The paper identifies and addresses cytosine-conversion errors in bisulphite sequencing caused by transposase activity, providing a Python package to correct these errors.

PLoS ONE · May 21, 2025Peer-reviewedGenomics

Life-history trade-offs explain local adaptation in Arabidopsis thaliana

Benjamin Brachi, Danièle L. Filiault, Rahul Pisupati, Tal Dahan‐Meir, Anna A. Igolkina, Alison Anastasio, Mathew S. Box, Susan Hanley Duncan, Talia L. Karasov, Envel Kerdaffrec, Laura Merwin, Timothy C. Morton, Viktoria Nizhynska, Polina Yu. Novikova, Fernando A. Rabanal, , Magnus Nordborg

This study shows that local adaptation in Arabidopsis thaliana involves strong and variable selection on multiple traits, with trade-offs and life-history strategies affecting fitness.

bioRxiv · May 18, 2025 · PreprintEvolutionary Biology

Population-level annotation of lncRNA transcription in Arabidopsis reveals extensive variation associated with TE-like silencing

Aleksandra E. Kornienko, Viktoria Nizhynska, Almudena Molla Morales, Rahul Pisupati, Magnus Nordborg

The paper annotates lncRNA loci in Arabidopsis thaliana across multiple natural accessions, revealing high expression variability and silencing linked to transposable elements.

bioRxiv · Mar 14, 2023 · PreprintGenomics

On the Causes of Gene-Body Methylation Variation in Arabidopsis thaliana

Rahul Pisupati, Viktoria Nizhynska, Almudena Molla Morales, Magnus Nordborg

This study investigates gene-body methylation variation in Arabidopsis thaliana by analyzing F2 plants from a cross between two Swedish lines, showing genetic and environmental influences on methylation patterns.

bioRxiv · Dec 4, 2022 · PreprintGenetics

Extensive gene duplication in Arabidopsis revealed by pseudo-heterozygosity

Benjamin Jaegle, Rahul Pisupati, Luz Mayela Soto-Jiménez, Robin Burns, Fernando A. Rabanal, Magnus Nordborg

The paper identifies 2500 putatively duplicated genes in Arabidopsis thaliana by analyzing SNP calls from short-read sequencing and validates them using de novo genome assemblies.

bioRxiv · Nov 15, 2021 · PreprintGenomics

Genomic evidence that governmentally produced Cannabis sativa poorly represents genetic variation available in state markets

Daniela Vergara, Ezra L. Huscher, Kyle G. Keepers, Rahul Pisupati, Anna L. Schwabe, Mitchell E. McGlaughlin, Nolan C. Kane

This study shows that NIDA-produced Cannabis sativa lacks genetic diversity compared to state market varieties, limiting the generalizability of research findings.

Frontiers in Plant Science · Sep 14, 2021Peer-reviewedGenomics

Stage-specific transcriptomes and DNA methylomes indicate an early and transient loss of transposon control in Arabidopsis shoot stem cells

Ruben Gutzat, Klaus Rembart, Thomas Nußbaumer, Rahul Pisupati, Falko Hofmann, Gabriele Bradamante, Nina Daubel, Angelika Gaidora, Nicole Lettner, Mattia Donà, Magnus Nordborg, Michael D. Nodine, Ortrun Mittelsten Scheid

The paper analyzes gene expression and DNA methylation in Arabidopsis shoot stem cells, revealing transient transposon activation and epigenetic reprogramming during their transition to reproductive lineage.

The EMBO Journal · Aug 20, 2020Peer-reviewedDevelopmental Biology

Verification of Arabidopsis stock collections using SNPmatch - an algorithm for genotyping high-plexed samples

Rahul Pisupati, Ilka Reichardt, Ümit Seren, Pamela Korte, Viktoria Nizhynska, Envel Kerdaffrec, Kristina Uzunova, Fernando A. Rabanal, Danièle L. Filiault, Magnus Nordborg

The paper introduces SNPmatch, an algorithm for genotyping Arabidopsis strains from low-coverage sequencing data, and validates its accuracy using over 2000 strains.

Scientific Data · Dec 19, 2017Peer-reviewedGenomics