ArticleGigaScience2018
A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- The Landscape of Long Non-Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Two telomere-to-telomere genome assemblies and comparative genomics reveal the conserved "toolkit" genes associated with sugar accumulation in the genus Rubus.Plant communications · 2026Article
- Genome-wide analysis of the NLR gene family in strawberry reveals a novel immune receptor architecture in Rosaceae.BMC genomics · 2026Article
- Multi-omics analyses shed lights on the evolution and fruit development of Chinese raspberries (Rubus spp.).Journal of integrative plant biology · 2026Article
- The chromosome-scale genome assembly and annotation of Rosa bracteata (Macartney Rose).Scientific data · 2026Article
- Orchard and storage-dependent metabolic and transcriptional regulation of superficial scald in 'Packham's Triumph' pears.Frontiers in plant science · 2026Article
- Improving the Antioxidant Potential of Berry Crops Through Genomic Advances and Modern Agronomic and Breeding Tools.Biotech (Basel (Switzerland)) · 2025Review
- A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Horticulture research · 2025Article
- The haplotype-phased genome assembly facilitated the deciphering of the bud dormancy-related QTLs in Prunus mume.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Genomic Introgression in the Hybrid zones at the Margins of the Species' Range Between Ecologically DistinctEcology and evolution · 2024Article
- A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'.G3 (Bethesda, Md.) · 2024Article
- Genomic data provides insights into the evolutionary history and adaptive differentiation of two tetraploid strawberries.Horticulture research · 2024Article
- Gene Duplication and Functional Diversification of MADS-Box Genes inInternational journal of molecular sciences · 2024Article
- Identifying potential anthocyanin biosynthesis regulator in Chinese cherry by comprehensive genome-wide characterization of the R2R3-MYB transcription factor gene family.BMC genomics · 2024Article
- Plant kleptomaniacs: geographical genetic patterns in the amphi-apomictic Rubus ser. Glandulosi (Rosaceae) reveal complex reticulate evolution of Eurasian brambles.Annals of botany · 2024Article
- Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.Nature genetics · 2024Article
- Chromosome-scale genome, together with transcriptome and metabolome, provides insights into the evolution and anthocyanin biosynthesis ofHorticulture research · 2024Article
- Haplotype-resolved genome ofHorticulture research · 2024Article
- Rosaceae fruit transcriptome database (ROFT)-a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry.Horticulture research · 2023Article
- Manual correction of genome annotation improved alternative splicing identification of Artemisia annua.Planta · 2023Article
1 more citing papers are in PubMed but not listed here.
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16 authors.
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Abstract
Background: The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies. Findings: Here, we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing an ∼200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high-quality V4 woodland strawberry genome (Fragaria vesca) revealed near-perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis. Conclusions: The improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.
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