A Reference-Free Algorithm Discovers Regulation in the Plant Transcriptome

Most plant genomes and their (post-)transcriptional regulation remain unknown. We used SPLASH—a new, reference genome-free sequence variation detection algorithm—to analyze transcriptional and post-transcriptional regulation from RNA-seq data. We discovered allelic variation in expression during maize pollen development and imbibition-dependent cryptic splicing in Arabidopsis seeds. SPLASH enables discovery of novel regulatory mechanisms, including differential regulation of genes from parental haplotypes of hybrids, without the use of alignment to a reference genome.