Alternative splicing enhances transcriptome complexity in desiccating seeds.
Before being dispersed in the environment, mature seeds need to be dehydrated. The survival of seeds after dispersal depends on their low hydration in combination with high desiccation tolerance. These characteristics are established during seed maturation. Some key seed maturation genes have been reported to be regulated by alternative splicing (AS). However, so far AS was described only for single genes and a comprehensive analysis of AS during seed maturation has been lacking. We investigated gene expression and AS during Arabidopsis thaliana seed development at a global level, before and after desiccation. Bioinformatics tools were developed to identify differentially spliced regions within genes. Our data suggest the importance and shows the peculiar features of AS during seed desiccation. We identified AS in 34% of genes that are expressed at both timepoints before and after desiccation. Most of these AS transcript variants had not been found before in other tissues. Among the AS genes some seed master regulators could be found. Interestingly, 6% of all expressed transcripts were not transcriptionally regulated during desiccation, but only modified by AS. We propose that AS should be more routinely taken into account in the analysis of transcriptomic data to prevent overlooking potentially important regulators.
Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.|Open Analytics, Antwerp, Belgium.
Arunkumar
A
Srinivasan
Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.|Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Versailles, France.
José M
JM
Jiménez-Gómez
University of Milan, Department of Biosciences, Milano 20133, Italy.
Fabio
F
Fornara
Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Wim J J
WJ
Soppe
Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.|University of Milan, Department of Biosciences, Milano 20133, Italy.|University of Milan, Department of Agricultural and Environmental Sciences, via Celoria 2, 20133 Milano, Italy.
Vittoria
V
Brambilla
D017398:Alternative Splicing / Q000235:genetics*; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology; D003890:Desiccation; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D015203:Reproducibility of Results; D012639:Seeds / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
D029681:Arabidopsis Proteins
Alternative splicing; Arabidopsis thaliana; seed desiccation