EuroPineDB: a high-coverage web database for maritime pine transcriptome

Fernández-Pozo, Noé; Canales, Javier; Guerrero-Fernández, Darío; Villalobos, David P.; Díaz-Moreno, Sara M.; Bautista, Rocí­o; Flores-Monterroso, Arantxa; Guevara, M. Ángeles; Perdiguero, Pedro; Collada, Carmen; Cervera, Marı́a Teresa; Soto, Álvaro; Ordás, Ricardo J.; Cantón, Francisco R.; Ávila, Concepción; Cánovas, Francisco M.; Claros, M. Gonzalo

doi:10.1186/1471-2164-12-366

Cited by 53 publications

(44 citation statements)

References 42 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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“…Conifers are widely distributed globally as the largest and most diverse group of gymnosperms [1] that evolved independently from angiosperms >300 million years ago [2]. Modern conifers are divided into eight families including 68 genera and 630 species, which form an integral part of the economy in many parts of the world [3].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinusphylogeny

Niu

Yuan

et al. 2013

BMC Genomics

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BackgroundThe Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcriptome data were obtained using a next-generation sequencing platform to compensate for the lack of P. tabuliformis genomic information.ResultsThe increasing amount of transcriptome data on Pinus provides an excellent resource for multi-gene phylogenetic analysis and studies on how conserved genes and functions are maintained in the face of species divergence. The first P. tabuliformis transcriptome from a normalised cDNA library of multiple tissues and individuals was sequenced in a full 454 GS-FLX run, producing 911,302 sequencing reads. The high quality overlapping expressed sequence tags (ESTs) were assembled into 46,584 putative transcripts, and more than 700 SSRs and 92,000 SNPs/InDels were characterised. Comparative analysis of the transcriptome of six conifer species yielded 191 orthologues, from which we inferred a phylogenetic tree, evolutionary patterns and calculated rates of gene diversion. We also identified 938 fast evolving sequences that may be useful for identifying genes that perhaps evolved in response to positive selection and might be responsible for speciation in the Pinus lineage.ConclusionsA large collection of high-quality ESTs was obtained, de novo assembled and characterised, which represents a dramatic expansion of the current transcript catalogues of P. tabuliformis and which will gradually be applied in breeding programs of P. tabuliformis. Furthermore, these data will facilitate future studies of the comparative genomics of P. tabuliformis and other related species.

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“…Publicly available databases have scarce information on conifer genes and 30% of these genes have little or no sequence similarity to plant genes of known function [11]. Useful initiatives have been created such as EuroPineDB, that aims at providing a high coverage database for maritime pine ( P. pinaster ) transcriptome genes [11].…”

Section: Introductionmentioning

confidence: 99%

“…Useful initiatives have been created such as EuroPineDB, that aims at providing a high coverage database for maritime pine ( P. pinaster ) transcriptome genes [11]. Different technologies have given us some insight regarding the pine genome and its response to biotic and abiotic stresses.…”

Section: Introductionmentioning

confidence: 99%

Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening

et al. 2012

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BackgroundPine wilt disease (PWD), caused by the pinewood nematode (PWN; Bursaphelenchus xylophilus), damages and kills pine trees and is causing serious economic damage worldwide. Although the ecological mechanism of infestation is well described, the plant’s molecular response to the pathogen is not well known. This is due mainly to the lack of genomic information and the complexity of the disease. High throughput sequencing is now an efficient approach for detecting the expression of genes in non-model organisms, thus providing valuable information in spite of the lack of the genome sequence. In an attempt to unravel genes potentially involved in the pine defense against the pathogen, we hereby report the high throughput comparative sequence analysis of infested and non-infested stems of Pinus pinaster (very susceptible to PWN) and Pinus pinea (less susceptible to PWN).ResultsFour cDNA libraries from infested and non-infested stems of P. pinaster and P. pinea were sequenced in a full 454 GS FLX run, producing a total of 2,083,698 reads. The putative amino acid sequences encoded by the assembled transcripts were annotated according to Gene Ontology, to assign Pinus contigs into Biological Processes, Cellular Components and Molecular Functions categories. Most of the annotated transcripts corresponded to Picea genes-25.4-39.7%, whereas a smaller percentage, matched Pinus genes, 1.8-12.8%, probably a consequence of more public genomic information available for Picea than for Pinus. The comparative transcriptome analysis showed that when P. pinaster was infested with PWN, the genes malate dehydrogenase, ABA, water deficit stress related genes and PAR1 were highly expressed, while in PWN-infested P. pinea, the highly expressed genes were ricin B-related lectin, and genes belonging to the SNARE and high mobility group families. Quantitative PCR experiments confirmed the differential gene expression between the two pine species.ConclusionsDefense-related genes triggered by nematode infestation were detected in both P. pinaster and P. pinea transcriptomes utilizing 454 pyrosequencing technology. P. pinaster showed higher abundance of genes related to transcriptional regulation, terpenoid secondary metabolism (including some with nematicidal activity) and pathogen attack. P. pinea showed higher abundance of genes related to oxidative stress and higher levels of expression in general of stress responsive genes. This study provides essential information about the molecular defense mechanisms utilized by P. pinaster and P. pinea against PWN infestation and contributes to a better understanding of PWD.

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EuroPineDB: a high-coverage web database for maritime pine transcriptome

Cited by 53 publications

References 42 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)

Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinusphylogeny

Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening

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