title: Profiling microRNAs and their targets in an important fleshy fruit: tomato (Solanum lycopersicum).
abstract: Tomato (Solanum lycopersicum) is an important and the most useful plant based diet. It is widely used for its antioxidant property. Presently, only two digits, tomato microRNAs (miRNAs) are reported in miRBase: a miRNA database. This study is aimed to profile and characterize more miRNAs and their targets in tomato. A comprehensive comparative genomic approach is applied and a total of 109 new miRNAs belonging to 106 families are identified and characterized from the tomato expressed sequence tags (ESTs). All these potential miRNAs are profiled for the first time in tomato. The profiled miRNAs are also observed with stable stem-loop structures (Precursor-miRNAs), whose length ranges from 45 to 329 nucleotides (nt) with an average of 125 nt. The mature miRNAs are found in the stem of pre-miRNAs and their length ranges from 19 to 24 nt with an average of 21 nt. Furthermore, twelve miRNAs are randomly selected and experimentally validated through RT-PCR. A total of 406 putative targets are also predicted for the newly 109 tomato miRNAs. These targets are involved in structural protein, metabolism, transcription factor, growth & development, stress related, signaling pathways, storage proteins and other vital processes. Some important proteins like; 9-cisepoxycarotenoid dioxygenase (NCED), transcription factor MYB, ATP-binding cassette transporters, terpen synthase, 14-3-3 and TIR-NBS proteins are also predicted as putative targets for tomato miRNAs. These findings improve a baseline data of miRNAs and their targets in tomato. This baseline data can be utilized to fine tune this important fleshy fruit for nutritional & antioxidant properties and also under biotic & abiotic stresses.
authors: Department of Botany, University of Balochistan, Sariab Road Quetta, Pakistan.
authors: Muhammad
authors: M
authors: Din
authors: Department of Botany, University of Balochistan, Sariab Road Quetta, Pakistan. Electronic address: barozaikhan@gmail.com.
authors: Muhammad Younas Khan
authors: MY
authors: Barozai
mesh_terms: D001483:Base Sequence; D020224:Expressed Sequence Tags; D005638:Fruit / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000145:classification / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D035683:MicroRNAs
keywords: Arabidopsis lyrata; Arabidopsis thaliana; BLAST; Basic Local Alignment Search Tool; Brachypodium distachyon; DCL1; Database of EST; Dicer-like Enzyme1; EST; ESTs; Expressed Sequence Tags; Glycine max; MFE; MIR; Messenger RNA; MicroRNA; MicroRNA Gene; Minimum Free Energy; NCBI; National Center for Biotechnology Information; Nucleotide; Opposite Strand of miRNA; Oryza sativa; Pol II; Pre-miRNA; Precursor-miRNA; Pri-miRNA; Primary Transcripts of Mature miRNA; RISC; RNA Induced Silencing Complex; RNA Polymerase II Enzyme; RT-PCR; Reference mRNA sequence; Refseq_rna; Reverse Transcription-Polymerase Chain Reaction; Tomato; aly; ath; bdi; dbEST; gma; mRNA; miRNA; miRNA*; nt; osa