Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia, College of Agriculture and Food Sciences, King Faisal University, Al Hofuf, Saudi Arabia
Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia, College of Agriculture and Food Sciences, King Faisal University, Al Hofuf, Saudi Arabia
Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil
Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia, Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane 4072, Australia
Advances in DNA sequencing have made it easier to sequence and assemble plant genomes. Here, we extend an earlier study, and compare recent methods for long read sequencing and assembly. Updated Oxford Nanopore Technology software improved assemblies. Using more accurate sequences produced by repeated sequencing of the same molecule (Pacific Biosciences HiFi) resulted in less fragmented assembly of sequencing reads. Using data for increased genome coverage resulted in longer contigs, but reduced total assembly length and improved genome completeness. The original model species, Macadamia jansenii, was also compared with three other Macadamia species, as well as avocado (Persea americana) and jojoba (Simmondsia chinensis). In these angiosperms, increasing sequence data volumes caused a linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity influenced the success of assembly. Advances in long read sequencing technology continue to improve plant genome sequencing and assembly. However, results were improved by greater genome coverage, with the amount needed to achieve a particular level of assembly being species dependent.
