title: ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome.
abstract: Plant reproductive transcriptomes have been analyzed in different species due to the agronomical and biotechnological importance of plant reproduction. Here we presented an olive tree reproductive transcriptome database with samples from pollen and pistil at different developmental stages, and leaf and root as control vegetative tissues http://reprolive.eez.csic.es). It was developed from 2,077,309 raw reads to 1,549 Sanger sequences. Using a pre-defined workflow based on open-source tools, sequences were pre-processed, assembled, mapped, and annotated with expression data, descriptions, GO terms, InterPro signatures, EC numbers, KEGG pathways, ORFs, and SSRs. Tentative transcripts (TTs) were also annotated with the corresponding orthologs in Arabidopsis thaliana from TAIR and RefSeq databases to enable Linked Data integration. It results in a reproductive transcriptome comprising 72,846 contigs with average length of 686 bp, of which 63,965 (87.8%) included at least one functional annotation, and 55,356 (75.9%) had an ortholog. A minimum of 23,568 different TTs was identified and 5,835 of them contain a complete ORF. The representative reproductive transcriptome can be reduced to 28,972 TTs for further gene expression studies. Partial transcriptomes from pollen, pistil, and vegetative tissues as control were also constructed. ReprOlive provides free access and download capability to these results. Retrieval mechanisms for sequences and transcript annotations are provided. Graphical localization of annotated enzymes into KEGG pathways is also possible. Finally, ReprOlive has included a semantic conceptualisation by means of a Resource Description Framework (RDF) allowing a Linked Data search for extracting the most updated information related to enzymes, interactions, allergens, structures, and reactive oxygen species.
authors: Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain ; Plataforma Andaluza de Bioinformática, Edificio de Bioinnovación, Universidad de Málaga Málaga, Spain.
authors: Rosario
authors: R
authors: Carmona
authors: Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain.
authors: Adoración
authors: A
authors: Zafra
authors: Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga Málaga, Spain.
authors: Pedro
authors: P
authors: Seoane
authors: Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain.
authors: Antonio J
authors: AJ
authors: Castro
authors: Plataforma Andaluza de Bioinformática, Edificio de Bioinnovación, Universidad de Málaga Málaga, Spain.
authors: Darío
authors: D
authors: Guerrero-Fernández
authors: Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga Málaga, Spain.
authors: Trinidad
authors: T
authors: Castillo-Castillo
authors: Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga Málaga, Spain.
authors: Ana
authors: A
authors: Medina-García
authors: Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga Málaga, Spain.
authors: Francisco M
authors: FM
authors: Cánovas
authors: Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga Málaga, Spain.
authors: José F
authors: JF
authors: Aldana-Montes
authors: Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga Málaga, Spain.
authors: Ismael
authors: I
authors: Navas-Delgado
authors: Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain.
authors: Juan de Dios
authors: Jde D
authors: Alché
authors: Plataforma Andaluza de Bioinformática, Edificio de Bioinnovación, Universidad de Málaga Málaga, Spain ; Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga Málaga, Spain.
authors: M Gonzalo
authors: MG
authors: Claros
keywords: annotation; database; olive; pistil; pollen; reproduction; transcriptome