Computational Identification of MicroRNAs in the Strawberry (Fragaria×ananassa) Genome Sequence and Validation of their Precise Sequences by MiR-RACE.

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dc.contributor.authorKorir, Nicholas Kibet
dc.contributor.authorHan, J.
dc.contributor.authorLi, A.
dc.contributor.authorLiu, H.
dc.contributor.authorWen, X.
dc.contributor.authorZhao, M.
dc.contributor.authorKorir, N. B.
dc.contributor.authorWang, C.
dc.contributor.authorFang, J.
dc.date.accessioned2014-01-14T08:44:58Z
dc.date.available2014-01-14T08:44:58Z
dc.date.issued2013
dc.descriptiondoi: 10.1016/j.gene.2013.11.023.en_US
dc.description.abstractIn 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.en_US
dc.identifier.urihttp://ir-library.ku.ac.ke/handle/123456789/8535
dc.language.isoenen_US
dc.publisherElsevier B.Ven_US
dc.subjectBioinformaticsen_US
dc.subjectCDSen_US
dc.subjectDCL1en_US
dc.subjectESTen_US
dc.subjectFragaria vesca microRNAen_US
dc.subjectFve-mirRNAen_US
dc.subjectGenome databaseen_US
dc.subjectLMWen_US
dc.subjectMicroRNAsen_US
dc.subjectRISCen_US
dc.subjectStrawberryen_US
dc.subjectUPEen_US
dc.subjectCoding sequenceen_US
dc.subjectExpressed sequence tagen_US
dc.subjectLow molecular weighten_US
dc.subjectMiRNA RACE,en_US
dc.subjectMiRNAsen_US
dc.subjectMicroRNAsen_US
dc.subjectQRT-PCRen_US
dc.subjectQuantitative real-time PCRen_US
dc.subjectThe RNA-induced silencing complexen_US
dc.subjectThe ribonuclease III-like enzyme Diceren_US
dc.subjectUnpaired energyen_US
dc.titleComputational Identification of MicroRNAs in the Strawberry (Fragaria×ananassa) Genome Sequence and Validation of their Precise Sequences by MiR-RACE.en_US
dc.typeArticleen_US
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