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 …

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 …

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 …

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 …

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 …

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 …

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 …

Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes

F Zhang, H Xue, X Dong, M Li, X Zheng, Z Li… - Genome …, 2022 - genome.cshlp.org
The concept of pan-genome, which is the collection of all genomes from a population, has
shown a great potential in genomics study, especially for crop sciences. The rice pan …

High-Quality Arabidopsis Thaliana Genome Assembly with Nanopore and HiFi Long Reads

B Wang, X Yang, Y Jia, Y Xu, P Jia… - Genomics …, 2022 - academic.oup.com
Arabidopsis thaliana is an important and long-established model species for plant molecular
biology, genetics, epigenetics, and genomics. However, the latest version of reference …

Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose …

X Han, Y Zhang, Q Zhang, N Ma, X Liu, W Tao, Z Lou… - Molecular Plant, 2023 - cell.com
Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and
nutritional value, especially because of the high content of vitamin C in its fruit. In this study …