Jeremy Schmutz

This study examines gene expression divergence in Panicum hallii using reciprocal transplants, finding constitutive divergence but no plastic responses, and links divergence to cis-regulatory factors.

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

The paper applies genomic selection to sugar kelp with a biphasic life cycle, predicting breeding values for gametophytes and achieving moderate prediction accuracy for yield and morphology traits.

GENESPACE provides pan-genome annotations to analyze syntenic relationships across diverse eukaryotic genomes, revealing structural variation at multiple biological scales.

This study uses whole-genome resequencing to analyze population structure, genomic diversity, and demographic history of American chestnut, identifying regions under positive selection for blight resistance.

The paper identifies master regulator genes and pathways involved in sex dimorphism in Salix purpurea using integrative genomics approaches.

The paper confirms a two-step hybridization model for the formation of hexaploidy in Brassiceae and shows subgenomes have distinct loss rates but functionally compatible genes.

This paper uses long-read genome sequencing to identify pathogenic variants in neurodevelopmental disorders, finding clinically relevant structural variants in two of six probands.

The paper uses genome resources from Setaria viridis to identify loci associated with climate response, seed shattering, and leaf angle, and validates a novel domestication gene.

The paper uses MET phenotypic data from common bean to discover genetic associations and genomic regions linked to agronomic traits over time.

The paper identifies large palindromic structures in the sex chromosome of Salix purpurea, showing convergent evolution with mammalian sex chromosomes.

The paper quantifies age-related somatic mutations and epimutations in a wild Populus trichocarpa tree over 330 years, showing lower mutation rates than annuals and distinct epimutation origins.

The paper reports the de novo genome sequencing and analysis of the rice variety KitaakeX, identifying genomic variations and providing a high-quality reference for rice functional genomics.

The paper uses genomic selection analyses to show that blight tolerance in chestnut hybrids is polygenic, not controlled by major genes, and that higher American chestnut genome inheritance correlates with lower blight tolerance.

The paper assembles and annotates the genome of the soybean cyst nematode, revealing duplications and horizontal gene transfer events in effector genes involved in parasitism.

The paper constructs a soybean haplotype map (GmHapMap) using whole-genome sequences, identifies a causal SNP for seed oil content, and predicts LOF mutations to aid in soybean genomics and breeding.

The paper integrates genomic, metabolomic, and network data to identify target genes involved in lignin biosynthesis/degradation in Populus trichocarpa.

This study compares DNA methylation patterns across 34 angiosperm species, revealing widespread variation in methylation patterns linked to evolutionary and life history traits.

The paper investigates the origin and evolutionary consequences of gene body DNA methylation by studying the loss of this feature in two angiosperms, finding that CMT3 is essential for its establishment.

The paper shows adaptation to copper-contaminated environments in Mimulus guttatus occurs through selection on pre-existing genetic variation rather than new mutations.