Supporting data for "Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry"

Dataset type: Genomic, Transcriptomic
Data released on January 17, 2019

Colle M; Leisner C; Wai CM; Ou S; Bird K; Wang J; Wisecaver J; Yocca A; Alger E; Tang H; Xiong Z; Callow P; Ben-Zvi G; Brodt A; Baruch K; Swale T; Shiue L; Song G; Childs K; Schilmiller A; Vorsa N; Buell CR; VanBuren R; Jiang N; Edger PP (2019): Supporting data for "Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry" GigaScience Database. http://dx.doi.org/10.5524/100537

DOI10.5524/100537

Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients, however, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources. The genome of highbush blueberry has been particularly challenging to assemble in large part to its polyploid nature and genome size. Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar Draper, which has the highest antioxidant levels among a diversity panel of seventyone cultivars and thirteen wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, analyses revealed the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. These findings and the reference genome will serve as a valuable resource for future genome-enabled breeding of important agronomic traits in highbush blueberry.

Additional details

Read the peer-reviewed publication(s):

Colle, M., Leisner, C. P., Wai, C. M., Ou, S., Bird, K. A., Wang, J., … Edger, P. P. (2019). Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. GigaScience, 8(3). doi:10.1093/gigascience/giz012

Additional information:

https://purr.purdue.edu/projects/blueberrygenome

https://phytozome.jgi.doe.gov/

https://genomevolution.org/coge/

Accessions (data generated as part of this study):

BioProject: PRJNA494180





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN1043884169266American blueberry Vaccinium corymbosum Description:RNA isolated from flower bud of Highbu...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
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SAMN1043884269266American blueberry Vaccinium corymbosum Description:RNA isolated from flower at anthesis o...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
+
SAMN1043884369266American blueberry Vaccinium corymbosum Description:RNA isolated from green fruit of Highb...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
+
SAMN1043884469266American blueberry Vaccinium corymbosum Description:RNA isolated during day from young lea...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
+
SAMN1043884569266American blueberry Vaccinium corymbosum Description:RNA isolated during night, from young ...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
+
SAMN1043884669266American blueberry Vaccinium corymbosum Description:RNA isolated from leaf (after 1hr of m...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
+
SAMN1043884769266American blueberry Vaccinium corymbosum Description:RNA isolated from leaf (after 8hrs of ...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
+
SAMN1043884869266American blueberry Vaccinium corymbosum Description:RNA isolated from leaf (after 24hrs of...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
+
SAMN1043884969266American blueberry Vaccinium corymbosum Description:RNA isolated from petal fall of Highbu...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
+
SAMN1043885069266American blueberry Vaccinium corymbosum Description:RNA isolated from pink fruit of Highbu...
Alternative accession-BioProject:PRJNA494180
Alternative names:Highbush blueberry
...
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Displaying 1-10 of 41 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular dataUNKNOWN351.11 KB 
Tabular dataUNKNOWN0.89 KB 
readmeTEXT2.45 KB2018-12-19
Tabular dataUNKNOWN0.75 KB 
Expression dataTEXT17.63 MB2018-12-19
Expression dataUNKNOWN10.94 MB2018-12-19
Genome sequenceFASTA1.73 GB2018-12-19
annotationGFF263.16 MB2018-12-19
protein sequenceFASTA61.86 MB2018-12-19
annotationGFF257.11 MB2018-12-19
Displaying 1-10 of 11 File(s).
Funding body Awardee Award ID Comments
United States Department of Agriculture P Edger 1015241 National Institute of Food and Agriculture AFRI
United States Department of Agriculture P Edger 1009804 National Institute of Food and Agriculture HATCH
United States Department of Agriculture J Wisecaver 1016057 National Institute of Food and Agriculture HATCH
National Natural Science Foundation of China Z Xiong 31560302
Inner Mongolia Major and Special Program of Science and Technology Z Xiong 5163901
Date Action
January 17, 2019 Dataset publish
January 27, 2019 Manuscript Link added : 10.1093/gigascience/giz012