Sandra Smit

KCFtools uses k-mer profiles for introgression screening and GWAS without sequence alignment, showing effectiveness in detecting introgressed segments and trait-associated loci in lettuce.

The Lettuce Expression Browser provides a high-resolution gene expression atlas for cultivated and wild lettuce, enabling exploration of gene activity across development and stress conditions.

The paper investigates the evolutionary dynamics of carotovoricin in Pectobacterium, finding that tail fiber gene exchange maintains diversity and influences community interactions.

MoGAAAP automates genome assembly and annotation using HiFi and other long-read data, producing quality assessments for comparative genomics.

This paper presents three new Capsicum genomes, expands the pangenome framework, and identifies genetic diversity and gene loci relevant to capsaicinoid biosynthesis.

PanVA is a visual analytics tool for exploring pangenomic variants in homologous sequences with metadata and phylogenies.

This study presents two high-quality rose genomes and constructs a Rosa pangenome to explore genetic diversity, evolution, and breeding potential in the genus Rosa.

The paper studies prophage dynamics in Pectobacterium species using a pangenome approach, finding that prophages contribute significantly to genome evolution and lineage diversification.

The paper introduces PanTools, a ploidy-aware pangenome analysis tool, and demonstrates its application to potato and apple genomes, revealing high allelic diversity and structural variants.

This study constructs a lettuce super-pangenome to reduce bias in reference genes, identifying novel QTLs for disease resistance and origins of non-reference resistance loci from wild relatives.

The paper compares transcriptomic responses to high light in Hirschfeldia incana and three Brassicaceae species to identify differences in photosynthetic pathways.

The paper presents a reference genome assembly of Hirschfeldia incana, showing its high photosynthetic efficiency compared to related Brassicaceae species and identifying genomic features potentially contributing to this trait.

Hecaton detects copy number variation in plant genomes using short read sequencing data, outperforming existing methods and accurately identifying dispersed duplications.

The paper introduces a multi-reference read mapping approach using PanTools, which is as accurate as existing methods but more efficient for large genome collections.

The paper shows that non-nodulating relatives of Parasponia lost key symbiosis genes, challenging the hypothesis that nodulation evolved independently multiple times.