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

SUMMARY Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for explo...

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Published inThe Plant journal : for cell and molecular biology Vol. 121; no. 6; pp. e70061 - n/a
Main Authors Villar, Emilie, Zweig, Nathanaël, Vincens, Pierre, Cruz de Carvalho, Helena, Duchene, Carole, Liu, Shun, Monteil, Raphael, Dorrell, Richard G., Fabris, Michele, Vandepoele, Klaas, Bowler, Chris, Falciatore, Angela
Format Journal Article
LanguageEnglish
Published England Blackwell Publishing Ltd 01.03.2025
Wiley
John Wiley and Sons Inc
Subjects
Annotations
Aquatic environment
Availability
Biochemistry, Molecular Biology
bioinformatics
Biotechnology
cell biology
Data analysis
data collection
Data Mining
Databases, Genetic
Datasets
diatoms
Diatoms - genetics
DNA methylation
ecotype variants
ecotypes
evolution
Experiments
gene expression regulation
gene models
Gene sequencing
genes
Genetic resources
Genome - genetics
genome browser
genome portal
Genomes
Genomics
histone marks
Histones
Life Sciences
Marine microorganisms
methylation
microalgae
Microbiology and Parasitology
Molecular Sequence Annotation
Network analysis
non‐coding RNAs
Phaeodactylum tricornutum
physiology
Plankton
protein domains
Proteomics
Quantitative Methods
Resource
Ribonucleic acid
RNA
RNA‐Seq datasets
sequence analysis
species
Thalassiosira pseudonana
Transcriptome - genetics
Transcriptomics
Thalassiosira pseudonana
ecotype variants
diatoms
RNA‐Seq datasets
Phaeodactylum tricornutum
genome portal
genome browser
gene models
histone marks
protein domains
non‐coding RNAs
RNA-Seq datasets
noncoding RNAs
Online AccessGet full text

