Identification of MicroRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods
Abstract
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.
- Authors:
- Montana State Univ., Bozeman, MT (United States)
- Chinese Academy of Sciences (CAS), Beijing (China)
- Publication Date:
- Research Org.:
- Donald Danforth Plant Science Center, St. Louis, MO (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1202364
- Grant/Contract Number:
- AR0000202
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 3; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS
Citation Formats
Poudel, Saroj, Aryal, Niranjan, Lu, Chaofu, and Wang, Tai. Identification of MicroRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods. United States: N. p., 2015.
Web. doi:10.1371/journal.pone.0121542.
Poudel, Saroj, Aryal, Niranjan, Lu, Chaofu, & Wang, Tai. Identification of MicroRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods. United States. doi:10.1371/journal.pone.0121542.
Poudel, Saroj, Aryal, Niranjan, Lu, Chaofu, and Wang, Tai. Tue .
"Identification of MicroRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods". United States. doi:10.1371/journal.pone.0121542. https://www.osti.gov/servlets/purl/1202364.
@article{osti_1202364,
title = {Identification of MicroRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods},
author = {Poudel, Saroj and Aryal, Niranjan and Lu, Chaofu and Wang, Tai},
abstractNote = {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 = {10.1371/journal.pone.0121542},
journal = {PLoS ONE},
number = 3,
volume = 10,
place = {United States},
year = {2015},
month = {3}
}
Web of Science
Works referenced in this record:
MicroRNAs: Target Recognition and Regulatory Functions
journal, January 2009
- Bartel, David P.
- Cell, Vol. 136, Issue 2
Characterization of the morphological changes and fatty acid profile of developing Camelina sativa seeds
journal, October 2013
- Rodríguez-Rodríguez, Manuel Fernando; Sánchez-García, Alicia; Salas, Joaquín J.
- Industrial Crops and Products, Vol. 50
Origin, Biogenesis, and Activity of Plant MicroRNAs
journal, February 2009
- Voinnet, Olivier
- Cell, Vol. 136, Issue 4
Modification of Seed Oil Composition in Arabidopsis by Artificial microRNA-Mediated Gene Silencing
journal, January 2012
- Belide, Srinivas; Petrie, James Robertson; Shrestha, Pushkar
- Frontiers in Plant Science, Vol. 3
PMRD: plant microRNA database
journal, October 2009
- Zhang, Zhenhai; Yu, Jingyin; Li, Daofeng
- Nucleic Acids Research, Vol. 38, Issue suppl_1
Rfam: an RNA family database
journal, January 2003
- Griffiths-Jones, S.
- Nucleic Acids Research, Vol. 31, Issue 1
The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure
journal, April 2014
- Kagale, Sateesh; Koh, Chushin; Nixon, John
- Nature Communications, Vol. 5, Issue 1
Polyploid genome of Camelina sativa revealed by isolation of fatty acid synthesis genes
journal, January 2010
- Hutcheon, Carolyn; Ditt, Renata F.; Beilstein, Mark
- BMC Plant Biology, Vol. 10, Issue 1
Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues
journal, July 2006
- Válóczi, Anna; Várallyay, Éva; Kauppinen, Sakari
- The Plant Journal, Vol. 47, Issue 1
Prediction of Plant MicroRNA Targets
journal, August 2002
- Rhoades, Matthew W.; Reinhart, Brenda J.; Lim, Lee P.
- Cell, Vol. 110, Issue 4
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009
- Langmead, Ben; Trapnell, Cole; Pop, Mihai
- Genome Biology, Vol. 10, Issue 3
Functions of microRNAs in plant stress responses
journal, April 2012
- Sunkar, Ramanjulu; Li, Yong-Fang; Jagadeeswaran, Guru
- Trends in Plant Science, Vol. 17, Issue 4
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview
journal, June 2006
- Al-Shehbaz, I. A.; Beilstein, M. A.; Kellogg, E. A.
- Plant Systematics and Evolution, Vol. 259, Issue 2-4
MicroRNA profiling: approaches and considerations
journal, April 2012
- Pritchard, Colin C.; Cheng, Heather H.; Tewari, Muneesh
- Nature Reviews Genetics, Vol. 13, Issue 5
Camelina seed transcriptome: a tool for meal and oil improvement and translational research
journal, April 2013
- Nguyen, Huu T.; Silva, Jillian E.; Podicheti, Ram
- Plant Biotechnology Journal, Vol. 11, Issue 6
Mfold web server for nucleic acid folding and hybridization prediction
journal, July 2003
- Zuker, M.
- Nucleic Acids Research, Vol. 31, Issue 13
Genetic mapping of agronomic traits in false flax (Camelina sativa subsp. sativa )
journal, December 2006
- Gehringer, A.; Friedt, W.; Lühs, W.
