Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis

TM Porter, M Hajibabaei - Molecular ecology, 2018 - Wiley Online Library
The purpose of this review is to present the most common and emerging DNA‐based
methods used to generate data for biodiversity and biomonitoring studies. As environmental …

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

AM Piper, J Batovska, NOI Cogan, J Weiss… - …, 2019 - academic.oup.com
Trap-based surveillance strategies are widely used for monitoring of invasive insect species,
aiming to detect newly arrived exotic taxa as well as track the population levels of …

[HTML][HTML] RESCRIPt: Reproducible sequence taxonomy reference database management

MS Robeson, DR O'Rourke, BD Kaehler… - PLoS computational …, 2021 - journals.plos.org
Nucleotide sequence and taxonomy reference databases are critical resources for
widespread applications including marker-gene and metagenome sequencing for …

[HTML][HTML] Assessment of BOLD and GenBank–Their accuracy and reliability for the identification of biological materials

KA Meiklejohn, N Damaso, JM Robertson - PloS one, 2019 - journals.plos.org
Taxonomic identification of biological materials can be achieved through DNA barcoding,
where an unknown “barcode” sequence is compared to a reference database. In many …

[HTML][HTML] Validation of COI metabarcoding primers for terrestrial arthropods

V Elbrecht, TWA Braukmann, NV Ivanova, SWJ Prosser… - PeerJ, 2019 - peerj.com
Metabarcoding can rapidly determine the species composition of bulk samples and thus
aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that …

A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

A Hakimzadeh, A Abdala Asbun… - Molecular Ecology …, 2024 - Wiley Online Library
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for
monitoring biodiversity in ecology. However, taxa identifications produced through …

[HTML][HTML] Soundscapes and deep learning enable tracking biodiversity recovery in tropical forests

J Müller, O Mitesser, HM Schaefer, S Seibold… - Nature …, 2023 - nature.com
Tropical forest recovery is fundamental to addressing the intertwined climate and
biodiversity loss crises. While regenerating trees sequester carbon relatively quickly, the …

[HTML][HTML] Over 2.5 million COI sequences in GenBank and growing

TM Porter, M Hajibabaei - PloS one, 2018 - journals.plos.org
The increasing popularity of cytochrome c oxidase subunit 1 (COI) DNA metabarcoding
warrants a careful look at the underlying reference databases used to make high-throughput …

PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

E Banchi, CG Ametrano, S Greco, D Stanković… - Database, 2020 - academic.oup.com
DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify
different taxa within environmental communities. The ITS has already been proposed and …

[HTML][HTML] COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems

M Hajibabaei, TM Porter, M Wright, J Rudar - PLoS One, 2019 - journals.plos.org
Mixed community or environmental DNA marker gene sequencing has become a commonly
used technique for biodiversity analyses in freshwater systems. Many cytochrome c oxidase …