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Bazakos C.,Mediterranean Agronomic Institute of Chania | Bazakos C.,Aristotle University of Thessaloniki | Manioudaki M.E.,Mediterranean Agronomic Institute of Chania | Therios I.,Aristotle University of Thessaloniki | And 4 more authors.
PLoS ONE | Year: 2012

Background: Olive (Olea europaea L.) cultivation is rapidly expanding and low quality saline water is often used for irrigation. The molecular basis of salt tolerance in olive, though, has not yet been investigated at a system level. In this study a comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt-tolerant and a salt-sensitive one. Methodology/Principal Findings: A 135-day long salinity experiment was conducted using one-year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period during the summer. A cDNA library made of olive seedling mRNAs was sequenced and an olive microarray was constructed. Total RNA was extracted from root samples after 15, 45 and 90 days of NaCl-treatment as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations. SAM analysis between the NaCl-stress and the post-stress time course resulted in the identification of 209 and 36 differentially expressed transcripts in the salt-tolerant and salt-sensitive cultivar, respectively. Hierarchical clustering revealed two major, distinct clusters for each cultivar. Despite the limited number of probe sets, transcriptional regulatory networks were constructed for both cultivars while several hierarchically-clustered interacting transcription factor regulators such as JERF and bZIP homologues were identified. Conclusions/Significance: A systems biology approach was used and differentially expressed transcripts as well as regulatory interactions were identified. The comparison of the interactions among transcription factors in olive with those reported for Arabidopsis might indicate similarities in the response of a tree species with Arabidopsis at the transcriptional level under salinity stress. © 2012 Bazakos et al.

Bazakos C.,Mediterranean Agronomic Institute of Chania | Bazakos C.,Aristotle University of Thessaloniki | Manioudaki M.,Mediterranean Agronomic Institute of Chania | Therios I.,Aristotle University of Thessaloniki | And 5 more authors.
Acta Horticulturae | Year: 2011

Olive (Olea europaea L.) is one of the most significant crops in the Mediterranean region. The expansion in cultivation of olive to areas irrigated with low quality water, mostly saline, limits growth and productivity. Although a number of studies have been conducted on the effects of salinity on olive growth, the molecular basis of salt tolerance has not been investigated. A five-month salt stress experiment was set up with one-year-old plants of the cultivar 'Kalamon', which exhibits tolerance to salinity. A custom olive cDNA microarray, composed of 1,121 cDNAs, was constructed and used for comparative transcriptome analysis of salt-treated and untreated roots. In addition, the expression profiles of selected cDNAs were further analyzed. Salt stress-related cDNA homologues through nucleotide bioinformatic analyses have been found.

Giraldo-Calderon G.I.,University of Notre Dame | Emrich S.J.,University of Notre Dame | MacCallum R.M.,Imperial College London | Maslen G.,European Bioinformatics Institute | And 45 more authors.
Nucleic Acids Research | Year: 2015

VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. Vector-Base also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/. © The Author(s) 2014.

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