- Genome, Vol. 49, Issue 12
Vienna RNA secondary structure server
journal, July 2003
- Hofacker, I. L.
- Nucleic Acids Research, Vol. 31, Issue 13
Acyl Editing and Headgroup Exchange Are the Major Mechanisms That Direct Polyunsaturated Fatty Acid Flux into Triacylglycerols
journal, August 2012
- Bates, Philip D.; Fatihi, Abdelhak; Snapp, Anna R.
- Plant Physiology, Vol. 160, Issue 3
De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers
journal, September 2013
- Mudalkar, Shalini; Golla, Ramesh; Ghatty, Sreenivas
- Plant Molecular Biology, Vol. 84, Issue 1-2
Conservation and divergence of plant microRNA genes
journal, April 2006
- Zhang, Baohong; Pan, Xiaoping; Cannon, Charles H.
- The Plant Journal, Vol. 46, Issue 2
MicroRNA networks and developmental plasticity in plants
journal, May 2011
- Rubio-Somoza, Ignacio; Weigel, Detlef
- Trends in Plant Science, Vol. 16, Issue 5
Oil-seed crop: Camelina sativa
journal, May 1997
- Zubr, Josef
- Industrial Crops and Products, Vol. 6, Issue 2
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes
journal, February 2007
- Fahlgren, Noah; Howell, Miya D.; Kasschau, Kristin D.
- PLoS ONE, Vol. 2, Issue 2
Identifying Conserved and Novel MicroRNAs in Developing Seeds of Brassica napus Using Deep Sequencing
journal, November 2012
- Körbes, Ana Paula; Machado, Ronei Dorneles; Guzman, Frank
- PLoS ONE, Vol. 7, Issue 11
In silico identification of conserved microRNAs in large number of diverse plant species
journal, January 2008
- Sunkar, Ramanjulu; Jagadeeswaran, Guru
- BMC Plant Biology, Vol. 8, Issue 1
A high-throughput method to monitor the expression of microRNA precursors
journal, February 2004
- Schmittgen, T. D.
- Nucleic Acids Research, Vol. 32, Issue 4
Camelina (Camelina sativa L.) oil as a biofuels feedstock: Golden opportunity or false hope?
journal, December 2010
- Moser, Bryan R.
- Lipid Technology, Vol. 22, Issue 12
Limitations and possibilities of small RNA digital gene expression profiling
journal, July 2009
- Linsen, Sam E. V.; de Wit, Elzo; Janssens, Georges
- Nature Methods, Vol. 6, Issue 7
Small RNA Profiling in Two Brassica napus Cultivars Identifies MicroRNAs with Oil Production- and Development-Correlated Expression and New Small RNA Classes
journal, December 2011
- Zhao, Ying-Tao; Wang, Meng; Fu, San-Xiong
- Plant Physiology, Vol. 158, Issue 2
Lipid Profiles in Wheat Cultivars Resistant and Susceptible to Tan Spot and the Effect of Disease on the Profiles
journal, January 2013
- Kim, Dongwon; Jeannotte, Richard; Welti, Ruth
- Phytopathology, Vol. 103, Issue 1
Agronomic evaluation of camelina genotypes selected for seed quality characteristics
journal, October 2007
- Vollmann, Johann; Moritz, Thomas; Kargl, Christine
- Industrial Crops and Products, Vol. 26, Issue 3
Acyl-Lipid Metabolism
journal, January 2013
- Li-Beisson, Yonghua; Shorrosh, Basil; Beisson, Fred
- The Arabidopsis Book, Vol. 11
miRBase: annotating high confidence microRNAs using deep sequencing data
journal, November 2013
- Kozomara, Ana; Griffiths-Jones, Sam
- Nucleic Acids Research, Vol. 42, Issue D1
Identification and Characterization of microRNAs from Peanut (Arachis hypogaea L.) by High-Throughput Sequencing
journal, November 2011
- Chi, Xiaoyuan; Yang, Qingli; Chen, Xiaoping
- PLoS ONE, Vol. 6, Issue 11
Identifying MicroRNAs and Transcript Targets in Jatropha Seeds
journal, February 2014
- Galli, Vanessa; Guzman, Frank; de Oliveira, Luiz F. V.
- PLoS ONE, Vol. 9, Issue 2
Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?
journal, February 2008
- Filipowicz, Witold; Bhattacharyya, Suvendra N.; Sonenberg, Nahum
- Nature Reviews Genetics, Vol. 9, Issue 2
Works referencing / citing this record:
High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying
journal, July 2017
- Feng, Jin-Ling; Yang, Zhi-Jian; Chen, Shi-Pin
- BMC Genomics, Vol. 18, Issue 1