RNA-Seq analysis and annotation of a draft blueberry genome assembly.

Dataset type: Genomic, Transcriptomic
Data released on January 30, 2015

Gupta V; Estrada AD; Blakley I; Reid R; Patel K; Meyer MD; Andersen SU; Brown AF; Lila MA; Loraine AE (2015): RNA-Seq analysis and annotation of a draft blueberry genome assembly. GigaScience Database. http://dx.doi.org/10.5524/100117

DOI10.5524/100117

Blueberries are a popular and commercially important fruit, rich in antioxidants and other beneficial compounds that can protect against disease. To understand and identify genes involved in synthesis of bioactive compounds that could enable breeding berry varieties with enhanced health benefits, a draft blueberry genome assembly was produced using RNA-Seq data from five stages of berry fruit development and ripening. Libraries were prepared from samples of green and ripe fruit from plants of the O’Neal variety of southern highbush blueberry (Vaccinium corymbosum). Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes.
All sequence data are available in the Short Read Archive under accessions SRP039977 and SRP039971. Files containing alignments, RNA-Seq coverage graphs, and output from TopHat2 are also available from a publicly accessible IGBQuickLoad site configured to serve data for visualization in Integrated Genome Browser (see:http://www.igbquickload.org/blueberry). RNA-Seq data are freely available for visualization in Integrated Genome Browser. Archives of Visualization of read alignments, gene models, GeneModelAnalysis, counts file of numbers of single-mapping reads for each annotated blueberry gene, differentially expressed genes, Gene Ontology categories and Blastx Analysis files are available for download here. A snapshot of the R Markdown files, python scripts, and shell scripts used in data analysis and data processing are archived here as a set of static files representing those as publlished. For the current up-to-date scripts please visit the BitBucket repository.

Additional details

Read the peer-reviewed publication(s):

Gupta, V., Estrada, A. D., Blakley, I., Reid, R., Patel, K., Meyer, M. D., … Loraine, A. E. (2015). RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing. GigaScience, 4(1). doi:10.1186/s13742-015-0046-9

Additional information:

http://www.igbquickload.org/blueberry/

Accessions (data generated as part of this study):

Sample: SRP039971
Sample: SRP039977

Accessions (data referenced by this study):

SRA: SRP022157





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
2-41 cup69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
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2-41 green69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
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2-41 pad69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
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2-41 pink69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
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2-41 ripe69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
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2-42 cup69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
+
2-42 green69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
+
2-42 pink69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
+
2-42 ripe69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
+
3-33 cup69266American blueberry Vaccinium corymbosum Age:6
Sample source:April Estrada
Collected by:April Estrada
...
+
Displaying 1-10 of 34 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
DirectoryUNKNOWN84 KB2015-01-22
DirectoryUNKNOWN1.3 MB2015-01-22
DirectoryUNKNOWN4.1 MB2015-01-22
DirectoryUNKNOWN40 MB2015-01-22
DirectoryUNKNOWN63 MB2015-01-22
Mixed archiveUNKNOWN464 MB2015-01-22
DirectoryUNKNOWN448 KB2015-01-22
DirectoryUNKNOWN1.9 MB2015-01-22
TextTEXT0.42 KB2015-01-22
DirectoryUNKNOWN5.5 MB2015-01-22
Displaying 1-10 of 21 File(s).
Date Action
April 27, 2015 Manuscript Link added : 10.1186/s13742-015-0046-9
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample Attribute added : of Sample Vaccinium corymbosum; Filtered Hiseq reads for blueberry
February 2, 2017 Sample updated : Vaccinium corymbosum Filtered reads