J Integr Plant Biol. ›› 2016, Vol. 58 ›› Issue (12): 947-958.DOI: 10.1111/jipb.12482

• Cell and Developmental Biology • Previous Articles     Next Articles

Alternative splicing enhances transcriptome complexity in desiccating seeds

Arunkumar Srinivasan1,2, José M. Jiménez-Gómez1,3, Fabio Fornara4, Wim J. J. Soppe1 and Vittoria Brambilla1,4,5,*   

  1. 1Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
    2Open Analytics, Antwerp, Belgium
    3Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Versailles, France
    4University of Milan, Department of Biosciences, Milano 20133, Italy
    5University of Milan, Department of Agricultural and Environmental Sciences, via Celoria 2, 20133 Milano, Italy

Abstract:

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.

Key words: Alternative splicing, Arabidopsis thaliana, seed desiccation

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