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Abstract SUMMARY Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome‐enabled datasets have been generated, based on RNA‐Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior‐art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non‐coding RNAs, and read densities from RNA‐Seq experiments. We developed a semi‐automatically updated transcriptomic module to explore both publicly available RNA‐Seq experiments and users' private datasets. Using gene‐level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co‐expression network analysis. Users can create heatmaps to visualize pre‐computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community. Significance Statement In recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsaturated fatty acids. Here, we present an interactive web‐based server that integrates public diatom omics (genomics, transcriptomics, epigenomics, proteomics, sequence variants) data to connect individual diatom genes to broader‐scale functional processes.
AbstractList Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users' private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize pre-computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community.
Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users' private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize pre-computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community.Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users' private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize pre-computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community.
Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome‐enabled datasets have been generated, based on RNA‐Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior‐art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non‐coding RNAs, and read densities from RNA‐Seq experiments. We developed a semi‐automatically updated transcriptomic module to explore both publicly available RNA‐Seq experiments and users' private datasets. Using gene‐level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co‐expression network analysis. Users can create heatmaps to visualize pre‐computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community.
Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome‐enabled datasets have been generated, based on RNA‐Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior‐art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non‐coding RNAs, and read densities from RNA‐Seq experiments. We developed a semi‐automatically updated transcriptomic module to explore both publicly available RNA‐Seq experiments and users' private datasets. Using gene‐level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co‐expression network analysis. Users can create heatmaps to visualize pre‐computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum , we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community. In recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsaturated fatty acids. Here, we present an interactive web‐based server that integrates public diatom omics (genomics, transcriptomics, epigenomics, proteomics, sequence variants) data to connect individual diatom genes to broader‐scale functional processes.
SUMMARYDiatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome‐enabled datasets have been generated, based on RNA‐Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior‐art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non‐coding RNAs, and read densities from RNA‐Seq experiments. We developed a semi‐automatically updated transcriptomic module to explore both publicly available RNA‐Seq experiments and users' private datasets. Using gene‐level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co‐expression network analysis. Users can create heatmaps to visualize pre‐computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community.
Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome‐enabled datasets have been generated, based on RNA‐Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior‐art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non‐coding RNAs, and read densities from RNA‐Seq experiments. We developed a semi‐automatically updated transcriptomic module to explore both publicly available RNA‐Seq experiments and users' private datasets. Using gene‐level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co‐expression network analysis. Users can create heatmaps to visualize pre‐computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum , we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community. In recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsaturated fatty acids. Here, we present an interactive web‐based server that integrates public diatom omics (genomics, transcriptomics, epigenomics, proteomics, sequence variants) data to connect individual diatom genes to broader‐scale functional processes.
SUMMARY Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome‐enabled datasets have been generated, based on RNA‐Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior‐art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non‐coding RNAs, and read densities from RNA‐Seq experiments. We developed a semi‐automatically updated transcriptomic module to explore both publicly available RNA‐Seq experiments and users' private datasets. Using gene‐level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co‐expression network analysis. Users can create heatmaps to visualize pre‐computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community. Significance Statement In recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsaturated fatty acids. Here, we present an interactive web‐based server that integrates public diatom omics (genomics, transcriptomics, epigenomics, proteomics, sequence variants) data to connect individual diatom genes to broader‐scale functional processes.
Author Vandepoele, Klaas
Cruz de Carvalho, Helena
Fabris, Michele
Vincens, Pierre
Zweig, Nathanaël
Bowler, Chris
Villar, Emilie
Monteil, Raphael
Dorrell, Richard G.
Liu, Shun
Falciatore, Angela
Duchene, Carole
AuthorAffiliation 3 Faculté des Sciences et Technologie Université Paris Est‐Créteil (UPEC) Créteil 94000 France
4 Institut de Biologie Physico‐Chimique, Laboratoire de Photobiologie et Physiologie des Plastes et des Microalgues, UMR7141 Centre National de la Recherche Scientifique (CNRS) Sorbonne Université Paris 75005 France
9 VIB Center for AI & Computational Biology, VIB Ghent Belgium
11 Present address: Guangzhou Marine Geological Survey Guangzhou China
1 Institut de Biologie de l'École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL Paris 75005 France
2 EV Consulting Marseille France
10 Present address: Department of Algal Development and Evolution Max Planck Institute for Biology Tuebingen 72076 Germany
5 CNRS, IBPS, CQSB‐ Department of Computational, Quantitative and Synthetic Biology, UMR7238 Sorbonne Université 4 place Jussieu Paris 75005 France
6 SDU Biotechnology, Department of Green Technology University of Southern Denmark Campusvej 55 Odense M 5230 Denmark
7 Depar
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– name: 4 Institut de Biologie Physico‐Chimique, Laboratoire de Photobiologie et Physiologie des Plastes et des Microalgues, UMR7141 Centre National de la Recherche Scientifique (CNRS) Sorbonne Université Paris 75005 France
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– name: 8 VIB‐UGent Center for Plant Systems Biology Technologiepark 71 Ghent 9052 Belgium
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  surname: Vincens
  fullname: Vincens, Pierre
  organization: Université PSL
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  surname: Cruz de Carvalho
  fullname: Cruz de Carvalho, Helena
  organization: Université Paris Est‐Créteil (UPEC)
– sequence: 5
  givenname: Carole
  surname: Duchene
  fullname: Duchene, Carole
  organization: Sorbonne Université
– sequence: 6
  givenname: Shun
  surname: Liu
  fullname: Liu, Shun
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  organization: Sorbonne Université
– sequence: 8
  givenname: Richard G.
  surname: Dorrell
  fullname: Dorrell, Richard G.
  organization: Sorbonne Université
– sequence: 9
  givenname: Michele
  orcidid: 0000-0003-2910-2089
  surname: Fabris
  fullname: Fabris, Michele
  organization: University of Southern Denmark
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  givenname: Klaas
  orcidid: 0000-0003-4790-2725
  surname: Vandepoele
  fullname: Vandepoele, Klaas
  organization: VIB Center for AI & Computational Biology, VIB
– sequence: 11
  givenname: Chris
  surname: Bowler
  fullname: Bowler, Chris
  email: cbowler@biologie.ens.fr
  organization: Université PSL
– sequence: 12
  givenname: Angela
  surname: Falciatore
  fullname: Falciatore, Angela
  email: angela.falciatore@ibpc.fr
  organization: Sorbonne Université
BackLink https://www.ncbi.nlm.nih.gov/pubmed/40089834$$D View this record in MEDLINE/PubMed
https://hal.science/hal-05027476$$DView record in HAL
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2025 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.
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Copyright_xml – notice: 2025 The Author(s). published by Society for Experimental Biology and John Wiley & Sons Ltd.
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– notice: 2025. This article is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Issue 6
Keywords Thalassiosira pseudonana
ecotype variants
diatoms
RNA‐Seq datasets
Phaeodactylum tricornutum
genome portal
genome browser
gene models
histone marks
protein domains
non‐coding RNAs
RNA-Seq datasets
noncoding RNAs
Language English
License Attribution-NonCommercial
2025 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.
Attribution - NonCommercial: http://creativecommons.org/licenses/by-nc
This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
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Snippet SUMMARY Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic...
Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom...
Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom...
SUMMARYDiatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources,...
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Aggregation Database
Index Database
Publisher
StartPage e70061
SubjectTerms Annotations
Aquatic environment
Availability
Biochemistry, Molecular Biology
bioinformatics
Biotechnology
cell biology
Data analysis
data collection
Data Mining
Databases, Genetic
Datasets
diatoms
Diatoms - genetics
DNA methylation
ecotype variants
ecotypes
evolution
Experiments
gene expression regulation
gene models
Gene sequencing
genes
Genetic resources
Genome - genetics
genome browser
genome portal
Genomes
Genomics
histone marks
Histones
Life Sciences
Marine microorganisms
methylation
microalgae
Microbiology and Parasitology
Molecular Sequence Annotation
Network analysis
non‐coding RNAs
Phaeodactylum tricornutum
physiology
Plankton
protein domains
Proteomics
Quantitative Methods
Resource
Ribonucleic acid
RNA
RNA‐Seq datasets
sequence analysis
species
Thalassiosira pseudonana
Transcriptome - genetics
Transcriptomics
Title DiatOmicBase: a versatile gene‐centered platform for mining functional omics data in diatom research
URI https://onlinelibrary.wiley.com/doi/abs/10.1111%2Ftpj.70061
https://www.ncbi.nlm.nih.gov/pubmed/40089834
https://www.proquest.com/docview/3182409719
https://www.proquest.com/docview/3177623768
https://www.proquest.com/docview/3200293901
https://hal.science/hal-05027476
https://pubmed.ncbi.nlm.nih.gov/PMC11910669
Volume 121
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