Hordeum vulgare subsp. vulgare cultivar 'Morex' assembly (MorexV3)

Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial compute resources and often several complementary sequencing and mapping approaches. The recent development of fast and accurate long-read sequence assembly by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies. The final Morex V3 assembly was constructed the following: As the CCS_Canu assembly outperformed the other assemblies in almost all regards, it was chosen as the primary contig assembly to construct chromosomal pseudomolecules. Pseudomolecule construction proceeded in the three steps: (i) scaffolding the CCS_Canu with Bionano contigs; (ii) removal of small redundant sequences; (iii) filling gaps in scaffolds with ONT_smartdenovo contigs and (iv) ordering and orienting scaffolds into chromosomal pseudomolecules.