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 …

Technology-enabled great leap in deciphering plant genomes

L **e, 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 …

A complete telomere-to-telomere assembly of the maize genome

J Chen, Z Wang, K Tan, W Huang, J Shi, T Li, J Hu… - Nature …, 2023 - nature.com
A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of
genomic research. Through generating deep coverage ultralong Oxford Nanopore …

quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

Y Lin, C Ye, X Li, Q Chen, Y Wu, F Zhang… - Horticulture …, 2023 - academic.oup.com
A high-quality genome is the basis for studies on functional, evolutionary, and comparative
genomics. The majority of attention has been paid to the solution of complex chromosome …

A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

Y Deng, S Liu, Y Zhang, J Tan, X Li, X Chu, B Xu… - Molecular plant, 2022 - cell.com
Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with
gaps and a narrow genetic base hinder functional genomics and genetic improvement of …

A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution

Y Bao, Q Zhang, J Huang, S Zhang, W Yao… - Nature …, 2024 - nature.com
Sugarcane is a vital crop with significant economic and industrial value. However, the
cultivated sugarcane's ultra-complex genome still needs to be resolved due to its high ploidy …

Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

W Chen, X Wang, J Sun, X Wang, Z Zhu… - Nature …, 2024 - nature.com
Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of
capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of …

Plant pan-genomics and its applications

J Shi, Z Tian, J Lai, X Huang - Molecular Plant, 2023 - cell.com
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are
not shared among individuals. The variable DNA sequences, along with the conserved core …

The integrated genomics of crop domestication and breeding

X Huang, S Huang, B Han, J Li - Cell, 2022 - cell.com
As a major event in human civilization, wild plants were successfully domesticated to be
crops, largely owing to continuing artificial selection. Here, we summarize new discoveries …

Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis

J Yue, Q Chen, Y Wang, L Zhang, C Ye… - Horticulture …, 2023 - academic.oup.com
Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents
of vitamin C. However, the previously released versions of kiwifruit genomes all have a mass …