Igor V. Grigoriev

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

Extended Tiberius models outscore Helixer and ANNEVO on all 33 genomes from the five clades all three tools cover, and approach BRAKER3 accuracy in four clades without extrinsic evidence.

Hypermutability of integrated sequences of viral origin in a Chlorarachniophyte

The paper identifies hypermutable regions in the nuclear genome of Bigelowiella natans, showing extreme mutation rate variation and a distinctive mutational signature in virus-derived sequences.

Plasticity of the mutation rate and spectrum in eukaryotic marine phytoplankton

This study measures mutation rate and spectrum plasticity in Ostreococcus tauri under different environmental conditions, finding significant variation in SNM rates and spectra.

Active histone modifications fine-tune DNA N-6 methyladenine deposition and maintain transcriptional stability

The paper characterizes the genome-wide interaction between active histone modifications and DNA 6mA in Rhizopus microsporus, showing they define chromatin domains and regulate transcriptional stability.

Fungal microbial enrichment method enables fungal metagenomics directly from human clinical samples

This paper introduces fMEM, a fungal microbial enrichment method that enables direct fungal metagenomic analysis from clinical samples, recovering MAGs with high completeness and resolving clinically relevant genes.

Spliceosome loss in the red tide ciliate Mesodinium rubrum presents a symbiotic cul-de-sac

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

Comparative genomics reveals shared accessory regions between members of two Fusarium species complexes virulent on garden pea

The paper identifies shared accessory regions between two Fusarium species complexes that cause garden pea disease, suggesting a common origin and horizontal transfer of virulence genes.

Global population structures and demographic history of Suillus luteus, a pine co-introduced ectomycorrhizal fungus associated with exotic forestry and invasion.

This study analyzes the population genetics of Suillus luteus, showing all introductions originated from Europe and showing genetic differentiation in introduced regions linked to forestry practices.

Prediction of Lignocellulose Degradation Potential of Wood Decay Fungi using Comparative Genomic Analysis

The paper predicts the lignocellulose degradation potential of Crepidotus cesatii by comparing its genomic features to white- and brown-rot fungi.

Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina

The paper presents haplotype-phased, near chromosome-scale genome assemblies for two poplar rust fungi species, improving contiguity and enabling analysis of genome architecture and virulence genes.

Identification and Classification of Fungal GPCR Gene Families

The paper identifies and classifies GPCRs in 1,357 fungal species, revealing Pth11-like GPCRs as predominant and identifying potential novel fungal GPCRs using a custom CNN and AlphaFold Multimer.

The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

The paper presents the first complete and annotated genome of Nereocystis luetkeana, a northeastern Pacific bull kelp, providing insights into its genomic diversity and evolutionary features.

MAESTRO uncovers tandem paralog dynamics as a core driver of fungal stress adaptation

MAESTRO identifies tandem paralog copy number variation as a key mechanism for stress adaptation in Pichia kudriavzevii, linking it to drug resistance and environmental tolerance.

A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing

The paper identifies NUC-1 as a bifunctional transcription factor regulating phosphate starvation response in Neurospora crassa, with NUC-3 acting as a brake on the response during prolonged starvation.

Virulence of Fusarium oxysporum strains causing corneal or plant disease is associated with their accessory chromosomes

This study compares two Fusarium oxysporum strains causing human and plant diseases, finding differences in virulence and accessory chromosomes associated with host adaptation.

Genomic and Transcriptomic Characterization of Carbohydrate-Active Enzymes in the Anaerobic Fungus Neocallimastix cameroonii var. constans

This paper characterizes the genomic and transcriptomic features of Neocallimastix cameroonii var. constans, an anaerobic fungus, revealing its capacity to degrade lignocellulose and identifying key carbohydrate-active enzymes.

The genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi has been driven by two major evolutionary lineages

This study analyzes the genetic diversity of Phakopsora pachyrhizi, identifying two major evolutionary lineages and suggesting a tetrapolar mating system.

Comparative transcriptomics uncovers plant and fungal genetic determinants of mycorrhizal compatibility

This study identifies plant and fungal genetic factors governing ectomycorrhizal compatibility through comparative transcriptomics in poplar and its fungal partners.

Genome-wide exploration of the transcriptional regulatory landscape in the early-diverging fungus R. microsporus reveals pervasive DNA methyl adenine regulatory network

The paper uses DAP-seq to analyze TF binding sites in R. microsporus, revealing DNA methylation's role in gene regulation and expanding fungal motif catalogs.

A chromosome-scale genome assembly of the flax rust fungus reveals the two unusually large effector proteins, AvrM3 and AvrN

This study presents a chromosome-scale genome assembly of the flax rust fungus, revealing two large effector proteins, AvrM3 and AvrN, and providing insights into its mating system.

Improved gene annotation of the fungal wheat pathogen Zymoseptoria tritici based on combined Iso-Seq and RNA-Seq evidence

The paper improves gene annotation of Zymoseptoria tritici by combining Iso-Seq and RNA-Seq data, resulting in more accurate gene models and new insights into its transcriptional landscape.

Comparative genomics of the extremophile Cryomyces antarcticus and other psychrophilic Dothideomycetes

The paper uses comparative genomics to analyze Cryomyces antarcticus and other psychrophilic fungi to identify genetic features associated with extremophilic traits.

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.

Unraveling Morphogenesis, Starvation, and Light Responses in a Mushroom-Forming Fungus, Coprinopsis cinerea, Using Long Read Sequencing and Extensive Expression Profiling

The paper improves the functional annotation of the mushroom-forming fungus Coprinopsis cinerea by integrating a chromosome-level genome assembly with extensive expression profiling across multiple conditions.

Purging genomes of contamination eliminates systematic bias from evolutionary analyses of ancestral genomes

The paper introduces ContScout, a tool to remove contamination from genomes, showing it reduces bias in evolutionary analyses by eliminating spurious gene origins and inflated gene loss rates.

Community-wide interactions sustain life in geothermal spring habitats

The paper studies how a geothermal spring community responds to diurnal stressors, revealing structured biotic interactions across domains of life.

Comparative transcriptomics provides insight into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus

This study identifies genes and mechanisms underlying zinc tolerance in Suillus luteus through comparative transcriptomics.

Omics driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

This paper develops a modular genetic part library for Xanthophyllomyces dendrorhous using transcriptomics and genomics, identifying 26 promoters and revealing light-responsive regulatory mechanisms.

Herpes-like viral elements and universal subtelomeric ribosomal RNA genes in a chromosome-scale thraustochytrid genome assembly

The paper presents a chromosome-scale genome assembly of Aurantiochytrium limacinum, revealing novel subtelomeric rDNA repeats and herpes-like viral elements.

Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex

This study examines transcription factor repertoires in the Fusarium oxysporum species complex, finding expanded families linked to host-specific adaptation and pathogenicity.