New whole-genome alignment tools are needed for tap** into plant diversity

B Song, ES Buckler, MC Stitzer - Trends in Plant Science, 2024 - cell.com
Genome alignment is one of the most foundational methods for genome sequence studies.
With rapid advances in sequencing and assembly technologies, these newly assembled …

The application gap: Genomics for biodiversity and ecosystem service management

M Heuertz, SB Carvalho, J Galindo, B Rinkevich… - Biological …, 2023 - Elsevier
The conservation of biodiversity from the genetic to the community levels is fundamental for
the continual provision of ecosystem services (ES), the benefits that ecosystems provide to …

Sensitive protein alignments at tree-of-life scale using DIAMOND

B Buchfink, K Reuter, HG Drost - Nature methods, 2021 - nature.com
We are at the beginning of a genomic revolution in which all known species are planned to
be sequenced. Accessing such data for comparative analyses is crucial in this new age of …

Representation and participation across 20 years of plant genome sequencing

RA Marks, S Hotaling, PB Frandsen, R VanBuren - Nature plants, 2021 - nature.com
The field of plant genome sequencing has grown rapidly in the past 20 years, leading to
increases in the quantity and quality of publicly available genomic resources. The growing …

Green plant genomes: What we know in an era of rapidly expanding opportunities

WJ Kress, DE Soltis, PJ Kersey… - Proceedings of the …, 2022 - National Acad Sciences
Green plants play a fundamental role in ecosystems, human health, and agriculture. As de
novo genomes are being generated for all known eukaryotic species as advocated by the …

CNSA: a data repository for archiving omics data

X Guo, F Chen, F Gao, L Li, K Liu, L You, C Hua… - Database, 2020 - academic.oup.com
With the application and development of high-throughput sequencing technology in life and
health sciences, massive multi-omics data brings the problem of efficient management and …

Designing future crops: challenges and strategies for sustainable agriculture

Z Tian, JW Wang, J Li, B Han - The Plant Journal, 2021 - Wiley Online Library
Crop production is facing unprecedented challenges. Despite the fact that the food supply
has significantly increased over the past half‐century,~ 8.9 and 14.3% people are still …

AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication

B Song, S Marco-Sola, M Moreto… - Proceedings of the …, 2022 - National Acad Sciences
Millions of species are currently being sequenced, and their genomes are being compared.
Many of them have more complex genomes than model systems and raise novel challenges …

[HTML][HTML] A conservation genomics workflow to guide practical management actions

M Rossetto, JYS Yap, J Lemmon, D Bain… - Global ecology and …, 2021 - Elsevier
Owing to decreasing costs and increased efficiency, it is now conceivable that conservation
genomic information can be used to improve the effectiveness of recovery programs for …