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A reference-free algorithm discovers regulation in the plant transcriptome

Meyer, E.; Saldivar, E.; Kokot, M.; Xue, B.; Deorowicz, S.; Rhee, S. Y.; Salzman, J.

2024-05-25 bioinformatics
10.1101/2024.05.23.595613 bioRxiv
Show 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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