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 …

[HTML][HTML] Factors affecting the optimisation and scale-up of lipid accumulation in oleaginous yeasts for sustainable biofuels production

R Robles-Iglesias, C Naveira-Pazos… - … and Sustainable Energy …, 2023 - Elsevier
The recent unprecedented increase in energy demand has led to a growing interest in
emerging alternatives such as the production of microbial lipids with high energy density …

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

JP Meier-Kolthoff, M Göker - Nature communications, 2019 - nature.com
Microbial taxonomy is increasingly influenced by genome-based computational methods.
Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS …

[HTML][HTML] What are the 100 most cited fungal genera?

CS Bhunjun, YJ Chen, C Phukhamsakda… - Studies in …, 2024 - ingentaconnect.com
The global diversity of fungi has been estimated between 2 to 11 million species, of which
only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they …

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 …

[HTML][HTML] Fungal diversity notes 1151–1276: taxonomic and phylogenetic contributions on genera and species of fungal taxa

KD Hyde, Y Dong, R Phookamsak, R Jeewon, DJ Bhat… - Fungal diversity, 2020 - Springer
Fungal diversity notes is one of the important journal series of fungal taxonomy that provide
detailed descriptions and illustrations of new fungal taxa, as well as providing new …

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 …

Tempo and mode of genome evolution in the budding yeast subphylum

XX Shen, DA Opulente, J Kominek, X Zhou… - Cell, 2018 - cell.com
Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as
genetically diverse as plants or animals. To understand budding yeast evolution, we …

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

M García-López, JP Meier-Kolthoff, BJ Tindall… - Frontiers in …, 2019 - frontiersin.org
Although considerable progress has been made in recent years regarding the classification
of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify …

Contentious relationships in phylogenomic studies can be driven by a handful of genes

XX Shen, CT Hittinger, A Rokas - Nature ecology & evolution, 2017 - nature.com
Phylogenomic studies have resolved countless branches of the tree of life, but remain
strongly contradictory on certain, contentious relationships. Here, we use a maximum …