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

Rosario Carmona,M Gonzalo Claros,Ismael Navas-Delgado,Antonio J Castro,Trinidad Castillo-Castillo,Adoración Zafra,Juan De Dios Alché,Ana Medina-García,Pedro Seoane,José F Aldana-Montes,Darío Guerrero-Fernández,Francisco M Cánovas

doi:10.3389/fpls.2015.00625

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.

Highlights

Research in plant reproduction is accelerating rapidly as a direct consequence of the technological progresses (Dickinson and Franklin-Tong, 2011)
ReprOlive: an olive tree reproductive transcriptome database use of transcriptomic approaches is unraveling the particular functionality of the key subsets of cells in charge of male and female gamete formation, and the complex interactions and signaling networks involved in the pollen–pistil interaction [reviewed in (Dukowic-Schulze and Chen, 2014)]
RNAs and mRNAs from mature pollen grains, in vitro germinated pollen at two different times after hydration (1 and 5 h), and pistils at developmental stages 2, 3, and 4 [as defined by (Zafra et al, 2010)] were isolated using RNeasy Plant and Oligotex PolyA+ kits (Qiagen), respectively. cDNA libraries to be sequenced with a Roche GS-FLX Titanium+ were generated using the cDNA Synthesis System Kit (Roche) and the raw read were uploaded to the SRA database with BioProject ID PRJNA2871073

Summary

Introduction

Research in plant reproduction is accelerating rapidly as a direct consequence of the technological progresses (Dickinson and Franklin-Tong, 2011). In good agreement with the degree of difficulty in isolating reproductive cells and extracting their RNAs, most studies up to date have reported gene expression in whole anther tissues, followed by male meiocytes, and female structures and meiocytes, being Arabidopsis thaliana the most widely studied, followed by lily, tobacco, brassica, petunia, maize, cotton, rice, and others (Dukowic-Schulze and Chen, 2014; Rutley and Twell, 2015) Those studies had shown that reproductive transcriptomes are substantially different from their vegetative counterparts, in concordance with the high proportion of specific transcripts present in these tissues, sometimes 4–11% of the total number of the genes expressed, depending on the normalization algorithms used and the number and diversity of sporophytic data sets used for comparison (Rutley and Twell, 2015). The peculiarity of reproductive tissues in terms of gene expression deserves a dedicated study for agronomical, biological, and biotechnological reasons and in search of putative new allergens in pollen (El Kelish et al, 2014; Villalba et al, 2014)

Methods

Results

Conclusion