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Updated: Apr 14, 2026

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
Published on: January 21, 2020
A Reference-Free Algorithm Discovers Regulation in the Plant Transcriptome
Elisabeth Meyer1,2, Evan V Saldivar3,4, Marek Kokot5
1Department of Biochemistry Stanford University Stanford California USA.
Abstract:
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.
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