Genomics in the long-read sequencing era
EL van Dijk, D Naquin, K Gorrichon, Y Jaszczyszyn… - Trends in Genetics, 2023 - cell.com
Long-read sequencing (LRS) technologies have provided extremely powerful tools to
explore genomes. While in the early years these methods suffered technical limitations, they …
explore genomes. While in the early years these methods suffered technical limitations, they …
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 …
not shared among individuals. The variable DNA sequences, along with the conserved core …
TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining
C Chen, Y Wu, J Li, X Wang, Z Zeng, J Xu, Y Liu… - Molecular plant, 2023 - cell.com
Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020, its
superior functionality in data analysis has been demonstrated by its widespread adoption by …
superior functionality in data analysis has been demonstrated by its widespread adoption by …
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 …
genomic research. Through generating deep coverage ultralong Oxford Nanopore …
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
Advancing crop genomics requires efficient genetic systems enabled by high-quality
personalized genome assemblies. Here, we introduce RagTag, a toolset for automating …
personalized genome assemblies. Here, we introduce RagTag, a toolset for automating …
Complete genomic and epigenetic maps of human centromeres
Existing human genome assemblies have almost entirely excluded repetitive sequences
within and near centromeres, limiting our understanding of their organization, evolution, and …
within and near centromeres, limiting our understanding of their organization, evolution, and …
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 …
gaps and a narrow genetic base hinder functional genomics and genetic improvement of …
The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding
Grapevine is one of the most economically important crops worldwide. However, the
previous versions of the grapevine reference genome tipically consist of thousands of …
previous versions of the grapevine reference genome tipically consist of thousands of …
Evolutionary analysis of a complete chicken genome
Z Huang, Z Xu, H Bai, Y Huang… - Proceedings of the …, 2023 - National Acad Sciences
Microchromosomes are prevalent in nonmammalian vertebrates [PD Waters et al., Proc.
Natl. Acad. Sci. USA 118 (2021)], but a few of them are missing in bird genome assemblies …
Natl. Acad. Sci. USA 118 (2021)], but a few of them are missing in bird genome assemblies …
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 …
genomics. The majority of attention has been paid to the solution of complex chromosome …