ArticleBMC genomics2011
EuroPineDB: a high-coverage web database for maritime pine transcriptome.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Stone Pine (Genes · 2024Review
- Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches.Plant molecular biology · 2021Article
- TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms.BMC bioinformatics · 2018Article
- Transcriptome sequencing of Pinus kesiya var. langbianensis and comparative analysis in the Pinus phylogeny.BMC genomics · 2018Article
- Article
- Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants.Nature chemical biology · 2017Article
- Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome.BMC genomics · 2015Article
- ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome.Frontiers in plant science · 2015Article
- Article
- Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.Genetics · 2014Article
- Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource.BMC genomics · 2013Article
- Transcriptomic analysis highlights epigenetic and transcriptional regulation during zygotic embryo development of Pinus pinaster.BMC plant biology · 2013Article
- Open access to tree genomes: the path to a better forest.Genome biology · 2013Article
- Article
- Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny.BMC genomics · 2013Article
- A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.BMC genomics · 2013Article
- Towards decoding the conifer giga-genome.Plant molecular biology · 2012Review
- Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening.BMC genomics · 2012Article
- Why assembling plant genome sequences is so challenging.Biology · 2012Article
- Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis).Plant cell reports · 2012Article
Corrections and comments
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. DESCRIPTION: EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided.
conclusionsThe EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deeper knowledge on the maritime pine transcriptome.
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