Transcriptome/degradome-wide identification of R. glutinosa miRNAs and their targets: the role of miRNA activity in the replanting disease
Rehmannia glutinosa, a traditional Chinese medicine herb, is unable to grow normally in a soil where the same species has recently been cultivated. The biological basis of this so called "replanting disease" is unknown, but it may involve the action of microRNAs (miRNAs), which are known t...
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| creator | Li, Ming Jie Yang, Yan Hui Chen, Xin Jian Wang, Feng Qing Lin, Wen Xiong Yi, Yan Jie Zeng, Lei Yang, Shuo Ye Zhang, Zhong Yi |
| description | Rehmannia glutinosa, a traditional Chinese medicine herb, is unable to grow normally in a soil where the same species has recently been cultivated. The biological basis of this so called "replanting disease" is unknown, but it may involve the action of microRNAs (miRNAs), which are known to be important regulators of plant growth and development. High throughput Solexa/Illumina sequencing was used to generate a transcript library of the R. glutinosa transcriptome and degradome in order to identify possible miRNAs and their targets implicated in the replanting disease. A total of 87,665 unigenes and 589 miRNA families (17 of which have not been identified in plants to date) was identified from the libraries made from a first year (FP) and a second year (SP) crop. A comparison between the FP and SP miRNAs showed that the abundance of eight of the novel and 295 of the known miRNA families differed between the FP and SP plants. Sequencing of the degradome sampled from FP and SP plants led to the identification of 165 transcript targets of 85 of the differentially abundant miRNA families. The interaction of some of these miRNAs with their target(s) is likely to form an important part of the molecular basis of the replanting disease of R. glutinosa. |
| doi_str_mv | 10.1371/journal.pone.0068531 |
| format | Article |
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The biological basis of this so called "replanting disease" is unknown, but it may involve the action of microRNAs (miRNAs), which are known to be important regulators of plant growth and development. High throughput Solexa/Illumina sequencing was used to generate a transcript library of the R. glutinosa transcriptome and degradome in order to identify possible miRNAs and their targets implicated in the replanting disease. A total of 87,665 unigenes and 589 miRNA families (17 of which have not been identified in plants to date) was identified from the libraries made from a first year (FP) and a second year (SP) crop. A comparison between the FP and SP miRNAs showed that the abundance of eight of the novel and 295 of the known miRNA families differed between the FP and SP plants. Sequencing of the degradome sampled from FP and SP plants led to the identification of 165 transcript targets of 85 of the differentially abundant miRNA families. The interaction of some of these miRNAs with their target(s) is likely to form an important part of the molecular basis of the replanting disease of R. glutinosa.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0068531</identifier><identifier>PMID: 23861915</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agriculture ; Allelopathy ; Analysis ; Arabidopsis ; Arabidopsis thaliana ; Bioengineering ; Biology ; Computational Biology ; Crop science ; Degradation ; Family ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing ; Identification ; Life sciences ; MicroRNA ; MicroRNAs ; MicroRNAs - genetics ; miRNA ; Molecular Sequence Annotation ; Oryza ; Plant growth ; Plants (botany) ; Proteins ; Regulators ; Revegetation ; Target recognition ; Tracheophyta - genetics ; Traditional Chinese medicine ; Transcription ; Transcriptome</subject><ispartof>PloS one, 2013-07, Vol.8 (7), p.e68531-e68531</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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>2013 Li et al 2013 Li et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-e45964805026ed44411c2161e5aeed6583a9b227e2fa661f445c559aab09d02e3</citedby><cites>FETCH-LOGICAL-c692t-e45964805026ed44411c2161e5aeed6583a9b227e2fa661f445c559aab09d02e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702588/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702588/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23861915$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Trujillo, Martha</contributor><creatorcontrib>Li, Ming Jie</creatorcontrib><creatorcontrib>Yang, Yan Hui</creatorcontrib><creatorcontrib>Chen, Xin Jian</creatorcontrib><creatorcontrib>Wang, Feng Qing</creatorcontrib><creatorcontrib>Lin, Wen Xiong</creatorcontrib><creatorcontrib>Yi, Yan Jie</creatorcontrib><creatorcontrib>Zeng, Lei</creatorcontrib><creatorcontrib>Yang, Shuo Ye</creatorcontrib><creatorcontrib>Zhang, Zhong Yi</creatorcontrib><title>Transcriptome/degradome-wide identification of R. glutinosa miRNAs and their targets: the role of miRNA activity in the replanting disease</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Rehmannia glutinosa, a traditional Chinese medicine herb, is unable to grow normally in a soil where the same species has recently been cultivated. The biological basis of this so called "replanting disease" is unknown, but it may involve the action of microRNAs (miRNAs), which are known to be important regulators of plant growth and development. High throughput Solexa/Illumina sequencing was used to generate a transcript library of the R. glutinosa transcriptome and degradome in order to identify possible miRNAs and their targets implicated in the replanting disease. A total of 87,665 unigenes and 589 miRNA families (17 of which have not been identified in plants to date) was identified from the libraries made from a first year (FP) and a second year (SP) crop. A comparison between the FP and SP miRNAs showed that the abundance of eight of the novel and 295 of the known miRNA families differed between the FP and SP plants. Sequencing of the degradome sampled from FP and SP plants led to the identification of 165 transcript targets of 85 of the differentially abundant miRNA families. The interaction of some of these miRNAs with their target(s) is likely to form an important part of the molecular basis of the replanting disease of R. glutinosa.</description><subject>Agriculture</subject><subject>Allelopathy</subject><subject>Analysis</subject><subject>Arabidopsis</subject><subject>Arabidopsis thaliana</subject><subject>Bioengineering</subject><subject>Biology</subject><subject>Computational Biology</subject><subject>Crop science</subject><subject>Degradation</subject><subject>Family</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genomes</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Identification</subject><subject>Life sciences</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>Molecular Sequence Annotation</subject><subject>Oryza</subject><subject>Plant growth</subject><subject>Plants (botany)</subject><subject>Proteins</subject><subject>Regulators</subject><subject>Revegetation</subject><subject>Target recognition</subject><subject>Tracheophyta - 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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>Li, Ming Jie</au><au>Yang, Yan Hui</au><au>Chen, Xin Jian</au><au>Wang, Feng Qing</au><au>Lin, Wen Xiong</au><au>Yi, Yan Jie</au><au>Zeng, Lei</au><au>Yang, Shuo Ye</au><au>Zhang, Zhong Yi</au><au>Trujillo, Martha</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptome/degradome-wide identification of R. glutinosa miRNAs and their targets: the role of miRNA activity in the replanting disease</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-07-05</date><risdate>2013</risdate><volume>8</volume><issue>7</issue><spage>e68531</spage><epage>e68531</epage><pages>e68531-e68531</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Rehmannia glutinosa, a traditional Chinese medicine herb, is unable to grow normally in a soil where the same species has recently been cultivated. The biological basis of this so called "replanting disease" is unknown, but it may involve the action of microRNAs (miRNAs), which are known to be important regulators of plant growth and development. High throughput Solexa/Illumina sequencing was used to generate a transcript library of the R. glutinosa transcriptome and degradome in order to identify possible miRNAs and their targets implicated in the replanting disease. A total of 87,665 unigenes and 589 miRNA families (17 of which have not been identified in plants to date) was identified from the libraries made from a first year (FP) and a second year (SP) crop. A comparison between the FP and SP miRNAs showed that the abundance of eight of the novel and 295 of the known miRNA families differed between the FP and SP plants. Sequencing of the degradome sampled from FP and SP plants led to the identification of 165 transcript targets of 85 of the differentially abundant miRNA families. The interaction of some of these miRNAs with their target(s) is likely to form an important part of the molecular basis of the replanting disease of R. glutinosa.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23861915</pmid><doi>10.1371/journal.pone.0068531</doi><tpages>e68531</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Agriculture Allelopathy Analysis Arabidopsis Arabidopsis thaliana Bioengineering Biology Computational Biology Crop science Degradation Family Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Genomes Genomics High-Throughput Nucleotide Sequencing Identification Life sciences MicroRNA MicroRNAs MicroRNAs - genetics miRNA Molecular Sequence Annotation Oryza Plant growth Plants (botany) Proteins Regulators Revegetation Target recognition Tracheophyta - genetics Traditional Chinese medicine Transcription Transcriptome |
| title | Transcriptome/degradome-wide identification of R. glutinosa miRNAs and their targets: the role of miRNA activity in the replanting disease |
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