Exploiting long-read sequence technology to resolve the hidden genomic landscape of complex crop genomes

Andrew and his team used long nanopore reads + 3C data to generate contiguous assemblies of Brassica crops black mustard and canola, cultivated lentil and a wild relative of lentil, and barley.

The long reads enabled large contig N50s, greater representation of full genomes including repetitive regions and analysis of SVs important in crop traits.

Black mustard genome scaffolded assembly N50 size of 44.6 Mb.

Analysis of CpG methylation in black mustard cultivar Ni100 genome data showed ‘very good correlation’ with short-read bisulfite data.

Drop in methylation and ALE-LTRs repeat class identified at putative centromeric region.

SVs, important in crop traits, characterised in Brassica assemblies – including in genic regions.

‘ONT provides robust assemblies of larger complex plant genomes’.