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

• DOI: 10.1093/g3journal/jkac289
• Publication Date: 2022-11-04T19:27:49Z
• Authors: Tomáš Brůna; Rishi Aryal; Olga Dudchenko; Daniel James Sargent; Daniel Mead; Matteo Buti; Andrea Cavallini; Timo Hytönen; Javier Andrés; Melanie Pham; David Weisz; Flavia Mascagni; Gabriele Usai; Lucia Natali; Nahla Bassil; Gina E Fernandez; Alexandre Lomsadze; Mitchell Armour; Bode Olukolu; Thomas Poorten; Caitlin Britton; Jahn Davik; Hamid Ashrafi; Erez Lieberman Aiden; Mark Borodovsky; Margaret Worthington
• Keywords: 0301 basic medicine; Biennial flowering; Rosoideae; Primocane-fruiting; Annotation; Chromosome-length genome assembly; QH426-470; Rubus; Hi-C; Rosaceae; Rosoideae; annotation; annual flowering; biennial flowering; blackberry; chromosome-length genome assembly; primocane-fruiting; repetitive content; Rubus; blackberry; Rosaceae; Rosoideae; biennial flowering; annual flowering; primocane-fruiting; chromosome-length genome assembly; Hi-C; annotation; repetitive content; Chromosomes, Plant; 03 medical and health sciences; Hi-C; Genetics; Repetitive content; Plant Genetics and Genomics; Rosaceae; Chromosome Mapping; Molecular Sequence Annotation; 15. Life on land; 11831 Plant biology; Blackberry; Tetraploidy; Plant Breeding; Annual flowering; Genetics, developmental biology, physiology; Rubus

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. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “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 Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 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-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. 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 possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.