A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

Authors: VANBUREN, ROBERT - Michigan State University; MAN WAI, CHING - Michigan State University; COLLE, MARIVI - Michigan State University; WANG, JIE - Michigan State University; SULLIVAN, SHAWN - Phase Genomics, Inc; Bushakra, Jill; LIACHKO, IVAN - Phase Genomics, Inc; VINING, KELLY - Oregon State University; DOSSETT, MICHAEL - British Columbia Blueberry Council; Finn, Chad; JIBRAN, RUBUNA - New Zealand Institute Of Plant & Food Research; CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research; CHILDS, KEVIN - Michigan State University; EDGER, PATRICK - Michigan State University; MOCKLER, TODD - Danforth Plant Science Center; Bassil, Nahla

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2018
Publication Date: 8/9/2018
Citation: Vanburen, R., Man Wai, C., Colle, M., Wang, J., Sullivan, S., Bushakra, J., Liachko, I., Vining, K., Dossett, M., Finn, C.E., Jibran, R., Chagne, D., Childs, K., Edger, P., Mockler, T., Bassil, N.V. 2018. A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. Gigascience. 7(8):giy094. https://doi.org/10.1093/gigascience/giy094.
DOI: https://doi.org/10.1093/gigascience/giy094

Interpretive Summary: Black raspberry is a niche fruit crop valued for its flavour and potential health benefits. The improvement of fruit quality and disease resistance traits via molecular breeding technologies has been hindered by the lack of a high-quality reference genome sequence. The recently released draft genome sequence for black raspberry needs improvement as a valuable reference for black raspberry and other closely related fruit crops like blackberry, and red raspberry. We used new techniques based on high-throughput chromatin conformation capture, Proximity-Guided Assembly, combined with long read sequencing to convert the existing draft genome assembly into seven pseudo-chromosomes. We demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for the woodland strawberry. This updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rose family and enable the development of marker assisted breeding in these berry fruit crops.

Technical Abstract: The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies. Here we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time (SMRT) PacBio sequencing and Hi-C genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing a ~200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high quality V4 woodland strawberry genome (Fragaria vesca) revealed near perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis. The improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.