Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Toward a fully resolved fungal tree of life

TY James, JE Stajich, CT Hittinger… - Annual Review of …, 2020 - annualreviews.org
In this review, we discuss the current status and future challenges for fully elucidating the
fungal tree of life. In the last 15 years, advances in genomic technologies have …

[HTML][HTML] Whitefly hijacks a plant detoxification gene that neutralizes plant toxins

J **a, Z Guo, Z Yang, H Han, S Wang, H Xu, X Yang… - Cell, 2021 - cell.com
Plants protect themselves with a vast array of toxic secondary metabolites, yet most plants
serve as food for insects. The evolutionary processes that allow herbivorous insects to resist …

[HTML][HTML] Heterotrophic nitrification–An eternal mystery in the nitrogen cycle

PJ Martikainen - Soil Biology and Biochemistry, 2022 - Elsevier
Despite the fact that heterotrophic nitrification was identified more than 100 years ago, the
biochemistry of heterotrophic nitrifiers is poorly known and their contribution to nitrification in …

Contamination detection in genomic data: more is not enough

L Cornet, D Baurain - Genome Biology, 2022 - Springer
The decreasing cost of sequencing and concomitant augmentation of publicly available
genomes have created an acute need for automated software to assess genomic …

Biosynthetic gene clusters and the evolution of fungal chemodiversity

A Rokas, ME Mead, JL Steenwyk, HA Raja… - Natural product …, 2020 - pubs.rsc.org
Covering: up to 2019 Fungi produce a remarkable diversity of secondary metabolites: small,
bioactive molecules not required for growth but which are essential to their ecological …

Domestication of industrial microbes

J Steensels, B Gallone, K Voordeckers, KJ Verstrepen - Current biology, 2019 - cell.com
Domestication refers to artificial selection and breeding of wild species to obtain cultivated
variants that thrive in man-made niches and meet human or industrial requirements. Several …

Interspecific hybridization as a driver of fungal evolution and adaptation

J Steensels, B Gallone, KJ Verstrepen - Nature Reviews Microbiology, 2021 - nature.com
Cross-species gene transfer is often associated with bacteria, which have evolved several
mechanisms that facilitate horizontal DNA exchange. However, the increased availability of …

Emerging mechanistic insights into the regulation of specialized metabolism in plants

LV Méteignier, HW Nützmann, N Papon, A Osbourn… - Nature plants, 2023 - nature.com
Plants biosynthesize a broad range of natural products through specialized and species-
specific metabolic pathways that are fuelled by core metabolism, together forming a …

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

DA Opulente, AL LaBella, MC Harrison, JF Wolters… - Science, 2024 - science.org
Organisms exhibit extensive variation in ecological niche breadth, from very narrow
(specialists) to very broad (generalists). Two general paradigms have been proposed to …