Sequencing and assembling highly heterozygous and/or repeat-rich plant genomes using Oxford Nanopore technology
Victor and his colleagues use long-read nanopore sequencing on PromethION to generate genome assemblies for a broad range of plants, even those with large, highly heterozygous/ repetitive genomes.
Assembled plant genomes include: East Asian pitcher plant, duckweed, butterwort, tembusu tree and, last but not least, giant corpse lily.
A nucleus-enriched prep method was used to extract HMW DNA, producing fragments >60 kbp for East Asian pitcher plant samples.
Tembusu tree assembly revealed plant ‘has had two polyploidy events since its common ancestor with a couple of close relatives and with coffee’.
Giant corpse lily assembly: ~8 Gb assembly, N50 179 kbp, identification of complex repeat structure.
‘Democracy is here: generate a reference quality genome in any lab, with low up-front equipment investment.’
