title: De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress.
abstract: Almond (Prunus dulcis Mill.), one of the most important nut crops, requires chilling during winter to develop fruiting buds. However, early spring chilling and late spring frost may damage the reproductive tissues leading to reduction in the rate of productivity. Despite the importance of transcriptional changes and regulation, little is known about the almond's transcriptome under the cold stress conditions. In the current research, we used RNA-seq technique to study the response of the reproductive tissues of almond (anther and ovary) to frost stress. RNA sequencing resulted in more than 20 million reads from anther and ovary tissues of almond, individually. About 40,000 contigs were assembled and annotated de novo in each tissue. Profile of gene expression in ovary showed significant alterations in 5,112 genes, whereas in anther 6,926 genes were affected by freezing stress. Around two thousands of these genes were common altered genes in both ovary and anther libraries. Gene ontology indicated the involvement of differentially expressed (DE) genes, responding to freezing stress, in metabolic and cellular processes. qRT-PCR analysis verified the expression pattern of eight genes randomly selected from the DE genes. In conclusion, the almond gene index assembled in this study and the reported DE genes can provide great insights on responses of almond and other Prunus species to abiotic stresses. The obtained results from current research would add to the limited available information on almond and Rosaceae. Besides, the findings would be very useful for comparative studies as the number of DE genes reported here is much higher than that of any previous reports in this plant.
authors.affiliation: Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran.
authors.forename: Sadegh
authors.initials: S
authors.lastname: Mousavi
authors.affiliation: Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran.
authors.forename: Arghavan
authors.initials: A
authors.lastname: Alisoltani
authors.affiliation: Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran; Institute of Biotechnology, Shahrekord University, Shahrekord, Iran.
authors.forename: Behrouz
authors.initials: B
authors.lastname: Shiran
authors.affiliation: Department of Biology, School of Sciences, Razi University, Bagh-e-Abrisham Kermanshah, Iran.
authors.forename: Hossein
authors.initials: H
authors.lastname: Fallahi
authors.affiliation: Department of Crop Production and Plant Breeding, Faculty of Agriculture, Shiraz University, Shiraz, Iran; School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia.
authors.forename: Esameil
authors.initials: E
authors.lastname: Ebrahimie
authors.affiliation: Department of Horticulture, Seed and Plant Improvement Institute (SPII), Karaj, Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Imani
authors.affiliation: Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran.
authors.forename: Saadollah
authors.initials: S
authors.lastname: Houshmand
mesh_terms: D005615:Freezing; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D058977:Molecular Sequence Annotation / Q000379:methods; D010940:Plant Proteins / Q000235:genetics; D027861:Prunus / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010940:Plant Proteins