title: 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.
abstract: BACKGROUND
  Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry varieties with enhanced health benefits.
  
  
  RESULTS
  Toward this end, we annotated a previously sequenced draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. 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. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up-regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up- and down-regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3' end formation.
  
  
  CONCLUSIONS
  We report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry.
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA ; Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark.
authors.forename: Vikas
authors.initials: V
authors.lastname: Gupta
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA.
authors.forename: April D
authors.initials: AD
authors.lastname: Estrada
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA.
authors.forename: Ivory
authors.initials: I
authors.lastname: Blakley
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Reid
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA ; NMRC-Frederick, 8400 Research Plaza, Ft. Detrick, MD 21702 USA.
authors.forename: Ketan
authors.initials: K
authors.lastname: Patel
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA.
authors.forename: Mason D
authors.initials: MD
authors.lastname: Meyer
authors.affiliation: Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark.
authors.forename: Stig Uggerhøj
authors.initials: SU
authors.lastname: Andersen
authors.affiliation: Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081 USA.
authors.forename: Allan F
authors.initials: AF
authors.lastname: Brown
authors.affiliation: Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081 USA.
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Lila
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA.
authors.forename: Ann E
authors.initials: AE
authors.lastname: Loraine
mesh_terms: D017398:Alternative Splicing; D000872:Anthocyanins / Q000096:biosynthesis; D001483:Base Sequence; D053898:Biosynthetic Pathways / Q000235:genetics*; D029798:Blueberry Plants / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D030541:Databases, Genetic; D005030:Ethylenes / Q000096:biosynthesis; D005638:Fruit / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D018749:RNA, Plant / Q000737:chemistry; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D000872:Anthocyanins; D005030:Ethylenes; D018749:RNA, Plant; C036216:ethylene
keywords: Alternative splicing; Blueberry; Fruit ripening; Genome; Metabolic pathways; RNA-Seq; Transcriptome
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