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.

doi:10.1101/2024.05.23.595613

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bioRxiv · 10.1101/2024.05.23.595613

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.

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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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Meyer, E., Saldivar, E., Kokot, M., Xue, B., Deorowicz, S., Rhee, S. Y., Salzman, J.. 2024-05-25. A reference-free algorithm discovers regulation in the plant transcriptome. https://doi.org/10.1101/2024.05.23.595613

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