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Updated: Jun 24, 2025

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, CA, 94305, USA.
Abstract:
Most plant genomes and their 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 differential homolog 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 hybrid parental haplotypes, without the use of alignment to a reference genome.
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