RESEARCH ARTICLE k

ro Alternative splicing (AS) is considered to be a key factor patterns of AS in plant species [9], but recent results Bao et al. BMC Genomics 2013, 14:359 http://www.biomedcentral.com/1471-2164/14/359non-IR AS, and within IR variants, a large number ofV6T1Z4, CanadaFull list of author information is available at the end of the articleunderlying increased cellular and functional complexity in higher eukaryotes and has been studied extensively on the genome-wide scale in humans, other animals, and plants [1-5]. In humans, RNA splice variants with alter-native exon configurations often accumulate differen-tially across different tissues and individuals [1,6-8] and such tissue-specific gene isoforms can have important functions in development and in the functioning of dif-ferent cell types. from Arabidopsis [10] and rice [11] have revealed high levels of AS that can vary in different organs and under different stress conditions. Next generation high throughput transcriptome sequencing (RNA-Seq) ana-lysis suggests that 42 % of the intron-containing genes in Arabidopsis undergo AS [10]. Using a normalized cDNA library derived from flower and seedling tissue, Marquez et al. [5] used deep RNA-Seq transcriptome analysis to show that over 60 % of Arabidopsis intron-containing genes are alternatively spliced, with intron retention (IR) being the most common form of AS. The analysis re-vealed, however, that over 50 % of genes surveyed displa