Computational identification of microRNAs in the strawberry (Fragaria x ananassa) genome sequence and validation of their precise sequences by miR-RACE

Gene
Jian HanJinggui Fang

Abstract

In plants, microRNAs (miRNAs) play significant roles in post-transcriptional gene regulation and have been found to control many genes involved in different biological and metabolic processes. Extensive studies were carried out to discover miRNAs and analyze their functions in model plant species, such as in Arabidopsis and rice that have been reported. In this research, we used bioinformatics to predict microRNAs in an important strawberry rootstock cultivar to discover and validate precise sequences of microRNAs in strawberry. By adopting a range of filtering criteria, we obtained 59 potential miRNAs belonging to 40 miRNA families from the Fragaria vesca genome. Using two specific 5' and 3' miRNA RACE PCR reactions and a sequence-directed cloning method, we accurately determined 34 precise sequences of candidate miRNAs, while six other sequences exhibited some minor divergence in their termini nucleotides, and 19 miRNAs that could not be cloned owing to expression abundance may be too low or these mirRNAs predicted could not be existing in strawberry. Potential target genes were further predicted for the miRNAs above. The expression of the 16 miRNAs unreported and having exact sequences and their targets by experiment could b...Continue Reading

References

Feb 7, 2001·Genes & Development·S M ElbashirT Tuschl
Aug 31, 2002·Cell·Matthew W RhoadesDavid P Bartel
Mar 6, 2003·Neuroscience Letters·Christian RamakersAntoon F M Moorman
Mar 17, 2004·Nucleic Acids Research·Jia-Fu WangLiang-Hu Qu
Apr 2, 2004·Nature·Sandra K Floyd, John L Bowman
Jun 18, 2004·Molecular Cell·Matthew W Jones-Rhoades, David P Bartel
Jul 20, 2004·The Plant Cell·Ramanjulu Sunkar, Jian-Kang Zhu
Aug 18, 2004·Proceedings of the National Academy of Sciences of the United States of America·Yukio Kurihara, Yuichiro Watanabe
Jan 7, 2005·The FEBS Journal·Michel J Weber
Apr 26, 2005·The Plant Cell·Michael J Axtell, David P Bartel
Apr 27, 2005·Cell·Edwards AllenJames C Carrington
Jun 17, 2005·Proceedings of the National Academy of Sciences of the United States of America·Nick LauterStephen P Moose
Jun 28, 2005·FEBS Letters·Hanjiang FuXiaofei Zheng
Sep 8, 2005·FEBS Letters·Xuemei Chen
Oct 21, 2005·BioTechniques·Rui Shi, Vincent L Chiang
Nov 30, 2005·Nucleic Acids Research·Caifu ChenKarl J Guegler
Feb 3, 2006·Bioinformatics·Ivo L Hofacker, Peter F Stadler
Apr 21, 2006·The Plant Journal : for Cell and Molecular Biology·Baohong ZhangTodd A Anderson
Jun 1, 2006·Nature Genetics·Eugene BerezikovRonald H A Plasterk
Jul 19, 2006·Birth Defects Research. Part C, Embryo Today : Reviews·Sungroh Yoon, Giovanni De Micheli
Nov 25, 2006·Computational Biology and Chemistry·Baohong ZhangTodd A Anderson
Jul 3, 2007·The Plant Cell·Michael J AxtellDavid P Bartel
Mar 4, 2008·BMC Plant Biology·Ramanjulu SunkarJian-Kang Zhu
Apr 18, 2008·BMC Plant Biology·Ramanjulu Sunkar, Guru Jagadeeswaran
May 17, 2008·Science·Peter BrodersenOlivier Voinnet
Feb 26, 2009·Cell·Richard W Carthew, Erik J Sontheimer
Jul 9, 2009·Planta·Changnian SongC Thomas Chao
Dec 28, 2010·Nature Genetics·Vladimir ShulaevKevin M Folta
May 31, 2011·Nucleic Acids Research·Xinbin Dai, Patrick Xuechun Zhao

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