10KP: A phylodiverse genome sequencing plan

S Cheng, M Melkonian, SA Smith, S Brockington… - …, 2018 - academic.oup.com
Understanding plant evolution and diversity in a phylogenomic context is an enormous
challenge due, in part, to limited availability of genome-scale data across phylodiverse …

GenBank is a reliable resource for 21st century biodiversity research

M Leray, N Knowlton, SL Ho… - Proceedings of the …, 2019 - National Acad Sciences
Traditional methods of characterizing biodiversity are increasingly being supplemented and
replaced by approaches based on DNA sequencing alone. These approaches commonly …

Fungal DNA barcoding

J Xu - Genome, 2016 - cdnsciencepub.com
Fungi are ubiquitous in both natural and human-made environments. They play important
roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus …

New primers to amplify the fungal ITS2 region–evaluation by 454-sequencing of artificial and natural communities

K Ihrmark, ITM Bödeker, K Cruz-Martinez… - FEMS microbiology …, 2012 - academic.oup.com
With recent methodological advances, molecular markers are increasingly used for semi-
quantitative analyses of fungal communities. The aim to preserve quantitative relationships …

Fungarium specimens: a largely untapped source in global change biology and beyond

C Andrew, J Diez, TY James… - … Transactions of the …, 2019 - royalsocietypublishing.org
For several hundred years, millions of fungal sporocarps have been collected and deposited
in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale …

ITS 1 versus ITS 2 as DNA metabarcodes for fungi

R Blaalid, S Kumar, RH Nilsson… - Molecular ecology …, 2013 - Wiley Online Library
Abstract The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a
DNA metabarcoding marker to characterize the diversity and composition of fungal …

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

DL Lindner, T Carlsen, R Henrik Nilsson… - Ecology and …, 2013 - Wiley Online Library
The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding
marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS …

Tissue storage and primer selection influence pyrosequencing‐based inferences of diversity and community composition of endolichenic and endophytic fungi

JM U'Ren, JM Riddle, JT Monacell… - Molecular Ecology …, 2014 - Wiley Online Library
Next‐generation sequencing technologies have provided unprecedented insights into
fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next …

Optimized metabarcoding with Pacific biosciences enables semi‐quantitative analysis of fungal communities

C Castaño, A Berlin, M Brandström Durling… - New …, 2020 - Wiley Online Library
Recent studies have questioned the use of high‐throughput sequencing of the nuclear
ribosomal internal transcribed spacer (ITS) region to derive a semi‐quantitative …

A genome-scale phylogeny of the kingdom Fungi

Y Li, JL Steenwyk, Y Chang, Y Wang, TY James… - Current Biology, 2021 - cell.com
Phylogenomic studies using genome-scale amounts of data have greatly improved
understanding of the tree of life. Despite the diversity, ecological significance, and …