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KMID : 0381120130350030377
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Genes and Genomics
2013 Volume.35 No. 3 p.377 ~ p.385
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Computational identification of microRNAs and their targets in apple
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Ye Keyong
Chen Yao
Hu Xinwen
Guo Jianchun
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Abstract
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MicroRNAs (miRNAs) are small RNAs approximately 21 nucleotides in length that regulate post-transcriptional gene expression by cleaving or inhibiting the translation of target gene transcripts. Based on the conservation of miRNAs in many plant species and the currently available genome sequence, 154 individual conserved miRNAs have been predicted in apple (Malus domestica), and found that these miRNAs belong to 26 families. 424 miRNA:target pairs between 150 miRNAs and 235 mRNAs have been predicted in apple, and these miRNA targets are involved in development, response to biotic and abiotic stresses, and other cellular processes. From studying the miR395 and miR399 clusters in apple, it was confirmed that the expansion of miRNA gene families in apple came about via segmental duplications. The study of divergence in homologous miRNA indicates that miRNA/miRNA* region is more conservative than loop-containing region.
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KEYWORD
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Apple, MiRNA, MiRNA precursor, MiRNA target, MiRNA clusters
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