{"doi":"10.1101/2022.04.28.489789","title":"A chromosome-length genome assembly and annotation of blackberry ( <i>Rubus argutus</i> , cv. ‘Hillquist’)","abstract":"Abstract Background 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 . Findings 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 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-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 using the assembly and Iso-Seq and RNA-seq data, of which 72% were functionally annotated. Conclusions 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 assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":300039,"datarank":0.22244887368078217,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.01450471951279854,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.01450471951279854,"corpus_percentile":37.5415796395142,"corpus_rank":8075,"citation_count":3,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9111,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":877231,"name":"Rishi Aryal","orcid":"0000-0001-5297-1528","position":1,"is_corresponding":false},{"id":292976,"name":"Olga Dudchenko","orcid":"0000-0001-9163-9544","position":2,"is_corresponding":false},{"id":877232,"name":"Daniel James Sargent","orcid":"0000-0002-6686-7147","position":3,"is_corresponding":false},{"id":51480,"name":"Daniel G. Mead","orcid":"0000-0001-7717-4330","position":4,"is_corresponding":false},{"id":877233,"name":"Matteo Buti","orcid":"0000-0002-1430-7826","position":5,"is_corresponding":false},{"id":877234,"name":"Andrea Cavallini","orcid":"0000-0003-4977-2696","position":6,"is_corresponding":false},{"id":877235,"name":"Timo Hytönen","orcid":"0000-0002-5231-4031","position":7,"is_corresponding":false},{"id":877236,"name":"Javier Andrés","orcid":"0000-0002-7769-9003","position":8,"is_corresponding":false},{"id":619051,"name":"Melanie Pham","orcid":"0000-0002-6083-271X","position":9,"is_corresponding":false},{"id":292983,"name":"David Weisz","orcid":"0000-0001-5868-6672","position":10,"is_corresponding":false},{"id":877237,"name":"Flavia Mascagni","orcid":"0000-0001-9747-8040","position":11,"is_corresponding":false},{"id":877238,"name":"Gabriele Usai","orcid":"0000-0001-9982-4883","position":12,"is_corresponding":false},{"id":877239,"name":"Lucia Natali","orcid":"0000-0003-3179-5910","position":13,"is_corresponding":false},{"id":877240,"name":"Nahla Bassil","orcid":"0000-0001-8625-2740","position":14,"is_corresponding":false},{"id":877241,"name":"Gina E. Fernandez","orcid":"0000-0002-9295-2687","position":15,"is_corresponding":false},{"id":17119,"name":"Alexandre Lomsadze","orcid":null,"position":16,"is_corresponding":false},{"id":877908,"name":"Mitchell Armour","orcid":null,"position":17,"is_corresponding":false},{"id":877242,"name":"Bode A. Olukolu","orcid":"0000-0003-4143-8909","position":18,"is_corresponding":false},{"id":877243,"name":"Thomas J. 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