London Calling 2023: How much is enough? A low-cost, rapid approach to generate non-model genomes for biodiversity and conservation genomics

We present high-quality de novo reference genomes for four flagship conservation species from Middle Eastern ecosystems, demonstrating how a small research team can generate high-quality reference genomes in less than two weeks, using just Oxford Nanopore long-read sequences. Although our genomes are not technically classified as chromosomal assemblies, they are vastly more contiguous to most chromosome-level genomes on NCBI. For example, only 6% of avian chromosome-level genomes have ungapped contig N50 > 30 Mb, and only 19% of fish genomes have ungapped contig N50 > 15 Mb. Most applications in biodiversity and conservation genomics rely on the analysis of large ungapped genome regions rather than chromosomes per se. Collectively, the approach presented here demonstrate that de novo reference genomes can be generated quickly in low-resource settings without the need for costly capital investment in sequencing and computation.