Twenty years of plant genome sequencing: achievements and challenges

Y Sun, L Shang, QH Zhu, L Fan, L Guo - Trends in plant science, 2021 - Elsevier
Publication of the complete genome sequence of Arabidopsis thaliana, the first plant
reference genome, in December 2000 heralded the beginning of the plant genome era …

Recent advances and future perspectives in cotton research

G Huang, JQ Huang, XY Chen… - Annual Review of Plant …, 2021 - annualreviews.org
Cotton is not only the world's most important natural fiber crop, but it is also an ideal system
in which to study genome evolution, polyploidization, and cell elongation. With the assembly …

[HTML][HTML] Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

JT Lovell, AH MacQueen, S Mamidi, J Bonnette… - Nature, 2021 - nature.com
Long-term climate change and periodic environmental extremes threaten food and fuel
security and global crop productivity–. Although molecular and adaptive breeding strategies …

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files

SS Dong, WM He, JJ Ji, C Zhang, Y Guo… - Briefings in …, 2021 - academic.oup.com
The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD)
pattern and haplotype block structure of SNPs is ubiquitous component of population-based …

The genomic basis of geographic differentiation and fiber improvement in cultivated cotton

S He, G Sun, X Geng, W Gong, P Dai, Y Jia, W Shi… - Nature Genetics, 2021 - nature.com
Large-scale genomic surveys of crop germplasm are important for understanding the
genetic architecture of favorable traits. The genomic basis of geographic differentiation and …

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 …

[HTML][HTML] Integrating multi-omics data for crop improvement

F Scossa, S Alseekh, AR Fernie - Journal of plant physiology, 2021 - Elsevier
Our agricultural systems are now in urgent need to secure food for a growing world
population. To meet this challenge, we need a better characterization of plant genetic and …

[HTML][HTML] Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids

X Jiang, Q Song, W Ye, ZJ Chen - Nature Ecology & Evolution, 2021 - nature.com
During evolution successful allopolyploids must overcome 'genome shock'between
hybridizing species but the underlying process remains elusive. Here, we report concerted …

Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

PE Bayer, A Scheben, AA Golicz… - Plant Biotechnology …, 2021 - Wiley Online Library
Plant genomes demonstrate significant presence/absence variation (PAV) within a species;
however, the factors that lead to this variation have not been studied systematically in …

[HTML][HTML] The miR319-targeted GhTCP4 promotes the transition from cell elongation to wall thickening in cotton fiber

JF Cao, B Zhao, CC Huang, ZW Chen, T Zhao, HR Liu… - Molecular plant, 2020 - Elsevier
Plant cell growth involves a complex interplay among cell-wall expansion, biosynthesis, and,
in specific tissues, secondary cell wall (SCW) deposition, yet the coordination of these …