Computational identification of microRNAs in apple expressed sequence tags and validation of their precise sequences by miR-RACE

Thirty‐one potential miRNAs that belong to 16 miRNA families were discovered from more than 324 000 EST sequences of apple (Malus domestica). In addition, precise sequences, especially terminal nucleotides of the 16 apple miRNAs (mdo‐miRNAs) in 16 families were validated by miR‐RACE, a newly develop...

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Published in:Physiologia plantarum 2011-01, Vol.141 (1), p.56-70
Main Authors: Yu, Huaping, Song, Changnian, Jia, Qidong, Wang, Chen, Li, Fei, Nicholas, Korir Kibet, Zhang, Xiaoying, Fang, Jinggui
Format: Article
Language:English
Subjects:
Base Sequence
Biological and medical sciences
Cloning, Molecular
Computational Biology - methods
Expressed Sequence Tags
Fundamental and applied biological sciences. Psychology
Gene Expression Regulation, Plant
Gene Library
Genes, Plant - genetics
Malus - genetics
MicroRNAs - genetics
MicroRNAs - metabolism
Molecular Sequence Data
Nucleic Acid Conformation
Plant physiology and development
Reproducibility of Results
Reverse Transcriptase Polymerase Chain Reaction - methods
Sequence Analysis, RNA - methods
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Summary:Thirty‐one potential miRNAs that belong to 16 miRNA families were discovered from more than 324 000 EST sequences of apple (Malus domestica). In addition, precise sequences, especially terminal nucleotides of the 16 apple miRNAs (mdo‐miRNAs) in 16 families were validated by miR‐RACE, a newly developed method for the determination of the potential miRNAs predicted computationally. The expression of these 16 microRNAs could be detected in apple young leaf, old leaf, young stem, flower bud, flower and developing fruits by quantitative RT‐PCR (qRT‐PCR) and some of them showed tissue‐specific expression. Fifty‐six potential targets were identified for the 16 apple miRNAs, most of which were transcription factors that play important roles in apple development. Twelve target genes were experimentally verified by qRT‐PCR, with some exhibiting different expression trends from their corresponding microRNAs, indicating the cleavage mode of miRNAs on their target genes.
ISSN:0031-9317
1399-3054
DOI:10.1111/j.1399-3054.2010.01411.x