title: Alternative splicing in tomato pollen in response to heat stress.
abstract: Alternative splicing (AS) is a key control mechanism influencing signal response cascades in different developmental stages and under stress conditions. In this study, we examined heat stress (HS)-induced AS in the heat sensitive pollen tissue of two tomato cultivars. To obtain the entire spectrum of HS-related AS, samples taken directly after HS and after recovery were combined and analysed by RNA-seq. For nearly 9,200 genes per cultivar, we observed at least one AS event under HS. In comparison to control, for one cultivar we observed 76% more genes with intron retention (IR) or exon skipping (ES) under HS. Furthermore, 2,343 genes had at least one transcript with IR or ES accumulated under HS in both cultivars. These genes are involved in biological processes like protein folding, gene expression and heat response. Transcriptome assembly of these genes revealed that most of the alternative spliced transcripts possess truncated coding sequences resulting in partial or total loss of functional domains. Moreover, 141 HS specific and 22 HS repressed transcripts were identified. Further on, we propose AS as layer of stress response regulating constitutively expressed genes under HS by isoform abundance.
authors.affiliation: Department of Biosciences, Molecular Cell Biology of Plants.
authors.forename: Mario
authors.initials: M
authors.lastname: Keller
authors.affiliation: Department of Biosciences, Molecular Cell Biology of Plants.
authors.forename: Yangjie
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Department of Biosciences, Molecular Cell Biology of Plants.
authors.forename: Anida
authors.initials: A
authors.lastname: Mesihovic
authors.affiliation: Department of Biosciences, Molecular Cell Biology of Plants.
authors.forename: Sotirios
authors.initials: S
authors.lastname: Fragkostefanakis
authors.affiliation: Department of Biosciences, Molecular Cell Biology of Plants.|Cluster of Excellence Frankfurt.|Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, D-60438 Frankfurt am Main, Germany.
authors.forename: Enrico
authors.initials: E
authors.lastname: Schleiff
authors.affiliation: Department of Biosciences, Molecular Cell Biology of Plants.|Cluster of Excellence Frankfurt.
authors.forename: Stefan
authors.initials: S
authors.lastname: Simm
mesh_terms: D017398:Alternative Splicing; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D006358:Hot Temperature; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D010940:Plant Proteins / Q000235:genetics; D011058:Pollen / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D015398:Signal Transduction; D013312:Stress, Physiological
chemical_list: D010940:Plant Proteins
keywords: RNA-seq; alternative splicing; assembly; heat stress; tomato pollen; transcriptome