London Calling 2023: Automated telomere-to-telomere crop genome assembly using only Oxford Nanopore sequencing

Recently, the combination of ultra-long Oxford Nanopore sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of the human genome and spurred similar efforts for many other species. However, the current recipe for telomere-to-telomere genome assembly relies on sequencing data from two different instruments, limiting its adoption. We generated Oxford Nanopore simplex and duplex data for two important crop species, Zea mays B73 and Solanum lycopersicum Heinz 1706. Assembling the Solanum lycopersicum Heinz 1706 data using Verkko followed by manual analysis, resulted in a complete, telomere-to-telomere genome assembly with only one gap, corresponding to the rDNA, remaining. Duplex data quality is similar to PacBio HiFi, although read lengths are tens of kilobases longer. The assembly has a base-accuracy exceeding 99.999% (Q50). We conclude that Oxford Nanopore duplex sequencing reads are a viable substitute for PacBio HiFi reads, and, in combination with simplex sequencing, have the potential to provide a single-instrument solution for complete genome assembly.