PlantTribes2: Tools for comparative gene family analysis in plant genomics

EK Wafula, H Zhang, G Von Kuster… - Frontiers in Plant …, 2023 - frontiersin.org
Plant genome-scale resources are being generated at an increasing rate as sequencing
technologies continue to improve and raw data costs continue to fall; however, the cost of …

Genome‐wide identification studies–A primer to explore new genes in plant species

I Safder, G Shao, Z Sheng, P Hu, S Tang - Plant Biology, 2022 - Wiley Online Library
Genome data have accumulated rapidly in recent years, doubling roughly after every 6
months due to the influx of next‐generation sequencing technologies. A plethora of plant …

PLAZA: a comparative genomics resource to study gene and genome evolution in plants

S Proost, M Van Bel, L Sterck, K Billiau… - The Plant …, 2009 - academic.oup.com
The number of sequenced genomes of representatives within the green lineage is rapidly
increasing. Consequently, comparative sequence analysis has significantly altered our view …

Tapping the promise of genomics in species with complex, nonmodel genomes

CN Hirsch, C Robin Buell - Annual review of plant biology, 2013 - annualreviews.org
Genomics is enabling a renaissance in all disciplines of plant biology. However, many plant
genomes are complex and remain recalcitrant to current genomic technologies. The …

GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

B Contreras-Moreira, S Saraf, G Naamati, AM Casas… - Genome Biology, 2023 - Springer
Crop pangenomes made from individual cultivar assemblies promise easy access to
conserved genes, but genome content variability and inconsistent identifiers hamper their …

[HTML][HTML] From plant genomes to phenotypes

M Bolger, R Schwacke, H Gundlach, T Schmutzer… - Journal of …, 2017 - Elsevier
Recent advances in sequencing technologies have greatly accelerated the rate of plant
genome and applied breeding research. Despite this advancing trend, plant genomes …

A graph-based pan-genome guides biological discovery

Y Tao, DR Jordan, ES Mace - Molecular Plant, 2020 - cell.com
The availability of reference genomes has been the foundation for genomics research in the
last decade. However, as reports of presence/absence variations of sequence and genes …

PlantGDB: a resource for comparative plant genomics

J Duvick, A Fu, U Muppirala, M Sabharwal… - Nucleic acids …, 2007 - academic.oup.com
Abstract PlantGDB (http://www. plantgdb. org/) is a genomics database encompassing
sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript …

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

A Sreedasyam, C Plott, MS Hossain… - Nucleic acids …, 2023 - academic.oup.com
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying
trait variation. Conversely, plant responses to environmental cues represent important …

Technology-enabled great leap in deciphering plant genomes

L Xie, X Gong, K Yang, Y Huang, S Zhang, L Shen… - Nature Plants, 2024 - nature.com
Plant genomes provide essential and vital basic resources for studying many aspects of
plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes …