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Article|07 Feb 2018|OPEN
Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data
Rubina Jibran1, Helge Dzierzon1, Nahla Bassil2, Jill M. Bushakra2, Patrick P. Edger3, Shawn Sullivan4, Chad E. Finn5, Michael Dossett6, Kelly J. Vining6, Robert VanBuren3, Todd C. Mockler7, Ivan Liachko4,8, Kevin M. Davies1, Toshi M. Foster1 & David Chagné1,
1The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4474, New Zealand
2USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
3Department of Horticulture, Michigan State University, East Lansing, MI 48824-2604, USA
4Phase Genomics, Seattle, WA 98195, USA
5USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97330, USA
6B.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research Centre, Agassiz, BC V0M 1A0, Canada
7The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
8Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA

Horticulture Research 5,
Article number: 8 (2018)
doi: 10.1038/hortres.2018.8
Views: 631

Received: 17 Sep 2017
Revised: 06 Dec 2017
Accepted: 10 Dec 2017
Published online: 07 Feb 2018

Abstract

Black raspberry (Rubus occidentalis L.) is a niche fruit crop valued for its flavor 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 9650 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 PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.