Supporting data for "A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome"

Dataset type: Genomic, Transcriptomic
Data released on July 09, 2018

VanBuren R; Wai CM; Colle M; Wang J; Sullivan S; Bushakra JM; Liachko I; Vining K; Dossett M; Finn C; Chagne D; Jibran R; Childs K; Edger PP; Mockler TC; Bassil NV (2018): Supporting data for "A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome" GigaScience Database. http://dx.doi.org/10.5524/100465

DOI10.5524/100465

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. Here we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time (SMRT) PacBio sequencing and Hi-C genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing a ~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. 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.

Keywords:

Additional details

Read the peer-reviewed publication(s):

VanBuren, R., Wai, C. M., Colle, M., Wang, J., Sullivan, S., Bushakra, J. M., … Bassil, N. V. (2018). A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. GigaScience, 7(8). doi:10.1093/gigascience/giy094

Genome browser:

https://www.rosaceae.org/jbrowse/index.html?data=data%2Frubus%2Froccidentalis_v3.0&loc=Ro01%3A137222

Accessions (data included in GigaDB):

BioProject: PRJNA430858
BioProject: PRJNA474906





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN0837912975079black raspberry Rubus occidentalis Description:Genomic DNA extracted from young leaf ...
Alternative names:black raspberry
Alternative accession-BioSample:SAMN08379129
...
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SAMN0937520175079black raspberry Rubus occidentalis Description:Total RNA extracted from leaf tissue o...
Common name:black raspberry
Alternative accession-BioSample:SAMN09375201
...
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SAMN0937520275079black raspberry Rubus occidentalis Description:Total RNA extracted from cane tissue o...
Common name:black raspberry
Alternative accession-BioSample:SAMN09375202
...
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SAMN0937520375079black raspberry Rubus occidentalis Description:Total RNA extracted from root of Rubus...
Common name:black raspberry
Alternative accession-BioSample:SAMN09375203
...
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SAMN0937520475079black raspberry Rubus occidentalis Description:Total RNA extracted from flower of Rub...
Common name:black raspberry
Alternative accession-BioSample:SAMN09375204
...
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SAMN0937520575079black raspberry Rubus occidentalis Description:Total RNA extracted from green berries...
Common name:black raspberry
Alternative accession-BioSample:SAMN09375205
...
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SAMN0937520675079black raspberry Rubus occidentalis Description:Total RNA extracted from red berries o...
Common name:black raspberry
Alternative accession-BioSample:SAMN09375206
...
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SAMN0937520775079black raspberry Rubus occidentalis Description:Total RNA extracted from ripe berries ...
Common name:black raspberry
Alternative accession-BioSample:SAMN09375207
...
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SAMN0937520875079black raspberry Rubus occidentalis Description:Total RNA extracted from jasmonate-tre...
Common name:black raspberry
Alternative accession-BioSample:SAMN09375208
...
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Displaying 1-9 of 9 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT2.74 KB2018-06-12
Sequence assemblyFASTA81.74 MB2018-06-12
annotationGFF38.88 MB2018-06-12
Coding SequenceFASTA37.4 MB2018-06-12
Repeat sequenceGFF9.62 MB2018-06-12
protein sequenceFASTA7.45 MB2018-06-12
transcriptome sequenceFASTA13.79 MB2018-06-12
Displaying 1-7 of 7 File(s).
Funding body Awardee Award ID Comments
USDA-NIFA P Edger 1009804 HATCH
USDA-NIFA R VanBuren 1013240 HATCH
Date Action
July 9, 2018 Dataset publish
August 22, 2018 Manuscript Link added : 10.1093/gigascience/giy094