Rubus ulmifolius Burbank Thornless Whole Genome v1.0 Assembly

Genome Overview
Analysis NameRubus ulmifolius Burbank Thornless Whole Genome v1.0 Assembly
MethodPacBio and HiC (Falcon assembly)
SourceBurbank Thornless
Date performed2020-01-15

R. ulmifolius Burbank Thornless Whole Genome v.1.0 assembly

Erez Aiden, Rishi Aryal, Hamid Ashrafi, Nahla Bassil, Mario Caccamo, Brian Crawford, Michael Dossett, Olga Dudchenko, Felicidad Fernandez-Fernandez, Gina Fernandez, Jodi Humann, Sook Jung, Dorrie Main, Dan Mead, Cherie Ochsenfeld, Gina Pham, Tom Poorten, Dan Sargent, Aabid Shariff, Margaret Worthington, Xiaoyu Zhang

Abstract

The global blackberry (Rubus subgenus Rubus) industry has experienced rapid growth during the past 15 years, driven by increased consumer demand, advanced production methods, year-round product availability, and new cultivars. Despite the growing economic importance of blackberries and their excellent nutritional properties, few genomic resources exist to facilitate molecular breeding. The application of molecular breeding in blackberry is a ‘thorny’ problem due to polyploidy, multisomic inheritance, and heterozygosity. While the red and black raspberries in subgenus Idaeobatus are diploids (2n = 2x = 14), cultivated blackberries in the subgenus Rubus are bred at the tetraploid (2n = 4x = 28) and higher order polyploid levels (Clark et al., 2007).

Today, we share the chromosome-length genome assembly for the diploid blackberry ‘Burbank Thornless’ (R. ulmifolius inermis, PI 554060), generated using plants donated by the USDA-ARS National Clonal Germplasm Repository in Corvallis, OR. ‘Burbank Thornless’ was chosen because is believed to be closely related to ‘John Innes’, the source of the recessive gene for thornlessness in ‘Merton Thornless’, which has been used widely in fresh-market blackberry breeding programs (Coyner et al., 2005; Scott et al., 1957). Botanically speaking, it would be more accurate to describe this accession as prickle-free than thornless.  Blackberries have prickles, outgrowths from epidermal tissue, instead of thorns or spines, which are connected to the vascular systems of the plant (https://ipm.missouri.edu/MEG/archive/2013/v19n1.pdf). Regardless of what they are called, anyone who has spent time picking berries in wild bramble patches can appreciate that picking from thornless cultivars is a much smoother experience!

The assembly was generated using PacBio and HiC sequencing data. The genome was assembled using Falcon software. The Falcon assembly was phased into haplotypes using Falcon-Unzip. And final error correction on the phased assembly was performed using Arrow. The Hi-C scaffolding was performed using the standard DNA Zoo workflow, based on in situ Hi-C library (Rao et al., 2014) prepared from fresh leaf samples. The tools used for Hi-C data processing included: Juicer (Durand et al., 2016), 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018).  

The whole-genome alignment was highly collinear with the black raspberry (R. occidentalis V. 3, VanBuren et al., 2018) and woodland strawberry (Fragaria vesca V. 4, Edger et al., 2017) genomes.  Inversions on chromosomes 1 and 7 were found woodland strawberry and both Rubus species. Interestingly, the inversions between R. occidentalis and F. vesca previously documented on chromosomes 4 and 6 were not seen in the new assembly of Burbank thornless.  These inversions likely represent errors in the chromosome scale assembly of R. occidentalis.

This work is part of a collaborative effort between the University of Arkansas, USDA-ARS, North Carolina State University, Baylor College of Medicine, NIAB-EMR, Pairwise Plants, and the Wellcome Sanger Institute.  The chromosome scale assembly is also available at the DNAzoo.

Non-hyperlinked Citations:

Scott, D.H., Darrrow G.M., and Ink D.P. (1957). ‘Merton Thornless’ as a parent in breeding thornless blackberries. Proc. Amer. Soc. Hort. Sci. 69,268-277.

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome