Twenty years of plant genome sequencing: achievements and challenges

Y Sun, L Shang, QH Zhu, L Fan, L Guo - Trends in Plant Science, 2022 - cell.com
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 …

Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium

M Wang, J Li, Z Qi, Y Long, L Pei, X Huang… - Nature Genetics, 2022 - nature.com
Phenotypic diversity and evolutionary innovation ultimately trace to variation in genomic
sequence and rewiring of regulatory networks. Here, we constructed a pan-genome of the …

GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

JT Lovell, A Sreedasyam, ME Schranz, M Wilson… - elife, 2022 - elifesciences.org
The development of multiple chromosome-scale reference genome sequences in many
taxonomic groups has yielded a high-resolution view of the patterns and processes of …

Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet

J Chen, Y Liu, M Liu, W Guo, Y Wang, Q He, W Chen… - Nature Genetics, 2023 - nature.com
Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve
cereal production and quality, and ensure food security. Here we present the genetic …

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 …

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 …

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

X Wen, Z Chen, Z Yang, M Wang, S **, G Wang… - Science China Life …, 2023 - Springer
Cotton is an irreplaceable economic crop currently domesticated in the human world for its
extremely elongated fiber cells specialized in seed epidermis, which makes it of high …

Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

S **, Z Han, Y Hu, Z Si, F Dai, L He, Y Cheng, Y Li… - Molecular Plant, 2023 - cell.com
Structural variations (SVs) have long been described as being involved in the origin,
adaption, and domestication of species. However, the underlying genetic and genomic …

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 …