Pushing the frontiers of biodiversity research: Unveiling the global diversity, distribution, and conservation of fungi

T Niskanen, R Lücking, A Dahlberg… - Annual review of …, 2023 - annualreviews.org
Fungi comprise approximately 20% of all eukaryotic species and are connected to virtually
all life forms on Earth. Yet, their diversity remains contentious, their distribution elusive, and …

Best practices in metabarcoding of fungi: from experimental design to results

L Tedersoo, M Bahram, L Zinger, RH Nilsson… - Molecular …, 2022 - Wiley Online Library
The development of high‐throughput sequencing (HTS) technologies has greatly improved
our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems …

GTDB-Tk v2: memory friendly classification with the genome taxonomy database

PA Chaumeil, AJ Mussig, P Hugenholtz… - …, 2022 - academic.oup.com
Abstract Summary The Genome Taxonomy Database (GTDB) and associated taxonomic
classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community …

PICRUSt2 for prediction of metagenome functions

GM Douglas, VJ Maffei, JR Zaneveld, SN Yurgel… - Nature …, 2020 - nature.com
To the Editor—One limitation of microbial community marker-gene sequencing is that it does
not provide information about the functional composition of sampled communities …

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

R Lücking, MC Aime, B Robbertse, AN Miller… - IMA fungus, 2020 - Springer
True fungi (Fungi) and fungus-like organisms (eg Mycetozoa, Oomycota) constitute the
second largest group of organisms based on global richness estimates, with around 3 …

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Y Turakhia, B Thornlow, AS Hinrichs, N De Maio… - Nature …, 2021 - nature.com
As the SARS-CoV-2 virus spreads through human populations, the unprecedented
accumulation of viral genome sequences is ushering in a new era of 'genomic contact …

Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community

A Canarini, H Schmidt, L Fuchslueger, V Martin… - Nature …, 2021 - nature.com
Climate change is altering the frequency and severity of drought events. Recent evidence
indicates that drought may produce legacy effects on soil microbial communities. However, it …

[HTML][HTML] Population genomics of post-glacial western Eurasia

ME Allentoft, M Sikora, A Refoyo-Martínez… - Nature, 2024 - nature.com
Western Eurasia witnessed several large-scale human migrations during the Holocene,,,–.
Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced …

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

AM Kozlov, D Darriba, T Flouri, B Morel… - …, 2019 - academic.oup.com
Motivation Phylogenies are important for fundamental biological research, but also have
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …

PICRUSt2: An improved and extensible approach for metagenome inference

GM Douglas, VJ Maffei, J Zaneveld, SN Yurgel… - BioRxiv, 2019 - biorxiv.org
One major limitation of microbial community marker gene sequencing is that it does not
provide direct information on the functional composition of sampled communities. Here, we …