Jeremy Schmutz

This study presents a chromosome-scale genome assembly of Edelweiss, revealing its recent allotetraploid origin and localized subgenome dominance.

The paper identifies a supernumerary B-Chromosome in Atlantic switchgrass, showing its evolutionary origin and impact on gene expression and genomic diversity.

The paper sequenced genomes of Poaceae sister species to identify metabolic innovations that predate grass evolution, revealing gene duplications linked to starch and lignin biosynthesis.

This study shows that cold acclimation in Brassica rapa involves diel retiming, paralog-specific regulation, and conserved regulatory programs masked by paralog diversification.

This study presents chromosome-level assemblies of two perennial Brachypodium species, revealing genomic features like polyploidy and transposable element dynamics that shaped genome evolution.

The paper analyzes the nuclear genomes of Mesodinium rubrum and finds it lacks spliceosomal introns and related machinery, suggesting introns hinder endosymbiotic genomic integration.

This study uses genome sequences from Cercis canadensis and Chamaecrista fasciculata to infer legume genome structures and histories, including the timing of whole genome duplications and the ancestral karyotype.

The paper identifies the genetic drivers of the G-locus in pecan trees using pangenome-integrated quantitative genomics, revealing a Mendelian super-gene responsible for dichogamy.

The paper catalogs structural and sequence variation in the pennycress pangenome, revealing contrasting evolutionary modes across genomic regions and highlighting the utility of pangenomic resources for crop development.

The paper shows that freshwater threespine stickleback fish have evolved expanded copies of the MYH3C gene family, which is linked to muscle development and adaptive divergence from marine populations.

The paper presents a chromosome-scale, haplotype-resolved genome assembly for Quercus virginiana, contributing to genomic resources for studying hybridization and structural genomic changes in oaks.

This study identifies hundreds of drought-responsive genes in sorghum using multi-season transcriptomic data from field experiments.

This paper uses whole-genome resequencing to analyze diversity and structure in crimson clover and develops a mid-density SNP capture panel for breeding applications.

This study uses over 700 pecan genotypes and a haplotype-resolved genome to identify gene pools, assess environmental adaptation, and predict future maladaptation risks.

This study investigates the origins and adaptive consequences of polyploidy in the prairie grass Andropogon gerardi, finding that whole genome duplication is common and provides fitness advantages in xeric climates.

This study presents a chromosome-level genome of Myrothamnus flabellifolia and transcriptomic data, revealing its desiccation tolerance mechanisms and sex determination system.

This paper constructs a sorghum pangenome and identifies trait-associated variants to inform climate-aware genome-enabled breeding strategies.

The paper uses long-read sequencing to analyze telomere-to-telomere assemblies in Populus trichocarpa, revealing complex KCS gene variation and its association with helitron transposons.

The paper presents an improved haplotype-resolved genome assembly for Eucalyptus grandis, increasing gene annotation completeness and revealing structural variations and tandem duplicates.

This paper identifies ECM29 as a key protein mediating microbial enhancement of plant heat stress tolerance through proteasome modulation in Arabidopsis.

The paper analyzes 739 Thlaspi arvense accessions to uncover genetic variation and adaptation mechanisms, identifying genomic regions linked to agronomic traits and climate resilience.

The paper develops genomic resources to improve American chestnut resistance to pathogens through breeding and gene editing.

This study uses CRISPR-Cas9 to generate sorghum mutants and analyzes their nitrogen response and growth trajectory using high-throughput phenotyping.

The paper presents a haplotype-resolved genome assembly of Amborella trichopoda, identifying a young ZW sex chromosome system with a 3-Megabase sex-determination region that shows limited degeneration.

The paper sequenced twelve Camelina sativa genomes to study pangenomic variation in an allohexaploid species, finding minimal gene presence-absence variation but subgenome-specific gene content.

This study shows that long-read genome sequencing improves diagnostic yield for neurodevelopmental disorders by identifying variants missed by short-read sequencing.

This paper presents an updated soybean genome assembly (Wm82.a6) and compares it with other assemblies and Fiskeby III, revealing genomic heterogeneity and polymorphisms.

This study presents genome assemblies of two homosporous lycophytes, revealing preserved gene collinearity and slow genome evolution over 350 million years.

The paper presents high-quality genomes and chromatin structure analyses of frogs, revealing conserved ancestral chromosomes and stable genome evolution.

The paper presents version 6 of the Chlamydomonas reinhardtii reference genome, improving assembly quality and revealing structural mutations in laboratory strains.