The paper develops crop-specific Nanopore basecalling models for Rosaceae species to improve sequencing quality and enables community use of these models.

Journal of Experimental Horticulture · Sep 24, 2026Peer-reviewedGenomics

Chromosome-level genome assemblies and annotations of Amaranthus spinosus, Amaranthus acanthochiton, Amaranthus arenicola, and Amaranthus floridanus

Damilola A. Raiyemo, Isabel Schlegel Werle, Ramandeep Kaur, Lauren Whitt, Sarah B. Carey, Haley J. Hale, Keyana J. Lewis, Lauren Womack, Alex Harkess, Víctor Llaca, Kevin A. Fengler, Eric L. Patterson, Todd Adam Gaines, Patrick J. Tranel

The paper presents chromosome-level genome assemblies for four Amaranthus species, revealing conserved sex chromosome inversions and providing resources for evolutionary and agronomic research.

bioRxiv · Aug 25, 2026 · PreprintGenomics

A newly arisen indel governs a leaf shape polymorphism in the Ivy Leaf Morning Glory (Ipomoea hederacea)

Amanda L. Peake, Emily Glasgow, Claire Abbasi, Yunchen Gong, Lauren Whitt, Melissa Williams, Jane Grimwood, Alex Harkess, John R. Stinchcombe

The paper identifies a 117 kb indel associated with leaf shape polymorphism in Ipomoea hederacea and shows it is a novel genetic mechanism distinct from related species.

bioRxiv · Jul 7, 2026 · PreprintPlant Biology

A comparative approach for selecting orthologous candidate genes in genome-wide associationstudies across multiple species

Lauren Whitt, Elizabeth H. Mahood, Greg Ziegler, Collin Luebbert, Jason D. Gillman, Gareth John Norton, Adam H. Price, David E. Salt, Brian P. Dilkes, Ivan R. Baxter

The paper develops a method to identify conserved causative genes across species using multi-species GWAS data, finding that conserved genes are more frequently associated with trait variation than expected by chance.

PLANT PHYSIOLOGY · May 22, 2026Peer-reviewedGenetics

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

Shengchen Shan, Edgardo Ortiz, Baylee Klein, Arthur Oganisyan, Gia Serrano, Bryanna Stults, Rubina Torkzadeh, Audrey Tucker, Ezra Linnan, Benjamin Pringle, Tyler Radtke, Moumita Hoque Rainy, Lia Swanson, Gabrielle Vines, Lauren Whitt, , Douglas E. Soltis

This paper presents the first chromosome-scale, haplotype-resolved genome assembly and annotation for Carya glabra, revealing it as an autotetraploid and providing resources for ecological and agricultural studies.

G3 Genes Genomes Genetics · May 20, 2026Peer-reviewedGenomics

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow

Ryan D. Kuster, Zane C Smith, Lauren Whitt, Margaret E. Staton, Ben N. Mansfeld, Christopher Gottschalk

RAGNAROK is a genome annotation pipeline that improves sensitivity, precision, and runtime for plant genomes compared to existing tools.

bioRxiv · Oct 3, 2025 · PreprintBioinformatics

Genome-Wide Associations within Diverse Wild Apple Germplasm for Postharvest Blue Mold Resistance to Penicillium expansum

Lauren Whitt, John S. Bennett, Tamara D. Collum, Breyn Evans, Doug Raines, Benjamin L. Gutierrez, Wojciech J. Janisiewicz, Wayne M. Jurick, Christopher Gottschalk

The paper identifies SNPs associated with postharvest blue mold resistance in wild apple germplasm using genomic sequencing and association mapping.

Postharvest Biology and Technology · Mar 18, 2025Peer-reviewedGenetics