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

Noé Fernández-Pozo1, Javier Canales, Darío Guerrero-Fernández

  • 1Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Campus de Teatinos s/n, Universidad de Málaga, 29071 Málaga, Spain.

BMC Genomics
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Summary

EuroPineDB is a new database for maritime pine (Pinus pinaster) transcriptomes, offering a valuable resource for genetic research. It provides extensive gene annotations and sequence data for this important conifer species.

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Forestry science

Background:

  • Pinus pinaster (maritime pine) is a key species for forestry and ecological research.
  • Its large genome size complicates whole-genome sequencing.
  • Characterizing the expressed genome and storing annotations is crucial for research.

Purpose of the Study:

  • To create a comprehensive database of maritime pine expressed sequences and annotations.
  • To facilitate research on Pinus pinaster by providing accessible genomic data.

Main Methods:

  • High-throughput sequencing of non-normalized cDNA libraries from various maritime pine tissues.
  • Bioinformatic processing including pre-processing, assembly, and extensive annotation (GO, EC, KEGG, SNPs, SSRs, InterPro).
  • Development of a scalable, maintainable, and expandable database (EuroPineDB).

Main Results:

  • EuroPineDB contains 951,641 raw sequence reads, assembled into 55,322 UniGenes, covering 10.5x of the P. pinaster genome.
  • 32,919 UniGenes (59.5%) were annotated, identifying at least 18,466 genes.
  • The database includes unique features like microarray data and a visualization tool for sequence assemblies and SNPs.

Conclusions:

  • EuroPineDB is the largest sequence collection for a single pine species, providing integrated information for new discoveries.
  • It serves as an accessible resource for experimental work, including microarray hybridizations.
  • The database enhances understanding of the maritime pine transcriptome.