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Title: Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

Author
item JIBRAN, RUBINA - New Zealand Institute Of Plant & Food Research
item DZIERZON, HELGE - New Zealand Institute Of Plant & Food Research
item Bassil, Nahla
item Bushakra, Jill
item EDGER, PATRICK - Michigan State University
item SULLIVAN, SHAWN - Phase Genomics, Inc
item Finn, Chad
item DOSSETT, MICHAEL - British Columbia Blueberry Council
item VINING, KELLY - Oregon State University
item VANBUREN, ROBERT - Michigan State University
item MOCKLER, TODD - Danforth Plant Science Center
item LIACHKO, IVAN - Phase Genomics, Inc
item DAVIES, KEVIN - New Zealand Institute Of Plant & Food Research
item FOSTER, TOSHI - New Zealand Institute Of Plant & Food Research
item CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2017
Publication Date: 2/7/2017
Citation: Jibran, R., Dzierzon, H., Bassil, N.V., Bushakra, J., Edger, P.P., Sullivan, S., Finn, C.E., Dossett, M., Vining, K.J., Vanburen, R., Mockler, T.C., Liachko, I., Davies, K.M., Foster, T.M., Chagne, D. 2017. Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data. Horticulture Research. 5:8. https://doi.org/10.1038/s41438-017-0013-y.
DOI: https://doi.org/10.1038/s41438-017-0013-y

Interpretive Summary: Black raspberry is a niche fruit crop valued for its flavour and potential health benefits. The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome. The recently released draft genome sequence for black raspberry (ORUS 4115-3) needs improvement as a valuable reference for blackberry, and red raspberry. We used new techniques based on high-throughput chromatin conformation capture (Hi-C) and Proximity-Guided Assembly (PGA) 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 protocol is a cost-effective and rapid method of generating chromosome-scale assemblies from short-read sequencing data.

Technical Abstract: Black raspberry (Rubus occidentalis L.) is a niche fruit crop valued for its flavour and potential health benefits. The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome. The recently released draft genome for black raspberry (ORUS 4115-3) lacks assembly of scaffolds to chromosome scale. We used high-throughput chromatin conformation capture (Hi-C) and Proximity-Guided Assembly (PGA) to cluster and order 9,650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes. The seven pseudo-chromosomes cover ~97.2% of the total contig length (~223.8 Mb). Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map. Centromeric regions were inferred from recombination frequencies of genetic markers, alignment of 303 bp centromeric sequence with the PGA, and heat map showing the physical contact matrix over the entire genome. We demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry (Fragaria vesca L.) assembled using only PacBio long-read sequences. We conclude that that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.