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

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

doi:10.3389/fpls.2015.00625

Cited by 42 publications

(50 citation statements)

References 43 publications

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“…It is noteworthy that all transcriptomes assembled in this study were hosted in a specific database named IsochrysisDB. The information was structured in a similar way to SoleaDB (Benzekri et al, 2014), EuroPineDB (Fernández-Pozo et al, 2011), EuroPineDB (Fernández-Pozo et al, 2011, and ReprOlive (Carmona et al, 2015). All transcriptomic information can be browsed by assemblies (with history versions) that contains all relevant information about bioinformatic pipeline, experimental conditions and main statistical features.…”

Section: Discussionmentioning

confidence: 99%

Characterization of Iodine-Related Molecular Processes in the Marine Microalga Tisochrysis lutea (Haptophyta)

et al. 2018

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Iodine metabolism is essential for the antioxidant defense of marine algae and in the biogeochemical cycle of iodine. Moreover, some microalgae can synthetize thyroid hormone-like compounds that are essential to sustain food webs. However, knowledge regarding iodine-related molecular processes in microalgae is still scarce. In this study, a de novo transcriptome of Tisochrysis lutea cultured under high iodide concentrations (5 mM) was assembled using both long and short reads. A database termed IsochrysisDB was established to host all genomic information. Gene expression analyses during microalgal growth showed that most of the antioxidant-(aryl, ccp, perox, sod1, sod2, sod3, apx3, ahp1) and iodide-specific deiodinase (dio) genes increased their mRNA abundance progressively until the stationary phase to cope with oxidative stress. Moreover, the increase of dio mRNA abundance in aging cultures indicated that this enzyme was also involved in senescence. Cell treatments with iodide modified the expression of perox whereas treatments with iodate changed the transcript levels of gpx1 and ccp. To test the dependence of perox on iodide, microalgae cells were treated with hydrogen peroxide (H 2 O 2 ) either in presence or absence of iodide observing that several genes related to reactive oxygen species (ROS) deactivation (perox, gpx1, apx2, apx3, ahp1, ahp2, sod1, sod3, and aryl) were transcriptionally activated although with some temporal differences. However, only the expression of perox was dependent on iodide levels indicating this enzyme, acquired by horizontal gene transfer (HGT), could act as a haloperoxidase. All these data indicate that T. lutea activates coordinately the expression of antioxidant genes to cope with oxidative stress. The identification of a phase-regulated deiodinase and a novel haloperoxidase provide new clues about the origin and evolution of thyroid signaling and the antioxidant role of iodine in the marine environment.

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Section: Discussionmentioning

confidence: 99%

Characterization of Iodine-Related Molecular Processes in the Marine Microalga Tisochrysis lutea (Haptophyta)

et al. 2018

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“…For a functional overview of the S. globulifera draft genome, predicted protein sequences were annotated with Full‐LengtherNEXT (as described in Carmona et al . ) and Sma3 (Muñoz‐Mérida et al . ) to provide protein orthologs, putative gene names, descriptions, Gene Ontology terms (GO terms), enzyme codes (EC numbers) for putative enzymes, and the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway in which they can be involved.…”

Section: Methodsmentioning

confidence: 99%

Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low‐coverage draft genome, SNP and SSR markers

Olsson

Zonjic

Bautista

et al. 2016

Molecular Ecology Resources

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Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, F = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.

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“…Transcriptomes used in this work were generated from pollen and pistil Sanger sequences and Roche/454 reads at different developmental stages, as described in ReprOlive (http://reprolive.eez.csic.es) [33].…”

Section: Pollen and Pistil Transcriptomesmentioning

confidence: 99%

“…As an example, differential gene expression analyses have been used to explore the involvement of NO in C. sinensis pollen tube growth at low temperature [20]. As per olive pollen, the ReprOlive database (http://reprolive.eez.csic.es/olivodb/) [33] is an easy-to-use olive tree (Olea europaea L.) database containing its reproductive transcriptome obtained from pollen and stigma (both together and separately). We have used the information stored and organized within this olive database to design new in silico strategies to explore the potential of both S-nitrosylation and Tyr-nitration in the olive pollen.…”

Section: Nano-lc-ms Identification Of S-nitrosylated/tyr-nitrated Promentioning

confidence: 99%

Generation of nitric oxide by olive (Olea europaea L.) pollen during in vitro germination and assessment of the S-nitroso- and nitro-proteomes by computational predictive methods

et al. 2017

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Nitric oxide is recognized as a signaling molecule involved in a broad range of physiological processes in plants including sexual reproduction. NO has been detected in the pollen grain at high levels and regulates pollen tube growth. Previous studies demonstrated that NO as well as ROS are produced in the olive reproductive tissues in a stage- and tissue-specific manner. The aim of this study was to assess the production of NO throughout the germination of olive (Olea europaea L.) pollen in vitro. The NO fluorescent probe DAF-2DA was used to image NO production in situ, which was correlated to pollen viability. Moreover, by means of a fluorimetric assay we showed that growing pollen tubes release NO. GSNO -a mobile reservoir of NO, formed by the S-nitrosylation of NO with reduced glutathione (GSH) - was for the first time detected and quantified at different stages of pollen tube growth using a LC-ES/MS analysis. Exogenous NO donors inhibited both pollen germination and pollen tube growth and these effects were partially reverted by the specific NO-scavenger c-PTIO. However, little is known about how NO affects the germination process. With the aim of elucidating the putative relevance of protein S-nitrosylation and Tyr-nitration as important post-translational modifications in the development and physiology of the olive pollen, a de novo assembled and annotated reproductive transcriptome from olive was challenged in silico for the putative capability of transcripts to become potentially modified by S-nitrosylation/Tyr-nitration according to well-established criteria. Numerous gene products with these characteristics were identified, and a broad discussion as regards to their potential role in plant reproduction was built after their functional classification. Moreover, the importance of both S-nitrosylation/Tyr-nitrations was experimentally assessed and validated by using Western blotting, immunoprecipitation and proteomic approaches.

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

Cited by 42 publications

References 43 publications

Characterization of Iodine-Related Molecular Processes in the Marine Microalga Tisochrysis lutea (Haptophyta)

Characterization of Iodine-Related Molecular Processes in the Marine Microalga Tisochrysis lutea (Haptophyta)

Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low‐coverage draft genome, SNP and SSR markers

Generation of nitric oxide by olive (Olea europaea L.) pollen during in vitro germination and assessment of the S-nitroso- and nitro-proteomes by computational predictive methods

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