Funct Integr Genomics. 2009 Nov;9(4):499-511. Epub 2009 Jun 5.

Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv.

Wei B, Cai T, Zhang R, Li A, Huo N, Li S, Gu YQ, Vogel J, Jia J, Qi Y, Mao L.

Source

National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, Pr China.

Abstract

The small RNA transcriptomes of bread wheat and its emerging model Brachypodium distachyon were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNAs) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of expressed sequence tags, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' rapid amplification of complementary DNA ends experiments demonstrated their capability to cleave predicted target genes including three disease-resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in B. distachyon.

PMID:: 19499258; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Supplemental Content

Save items

Related citations in PubMed

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. [BMC Genomics. 2009]
Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response.
Zhang J, Xu Y, Huan Q, Chong K. BMC Genomics. 2009 Sep 23; 10:449. Epub 2009 Sep 23.
Computational identification of microRNAs and their targets in wheat (Triticum aestivum L.). [Sci China C Life Sci. 2009]
Computational identification of microRNAs and their targets in wheat (Triticum aestivum L.).
Han Y, Luan F, Zhu H, Shao Y, Chen A, Lu C, Luo Y, Zhu B. Sci China C Life Sci. 2009 Nov; 52(11):1091-100. Epub 2009 Nov 24.
Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). [Genome Biol. 2007]
Cloning and characterization of microRNAs from wheat (Triticum aestivum L.).
Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q. Genome Biol. 2007; 8(6):R96.
Review MicroRNAs and mammalian ovarian development. [Semin Reprod Med. 2008]
Review MicroRNAs and mammalian ovarian development.
Zhao H, Rajkovic A. Semin Reprod Med. 2008 Nov; 26(6):461-8. Epub 2008 Oct 24.
Review Expression profiling of microRNAs by deep sequencing. [Brief Bioinform. 2009]
Review Expression profiling of microRNAs by deep sequencing.
Creighton CJ, Reid JG, Gunaratne PH. Brief Bioinform. 2009 Sep; 10(5):490-7. Epub 2009 Mar 30.

See reviews... See all...

Cited by 7 PubMed Central articles

High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.). [PLoS One. 2011]
High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.).
Donaire L, Pedrola L, Rosa Rde L, Llave C. PLoS One. 2011; 6(11):e27916. Epub 2011 Nov 28.
First survey of the wheat chromosome 5A composition through a next generation sequencing approach. [PLoS One. 2011]
First survey of the wheat chromosome 5A composition through a next generation sequencing approach.
Vitulo N, Albiero A, Forcato C, Campagna D, Dal Pero F, Bagnaresi P, Colaiacovo M, Faccioli P, Lamontanara A, Šimková H, et al. PLoS One. 2011; 6(10):e26421. Epub 2011 Oct 18.
Function and evolution of a MicroRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. [Plant Cell. 2011]
Function and evolution of a MicroRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth.
Wang Y, Itaya A, Zhong X, Wu Y, Zhang J, van der Knaap E, Olmstead R, Qi Y, Ding B. Plant Cell. 2011 Sep; 23(9):3185-203. Epub 2011 Sep 13.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
GEO DataSets
Gene expression and molecular abundance data reported in the current articles that are also included in the curated Gene Expression Omnibus (GEO) DataSets.
Related Project
Related Projects
SRA
Massively-parallel sequencing project data in the Short Read Archive (SRA) that are reported in the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in brea...
Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv.
Funct Integr Genomics. 2009 Nov ;9(4):499-511. Epub 2009 Jun 5 .

PubMed
A new view of radiation-induced cancer: integrating short- and long-term process...
A new view of radiation-induced cancer: integrating short- and long-term processes. Part II: second cancer risk estimation.
Radiat Environ Biophys. 2009 Aug ;48(3):275-86. Epub 2009 Jun 5 .

PubMed
Transport advances in disposable bioreactors for liver tissue engineering.
Transport advances in disposable bioreactors for liver tissue engineering.
Adv Biochem Eng Biotechnol. 2010 ;115:117-43.

PubMed
An experimental intraarticular implantation of woven carbon fiber pad into osteo...
An experimental intraarticular implantation of woven carbon fiber pad into osteochondral defect of the femoral condyle in rabbit.
Yonsei Med J. 1991 Jun ;32(2):108-16.

PubMed
Potential microbial origins of schizophrenia and their treatments.
Potential microbial origins of schizophrenia and their treatments.
Drugs Today (Barc). 2009 Apr ;45(4):305-18.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: