A. Lipzen

Multi-omics analysis of a traditional fermented food reveals a byproduct-associated subpopulation of Neurospora intermedia for waste-to-food upcycling

This study uses multi-omics analysis to characterize Neurospora intermedia in oncom, revealing its role in byproduct conversion and potential for waste-to-food upcycling.

JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom

The paper introduces the JGI Plant Gene Atlas, a resource that improves gene function annotations by analyzing transcript abundance across 18 species and 604 tissues, identifying 64,620 genes with unknown functions.

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

This study analyzes genome and transcriptome data from 30 Colletotrichum species to show evolutionary adaptations to monocot and eudicot hosts, including gene expansion and expression changes.

Divergent evolution of early terrestrial fungi reveals the evolution of Mucormycosis pathogenicity factors

This study investigates the divergent evolution of zygomycete fungi, identifying lineage-specific genomic elements and evolutionary relationships that contribute to Mucormycosis pathogenicity.

Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche

This study characterizes a novel polyextremotolerant fungus, Exophiala viscosa, revealing its metabolic flexibility, abiotic stress tolerance, and melanin production capabilities.

Experimental evolution of extremophile levels of radiation resistance in Escherichia coli

This study uses experimental evolution to generate E. coli with radiation resistance similar to Deinococcus radiodurans, revealing multiple genomic and proteomic changes involved in IR resistance.

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.

Genetic determinants of endophytism in the Arabidopsis root mycobiome

The paper identifies genetic factors associated with endophytism in Arabidopsis root fungi, showing specific gene families linked to aggressive colonization and plant health.

Genomic signatures of a major adaptive event in the pathogenic fungus Melampsora larici-populina

The paper identifies a genomic signature of a recent adaptive event in the fungus Melampsora larici-populina, pinpointing a single amino acid change associated with overcoming host resistance.

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.

Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement?

This study identifies genomic features of the transition to ectomycorrhizal habit in Russulaceae fungi, finding gene loss, TE expansion, and secreted protein associations with TE nests.

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.

Identification of enzymes for lignocellulose degradation in the genome and transcriptome of the aquatic hyphomycete Clavariopsis aquatica.

The paper identifies enzymes for lignocellulose degradation in Clavariopsis aquatica by analyzing its genome and transcriptome under different substrates.

Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria

The paper shows that enhanced nutrient uptake by recipient bacteria, not increased excretion by producers, drives emergent cross-feeding in microbial communities.

The genome of Auriculariopsis ampla sheds light on fruiting body development and wood-decay of bark-inhabiting fungi

This study sequenced the genome of Auriculariopsis ampla and analyzed its transcriptome to uncover genetic features related to wood-decay and fruiting body development in fungi.

Transcriptomic atlas of mushroom development highlights an independent origin of complex multicellularity

This study constructs a transcriptomic atlas of mushroom development using six species and genome comparisons to identify conserved genes involved in complex multicellularity.

Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass.

This study identifies the oxidative enzyme systems in Polyporus brumalis that enable efficient lignin degradation during wheat straw fermentation.