ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome

Frontiers in Plant Science
Rosario CarmonaM Gonzalo Claros

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....Continue Reading

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Citations

Apr 2, 2016·BioMed Research International·Jose C Jimenez-LopezJuan de Dios Alché
Jun 14, 2019·The Plant Journal : for Cell and Molecular Biology·Muriel Gros-BalthazardBouchaib Khadari
May 4, 2017·The Plant Genome·Jaime Jiménez-RuizFrancisco Luque
May 26, 2017·Proteomics·Carlos S Casimiro-SoriguerAntonio J Pérez-Pulido
Jun 14, 2019·Journal of Proteome Research·Pablo San Segundo-AcostaRodrigo Barderas

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Datasets Mentioned

BETA
PRJNA287107
SRX193576
SRR592583

Methods Mentioned

BETA
RNA-seq

Software Mentioned

blastx
Euler
Linux
Blast
D2RQ
Apache HTTP Server
MySQL
AutoFlow
MREPS
BioRuby

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