title: Genome-wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron-based splicing and its possible function through network analysis.
abstract: In this study, using homology mapping of assembled expressed sequence tags against the genomic data, we identified alternative splicing events in barley. Results demonstrated that intron retention is frequently associated with specific abiotic stresses. Network analysis resulted in discovery of some specific sub-networks between miRNAs and transcription factors in genes with high number of alternative splicing, such as cross talk between SPL2, SPL10 and SPL11 regulated by miR156 and miR157 families. To confirm the alternative splicing events, elongation factor protein (MLOC_3412) was selected followed by experimental verification of the predicted splice variants by Semi quantitative Reverse Transcription PCR (qRT-PCR). Our novel integrative approach opens a new avenue for functional annotation of alternative splicing through regulatory-based network discovery.
authors.affiliation: Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran. Electronic address: panahibahman@ymail.com.
authors.forename: Bahman
authors.initials: B
authors.lastname: Panahi
authors.affiliation: Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
authors.forename: Seyed Abolghasem
authors.initials: SA
authors.lastname: Mohammadi
authors.affiliation: Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran.
authors.forename: Reyhaneh
authors.initials: R
authors.lastname: Ebrahimi Khaksefidi
authors.affiliation: Department of Biology, School of Basic Science, University of Qom, Qom, Iran.
authors.forename: Jalil
authors.initials: J
authors.lastname: Fallah Mehrabadi
authors.affiliation: School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, Australia; Institute of Biotechnology, Shiraz University, Shiraz, Iran; Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, Australia; School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia.
authors.forename: Esmaeil
authors.initials: E
authors.lastname: Ebrahimie
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001483:Base Sequence; D005091:Exons / Q000235:genetics; D063990:Gene Ontology; D053263:Gene Regulatory Networks / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D001467:Hordeum / Q000166:cytology / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D007210:Indoleacetic Acids / Q000378:metabolism; D007438:Introns / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics; D013312:Stress, Physiological / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D007210:Indoleacetic Acids; D035683:MicroRNAs; D014157:Transcription Factors
keywords: Alternative splicing; Functional diversity; Hordeum vulgare; Network discovery; Semi quantitative Reverse Transcription PCR