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Title: RNA-Seq analysis and annotation of a draft blueberry genome assembly.      
dateReleased:
02-24-2015
privacy:
not applicable
aggregation:
instance of dataset
dateCreated:
02-24-2015
refinement:
curated
ID:
doi:10.5524/100117
creators:
Gupta, V
Estrada, AD
Blakley, I
Reid, R
Patel, K
,
Andersen, SU
Brown, AF
Lila, MA
Loraine, AE
availability:
available
types:
sequence
description:
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.
accessURL: https://doi.org/10.5524/100117
storedIn:
GigaScience Database
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
GigaDB
homePage: http://gigadb.org/
ID:
SCR:006565
name:
Giga Science Database

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