J. Schmutz

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

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

The Marchantia pangenome reveals ancient mechanisms of plant adaptation to the environment

This study analyzes the pangenome of Marchantia polymorpha to identify genetic features involved in plant adaptation to terrestrial environments, finding shared and lineage-specific genes with flowering plants.

Evolutionary analyses of gene expression divergence in Panicum hallii: exploring constitutive and plastic responses using reciprocal transplants

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.

Seagrass genomes reveal a hexaploid ancestry facilitating adaptation to the marine environment

This study presents chromosome-level genome assemblies of seagrass species and identifies ancient and recent genome duplication events linked to adaptation to marine environments.

Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina)

The paper reconstructs the colonization history of eelgrass using genomic data, showing trans-Pacific currents drove its spread and Atlantic populations arrived more recently with lower genetic diversity.

The western redcedar genome reveals low genetic diversity in a self-compatible conifer

The paper assembles the western redcedar genome and finds it has low genetic diversity, suggesting mechanisms like associative overdominance maintain genetic variation despite selfing.

High-throughput Identification of Novel Heat Tolerance Genes via Genome-wide Pooled Mutant Screens in the Model Green Alga Chlamydomonas reinhardtii

This study identifies 933 heat tolerance genes in Chlamydomonas reinhardtii through genome-wide mutant screens, showing 50% have orthologs in crops and Arabidopsis mutants are heat sensitive.

Heritability and host genomic determinants of switchgrass root-associated microbiota in field sites spanning its natural range.

This study examines how host genetics and environmental factors shape root microbiota in switchgrass across its native range, finding heritable variation and local microbial recruitment.

Transcriptome and DNA methylome dynamics reveal differential characteristics of inflorescence development between two ecotypes in Panicum hallii

A comparative transcriptome and DNA methylome analysis of inflorescence between upland and lowland ecotypes reveals gene expression and DNA methylation variation underlying inflorescence divergence in Panicum hallii.

Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA

A single gRNA targeting conserved sequences enabled efficient mutagenesis of a multigene family, resulting in trichomeless and triterpene-free poplar mutants.

The genome of stress tolerant crop wild relativePaspalum vaginatum leads to increased biomassproductivity in the crop Zea mays

This study sequenced Paspalum vaginatum, a stress-tolerant wild relative of maize, and found that inducing trehalose accumulation in maize increases biomass through autophagy.

Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae

The paper identifies horizontal gene transfer as a driver of convergent evolution in Arctic microalgae, highlighting ice-binding domain gene transfers between distantly related species.

The transcription factor Roc1 is a regulator of cellulose degradation in the wood-decaying mushroom Schizophyllum commune

This study identifies Roc1 as a key transcription factor regulating cellulose degradation in the wood-decaying fungus Schizophyllum commune through genomic and transcriptomic analyses.

The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange

The paper identifies a globally rare East African allele of RMES1 that conferred resistance to sugarcane aphids in Haitian sorghum, demonstrating the importance of global germplasm exchange for evolutionary rescue.

Novel insights into joint estimations of demography, mutation rate, and selection using UV sex chromosomes

This study examines how anisogamy influences genetic variation in moss using UV sex chromosomes, finding sex-biased mutation and selection but no model explaining observed diversity ratios.

Sphagnum peat moss thermotolerance is modulated by the microbiome

This study shows that Sphagnum moss thermotolerance can be modulated by the microbiome, with warming-origin microbes restoring plant growth after heat stress.

The Ceratodon purpureus genome uncovers structurally complex, gene rich sex chromosomes

The paper compares genomes of male and female mosses to study sex chromosome evolution, finding gene-rich, non-degenerated UV sex chromosomes.

Hybridization history and repetitive element content in the genome of a homoploid hybrid, Yucca gloriosa (Asparagaceae)

This study investigates the hybridization history and transposon dynamics in Yucca gloriosa, a homoploid hybrid, using whole genome resequencing and mRNA-seq.

Assembly of a young vertebrate Y chromosome reveals convergent signatures of sex chromosome evolution

The paper assembles a young Y chromosome from threespine stickleback, revealing convergent evolutionary features with older sex chromosomes.

Soybean Haplotype Map (GmHapMap): A Universal Resource for Soybean Translational and Functional Genomics

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 Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history

The paper presents the genome of Aquilegia coerulea and shows extensive allele sharing and introgression among species, with a unique chromosome evolutionary history.

The genetic architecture of shoot and root trait divergence between upland and lowland ecotypes of a perennial grass.

The paper investigates the genetic basis of trait divergence between upland and lowland ecotypes of a perennial grass, focusing on adaptation to soil water availability.

The Sequence of 1504 Mutants in the Model Rice Variety Kitaake Facilitates Rapid Functional Genomic Studies

The paper sequenced 1,504 mutant lines in the rice variety Kitaake and established a database to enable rapid functional genomic studies.

The Sorghum bicolor reference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization

This paper improves the Sorghum bicolor reference genome, annotates it, and constructs a transcriptome atlas, revealing genomic features and gene expression patterns across developmental stages.