We had a productive and fun day working in Minneapolis on the PALM and Vision and Change project! I am glad I was able to come here and work with friends. Tonight, I watched the London Calling 2024 session “Plant T2T genome assembly using ultra-long and adaptive nanopore sequencing” by Bosheng Li from the Institute of Advanced Agricultural Services at Peking University in China. They are using ultra-long reads to complete the telomere-to-telomere genome assembly in plants. Ultra-long reads are above 100 kb. They have optimized extraction and library preparation to obtain longer reads and more throughput. DNA extraction, they homogenize to release the cell nucleus and gently filter. Young tissue was able to yield longer DNA. They optimized library preparation with adjustments to input and library preparation. The output for pepper, for example, was used to complete the genome assembly. For several plants, the yield was improved, and N50 mainly was above 100 kb. The team used adaptive sampling to fill in the gaps in Arabidopsis genome assembly. Li noted that they collaborated with several companies to improve the protocols. I would like to learn their protocols and if additional equipment is needed to achieve ultra-long reads.
