tissue-specific expression.</abstract><cop>Germany</cop><pub>Elsevier GmbH</pub><pmid>23107282</pmid><doi>10.1016/j.jplph.2012.08.021</doi><tpages>13</tpages></addata></record> |
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| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | bioinformatics Cloning complementary DNA Computational Biology Computational prediction developmental stages DNA, Complementary - genetics flowers Flowers - genetics Flowers - growth & development Fruit - genetics Fruit - growth & development fruits Gene expression Gene Expression Regulation, Plant - genetics Gene Library Gene sequencing genes Genome, Plant - genetics Genomes leaves microRNA microRNAs MicroRNAs - genetics miR-RACE Nucleotides Organ Specificity Peaches Physiology Plant Leaves - genetics Plant Leaves - growth & development prediction Prunus Prunus - genetics Prunus - growth & development Prunus persica qRT-PCR quantitative polymerase chain reaction rapid amplification of cDNA ends Real-Time Polymerase Chain Reaction Reverse Transcriptase Polymerase Chain Reaction Ribonucleic acids RNA, Plant - genetics |
| title | Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE |
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