AppleGFDB:The Apple Gene Function & Gene Family DataBase v1.0
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Apple MicroRNA Database

MicroRNAs (miRNA) are important regulators of post-transcriptional and translational gene expression. A total of 165 apple miRNAs were collected from the publication and the miRNA database and divided into 56 families in AppleGADB. This database provides information on genomic location, target gene, sequence of pre-miRNA and mature miRNA, the structure of the Pre-miRNA and so on.

The prediction of conserved miRNAs was conducted by miRPI software (Vignesh et al., 2011). It identifies the highly conserved mature miRNA sequences without any mismatches against the apple genomic sequences and, in addition, the pre-miRNA sequences was extracted for calculating of GC contents, MFE and MFEI, in order to evaluate the hairpin sequences. Sequence alignment was performed by clustalw software (http://www.ebi.ac.uk/Tools/msa/clustalw2/), and the second structural alignment was conducted by R-coffee software (Moretti et al., 2008). miRNAs were clustered using Blastclust software with CS setting as 0.95. Targets were predicted by psRNATarget web server using predicted consensus gene set CDS sequences of apple genome v1.0 as target datasets (http://plantgrn.noble.org/psRNATarget/) (Dai and Zhao, 2011). Sequences of targets were retrieved from apple CDS database, then send to mapping in GO, KOG and KEGG databases using blast2go software (Conesa et al., 2005). KEGG pathway enrichment analysis was conducted by KAAS server (http://www.genome.jp/tools/kaas/). miRNA-target network constructed by Cytoscape 2.7.0 (Shannon et al., 2003).

 

The Micro RNA data was collected according the following referrence :

Gleave, A., Ampomah-Dwamena, C., Berthold, S., Dejnoprat, S., Karunairetnam, S., Nain, B., Wang, Y.-Y., Crowhurst, R., and MacDiarmid, R. (2008). Identification and characterisation of primary microRNAs from apple ( Malus domestica cv. Royal Gala) expressed sequence tags. Tree Genetics & Genomes 4, 343-358.

Varkonyi-Gasic, E., Gould, N., Sandanayaka, M., Sutherland, P., and MacDiarmid, R.M. (2010). Characterisation of microRNAs from apple (Malus domestica 'Royal Gala') vascular tissue and phloem sap. BMC Plant Biol 10, 159.

Yu, H., Song, C., Jia, Q., Wang, C., Li, F., Nicholas, K.K., Zhang, X., and Fang, J. (2011). Computational identification of microRNAs in apple expressed sequence tags and validation of their precise sequences by miR-RACE. Physiol Plant 141, 56-70.

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