Plant pangenomes for crop improvement, biodiversity and evolution

M Schreiber, M Jayakodi, N Stein… - Nature Reviews Genetics, 2024 - nature.com
Plant genome sequences catalogue genes and the genetic elements that regulate their
expression. Such inventories further research aims as diverse as map** the molecular …

Genomes on a Tree (GoaT): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life

R Challis, S Kumar, C Sotero-Caio… - Wellcome Open …, 2023 - pmc.ncbi.nlm.nih.gov
As genomic data transform our understanding of biodiversity, the Earth BioGenome Project
(EBP) has set a goal of generating reference quality genome assemblies for all~ 1.9 million …

[HTML][HTML] A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project

AD Twyford, J Beasley, I Barnes, H Allen… - Wellcome Open …, 2024 - pmc.ncbi.nlm.nih.gov
Biodiversity genomics research requires reliable organismal identification, which can be
difficult based on morphology alone. DNA-based identification using DNA barcoding can …

Hi-C techniques: from genome assemblies to transcription regulation

H Šimková, AS Câmara… - Journal of Experimental …, 2024 - academic.oup.com
The invention of chromosome conformation capture (3C) techniques, in particular the key
method Hi-C providing genome-wide information about chromatin contacts, revolutionized …

Quality assessment of gene repertoire annotations with OMArk

Y Nevers, A Warwick Vesztrocy, V Rossier… - Nature …, 2025 - nature.com
In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding
gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure …

A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

B Ranawaka, J An, MT Lorenc, H Jung, M Sulli… - Nature Plants, 2023 - nature.com
Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a~ 3
Gb allotetraploid genome. To further improve its usefulness and versatility, we have …

Toward a national eDNA strategy for the United States

RP Kelly, DM Lodge, KN Lee, S Theroux… - Environmental …, 2024 - Wiley Online Library
Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at
unprecedented resolution and scale. As use‐cases multiply and scientific consensus grows …

Galba: genome annotation with miniprot and AUGUSTUS

T Brůna, H Li, J Guhlin, D Honsel, S Herbold… - BMC …, 2023 - Springer
Abstract Background The Earth Biogenome Project has rapidly increased the number of
available eukaryotic genomes, but most released genomes continue to lack annotation of …

Threatened Species Initiative: Empowering conservation action using genomic resources

CJ Hogg, K Ottewell, P Latch, M Rossetto… - Proceedings of the …, 2022 - pnas.org
Globally, 15,521 animal species are listed as threatened by the International Union for the
Conservation of Nature, and of these less than 3% have genomic resources that can inform …

Structural variation in the pangenome of wild and domesticated barley

M Jayakodi, Q Lu, H Pidon, MT Rabanus-Wallace… - Nature, 2024 - nature.com
Pangenomes are collections of annotated genome sequences of multiple individuals of a
species. The structural variants uncovered by these datasets are a major asset to genetic …