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DiatOmicBase: a versatile gene-centered platform for mining functional omics data in diatom research.

Emilie Villar1,2, Nathanaël Zweig1, Pierre Vincens1

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Diatoms are key microalgae. DiatOmicBase centralizes omics data for Phaeodactylum tricornutum and Thalassiosira pseudonana, aiding research in evolution, cell biology, and biotechnology.

Keywords:
Phaeodactylum tricornutumRNA‐Seq datasetsThalassiosira pseudonanadiatomsecotype variantsgene modelsgenome browsergenome portalhistone marksnon‐coding RNAsprotein domains

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Area of Science:

  • Marine biology and genomics.
  • Microalgal research.
  • Bioinformatics and computational biology.

Background:

  • Diatoms are vital microalgae in aquatic ecosystems.
  • Phaeodactylum tricornutum and Thalassiosira pseudonana are established model organisms.
  • Extensive omics data exists but is fragmented and difficult to access.

Purpose of the Study:

  • To create DiatOmicBase, a centralized genome portal for diatom omics data.
  • To facilitate exploration of dispersed public datasets for Phaeodactylum tricornutum and Thalassiosira pseudonana.
  • To support new experimental designs in diatom research.

Main Methods:

  • Integrated gene annotations, transcriptomic profiles, and a genome browser.
  • Included data on ecotype variants, epigenetics, and RNA-Seq.
  • Developed a transcriptomic module for public and private RNA-Seq data analysis.

Main Results:

  • DiatOmicBase offers comprehensive omics resources for two key diatom species.
  • The portal enables advanced analyses like differential expression and co-expression network analysis.
  • Examples demonstrate strengthened molecular research capabilities for diatoms.

Conclusions:

  • DiatOmicBase significantly enhances accessibility and analysis of diatom omics data.
  • The portal empowers a broader research community to study diatoms.
  • Facilitates comparative and functional genomics research in diatoms.