title: Computational identification of microRNAs in the strawberry (Fragaria x ananassa) genome sequence and validation of their precise sequences by miR-RACE.
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 be detected in different tissues of strawberry ranging from roots, stems, leaves, flowers and fruits by qRT-PCR and some of them showed differential expression in various tissues. The functional analysis of 16 miRNAs and their targets was carried out. Finally, we conclude that there are 34 mirRNAs in strawberry and their targets play vital roles not only in growth and development, but also in diverse physiological processes. These results show that regulatory miRNAs exist in agronomically important strawberry and might have an important function in strawberry growth and development.
authors: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors: Jian
authors: J
authors: Han
authors: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors: Aying
authors: A
authors: Li
authors: Department of Horticulture, Nanjing Jinling Institute of Technology, Nanjing 210038, China.
authors: Hong
authors: H
authors: Liu
authors: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors: Xicheng
authors: X
authors: Wen
authors: Department of Horticulture, Nanjing Jinling Institute of Technology, Nanjing 210038, China.
authors: Mizhen
authors: M
authors: Zhao
authors: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors: Nadira Bilkish
authors: NB
authors: Korir
authors: Department of Agricultural Technology, Kenyatta University, P.O. Box, 43844-00100 Nairobi, Kenya.
authors: Nicholas Kibet
authors: NK
authors: Korir
authors: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors: Chen
authors: C
authors: Wang
authors: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: fanggg@njau.edu.cn.
authors: Jinggui
authors: J
authors: Fang
mesh_terms: D003001:Cloning, Molecular; D019295:Computational Biology; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D031985:Fragaria / Q000235:genetics* / Q000254:growth & development; D005638:Fruit / Q000235:genetics / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA; D014018:Tissue Distribution
chemical_list: D035683:MicroRNAs
keywords: Bioinformatics; CDS; DCL1; EST; Fragaria vesca microRNA; Fve-mirRNA; Genome database; LMW; MicroRNAs; RISC; Strawberry; UPE; coding sequence; expressed sequence tag; low molecular weight; miRNA RACE; miRNAs; microRNAs; qRT-PCR; quantitative real-time PCR; the RNA-induced silencing complex; the ribonuclease III-like enzyme Dicer; unpaired energy