Proteinaceous effector discovery and characterization in filamentous plant pathogens

C Kanja, KE Hammond‐Kosack - Molecular Plant Pathology, 2020 - Wiley Online Library
The complicated interplay of plant–pathogen interactions occurs on multiple levels as
pathogens evolve to constantly evade the immune responses of their hosts. Many …

Recent advances in oomycete genomics

J McGowan, DA Fitzpatrick - Advances in genetics, 2020 - Elsevier
The oomycetes are a class of ubiquitous, filamentous microorganisms that include some of
the biggest threats to global food security and natural ecosystems. Within the oomycete …

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC

P Saary, AL Mitchell, RD Finn - Genome biology, 2020 - Springer
Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained
more attention, but the recovery of high-quality metagenomic assembled eukaryotic …

UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi

D Kim, CLM Gilchrist, J Chun… - Nucleic Acids …, 2023 - academic.oup.com
In phylogenomics the evolutionary relationship of organisms is studied by their genomic
information. A common approach to phylogenomics is to extract related genes from each …

[PDF][PDF] Predicted input of uncultured fungal symbionts to a lichen symbiosis from metagenome-assembled genomes

G Tagirdzhanova, P Saary, JP Tingley… - Genome Biology and …, 2021 - academic.oup.com
Basidiomycete yeasts have recently been reported as stably associated secondary fungal
symbionts of many lichens, but their role in the symbiosis remains unknown. Attempts to …

Genomic insights into the host specific adaptation of the Pneumocystis genus

OH Cissé, L Ma, JP Dekker, PP Khil, JH Youn… - Communications …, 2021 - nature.com
Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely
related to macaque Pneumocystis. Little is known about other Pneumocystis species in …

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

JL Espinoza, CL Dupont - BMC bioinformatics, 2022 - Springer
Background With the advent of metagenomics, the importance of microorganisms and how
their interactions are relevant to ecosystem resilience, sustainability, and human health has …

What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

B Greshake Tzovaras, FHID Segers… - Genome Biology and …, 2020 - academic.oup.com
Lichens are valuable models in symbiosis research and promising sources of biosynthetic
genes for biotechnological applications. Most lichenized fungi grow slowly, resist …

Metabolic engineering of filamentous fungi

V Meyer - Metabolic engineering: concepts and applications, 2021 - Wiley Online Library
Filamentous fungi have been harnessed for the production of organic acids, antibiotics,
drugs, and enzymes for the last 100 years. Fungal biotechnology is currently undergoing a …

Comparative genomics and phylogenomic investigation of the class Geoglossomycetes provide insights into ecological specialization and the systematics of …

T Melie, S Pirro, AN Miller, SD Smith, KS Schutz… - Mycologia, 2023 - Taylor & Francis
Despite their global presence and ubiquity, members of the class Geoglossomycetes
(Pezizomycotina, Ascomycota) are understudied systematically and ecologically. These …