A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist")

Authors: BRUNA, TOMAS - Georgia Tech; ARYAL, RISHI - North Carolina State University; DUDCHENKO, OLGA - Baylor College Of Medicine; SARGENT, DANIEL - National Institute Of Agricultural Botany (NIAB); MEAD, DANIEL - Wellcome Trust Sanger Institute; BUTI, MATTEO - University Of Florence; CAVALLINI, ANDREA - Universita Di Pisa; HYTONEN, TIMO - University Of Helsinki; ANDRES, JAVIER - University Of Helsinki; PHAM, MELANIE - Baylor College Of Medicine; WEISZ, DAVID - Baylor College Of Medicine; MASCAGNI, FLAVIA - Universita Di Pisa; USAI, GABRIELE - Universita Di Pisa; NATALI, LUCIA - Universita Di Pisa; Bassil, Nahla; FERNANDEZ, GINA - North Carolina State University; LOMSADZE, ALEXANDRE - Georgia Tech; ARMOUR, MITCHELL - University Of Arkansas; OLUKOLU, BODE - University Of Tennessee; POORTEN, TOM - Pairwise; BRITTON, CAITLIN - Pairwise; DAVIK, JAHN - Norwegian Institute Of Bioeconomy Research(NIBIO); ASHRAFI, HAMID - North Carolina State University; AIDEN, EREZ - Baylor College Of Medicine; BORODOVSKY, MARK - Georgia Tech; WORTHINGTON, MARGARET - University Of Arkansas

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/26/2022
Publication Date: 11/4/2022
Citation: Bruna, T., Aryal, R., Dudchenko, O., Sargent, D.J., Mead, D., Buti, M., Cavallini, A., Hytonen, T., Andres, J., Pham, M., Weisz, D., Mascagni, F., Usai, G., Natali, L., Bassil, N.V., Fernandez, G.E., Lomsadze, A., Armour, M., Olukolu, B., Poorten, T., Britton, C., Davik, J., Ashrafi, H., Aiden, E.L., Borodovsky, M., Worthington, M. 2022. A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist"). Genes, Genomes, Genetics. 13(2). Article jkac289. https://doi.org/10.1093/g3journal/jkac289.
DOI: https://doi.org/10.1093/g3journal/jkac289

Interpretive Summary: Blackberries are the fourth most economically important berry crop worldwide. Very few genomic resources exist for blackberries. Here we present a chromosome-length scale genome assembly and annotation of the diploid blackberry germplasm accession ‘Hillquist’. ‘Hillquist’ is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The genome sequence was highly collinear with a new map of the tetraploid blackberry selection A-2551TN and available genome assemblies of related raspberry crops. A total of 38,503 protein protein-coding genes were predicted using the assembly. The utility of the ‘Hillquist’ genome has been demonstrated here by the development of the first genetic linkage map of tetraploid blackberry and the identification of several possible candidate genes for primocane-fruiting within the previously mapped locus. This chromosome-length scale assembly will facilitate future studies in raspberry and blackberry biology, genetics, and genomics and strengthen applied breeding programs.

Technical Abstract: Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus Watson. Here we present a chromosome-length scale assembly and annotation of the diploid blackberry germplasm accession ‘Hillquist’ (R. argutus Link.). ‘Hillquist’ is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The ‘Hillquist’ assembly, generated using PacBio long reads scaffolded with Hi-C sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on seven chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein protein-coding genes were predicted using the assembly and Iso-Seq and RNA-seq data, of which 72% were functionally annotated. The utility of the ‘Hillquist’ genome has been demonstrated here by the development of the first genotyping-by-sequencing based linkage map of tetraploid blackberry and the identification of several possible candidate genes for primocane-fruiting within the previously mapped locus. This chromosome-length scale assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.