Identification of microRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods
Camelina sativa is an annual oilseed crop that is under intensive development for renewable resources of biofuels and industrial oils. MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA...
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| Veröffentlicht in: | PloS one 2015-03, Vol.10 (3), p.e0121542-e0121542 |
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| creator | Poudel, Saroj Aryal, Niranjan Lu, Chaofu |
| description | Camelina sativa is an annual oilseed crop that is under intensive development for renewable resources of biofuels and industrial oils. MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA libraries prepared from camelina leaves, flower buds and two stages of developing seeds corresponding to initial and peak storage products accumulation. Computational analyses identified 207 known miRNAs belonging to 63 families, as well as 5 novel miRNAs. These miRNAs, especially members of the miRNA families, varied greatly in different tissues and developmental stages. The predicted miRNA target genes are involved in a broad range of physiological functions including lipid metabolism. This report is the first step toward elucidating roles of miRNAs in C. sativa and will provide additional tools to improve this oilseed crop for biofuels and biomaterials. |
| doi_str_mv | 10.1371/journal.pone.0121542 |
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MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA libraries prepared from camelina leaves, flower buds and two stages of developing seeds corresponding to initial and peak storage products accumulation. Computational analyses identified 207 known miRNAs belonging to 63 families, as well as 5 novel miRNAs. These miRNAs, especially members of the miRNA families, varied greatly in different tissues and developmental stages. The predicted miRNA target genes are involved in a broad range of physiological functions including lipid metabolism. This report is the first step toward elucidating roles of miRNAs in C. sativa and will provide additional tools to improve this oilseed crop for biofuels and biomaterials.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0121542</identifier><identifier>PMID: 25826400</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>09 BIOMASS FUELS ; Arabidopsis ; Arabidopsis thaliana ; BASIC BIOLOGICAL SCIENCES ; Biodiesel fuels ; Biofuels ; Biological activity ; Biomaterials ; Biomedical materials ; Brassicaceae - genetics ; Camelina ; Camelina sativa ; Coding ; Computation ; Computational Biology ; Computer applications ; Crops ; Developmental stages ; Fatty acids ; Flowers & plants ; Gene expression ; Gene sequencing ; Genomes ; High-Throughput Nucleotide Sequencing ; Identification ; Leaves ; Lipid metabolism ; Lipids ; Loam soils ; Metabolism ; MicroRNAs ; MicroRNAs - genetics ; miRNA ; Petroleum production ; Plant pathology ; Plant sciences ; Plant tissues ; Renewable resources ; Ribonucleic acid ; RNA ; RNA, Messenger - genetics ; Seeds ; Sustainable yield ; Transcription ; Transfer RNA ; Wheat</subject><ispartof>PloS one, 2015-03, Vol.10 (3), p.e0121542-e0121542</ispartof><rights>2015 Poudel et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://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>2015 Poudel et al 2015 Poudel et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c553t-c77cd8e16dd86556b1487d189d6dd5ff7a5f5408463da25aa644d17dd84c0133</citedby><cites>FETCH-LOGICAL-c553t-c77cd8e16dd86556b1487d189d6dd5ff7a5f5408463da25aa644d17dd84c0133</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/PMC4380411/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380411/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25826400$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1202364$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><contributor>Wang, Tai</contributor><creatorcontrib>Poudel, Saroj</creatorcontrib><creatorcontrib>Aryal, Niranjan</creatorcontrib><creatorcontrib>Lu, Chaofu</creatorcontrib><creatorcontrib>Donald Danforth Plant Science Center, St. Louis, MO (United States)</creatorcontrib><title>Identification of microRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Camelina sativa is an annual oilseed crop that is under intensive development for renewable resources of biofuels and industrial oils. MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA libraries prepared from camelina leaves, flower buds and two stages of developing seeds corresponding to initial and peak storage products accumulation. Computational analyses identified 207 known miRNAs belonging to 63 families, as well as 5 novel miRNAs. These miRNAs, especially members of the miRNA families, varied greatly in different tissues and developmental stages. The predicted miRNA target genes are involved in a broad range of physiological functions including lipid metabolism. This report is the first step toward elucidating roles of miRNAs in C. sativa and will provide additional tools to improve this oilseed crop for biofuels and biomaterials.</description><subject>09 BIOMASS FUELS</subject><subject>Arabidopsis</subject><subject>Arabidopsis thaliana</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Biodiesel fuels</subject><subject>Biofuels</subject><subject>Biological activity</subject><subject>Biomaterials</subject><subject>Biomedical materials</subject><subject>Brassicaceae - genetics</subject><subject>Camelina</subject><subject>Camelina sativa</subject><subject>Coding</subject><subject>Computation</subject><subject>Computational Biology</subject><subject>Computer applications</subject><subject>Crops</subject><subject>Developmental stages</subject><subject>Fatty acids</subject><subject>Flowers & plants</subject><subject>Gene expression</subject><subject>Gene sequencing</subject><subject>Genomes</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Identification</subject><subject>Leaves</subject><subject>Lipid metabolism</subject><subject>Lipids</subject><subject>Loam soils</subject><subject>Metabolism</subject><subject>MicroRNAs</subject><subject>MicroRNAs - 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MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA libraries prepared from camelina leaves, flower buds and two stages of developing seeds corresponding to initial and peak storage products accumulation. Computational analyses identified 207 known miRNAs belonging to 63 families, as well as 5 novel miRNAs. These miRNAs, especially members of the miRNA families, varied greatly in different tissues and developmental stages. The predicted miRNA target genes are involved in a broad range of physiological functions including lipid metabolism. This report is the first step toward elucidating roles of miRNAs in C. sativa and will provide additional tools to improve this oilseed crop for biofuels and biomaterials.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25826400</pmid><doi>10.1371/journal.pone.0121542</doi><oa>free_for_read</oa></addata></record> |
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| subjects | 09 BIOMASS FUELS Arabidopsis Arabidopsis thaliana BASIC BIOLOGICAL SCIENCES Biodiesel fuels Biofuels Biological activity Biomaterials Biomedical materials Brassicaceae - genetics Camelina Camelina sativa Coding Computation Computational Biology Computer applications Crops Developmental stages Fatty acids Flowers & plants Gene expression Gene sequencing Genomes High-Throughput Nucleotide Sequencing Identification Leaves Lipid metabolism Lipids Loam soils Metabolism MicroRNAs MicroRNAs - genetics miRNA Petroleum production Plant pathology Plant sciences Plant tissues Renewable resources Ribonucleic acid RNA RNA, Messenger - genetics Seeds Sustainable yield Transcription Transfer RNA Wheat |
| title | Identification of microRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods |
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