ArticleScientific reports2018
Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 133 citations in OpenAlex.
- Mesoporous PU/PEDOT:PSS Electrodes Reveal Population-Level Stochastic Bioelectrical Dynamics in Marine Diatoms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- NPF2 is involved in intracellular pH regulation and ion balance in the diatom Phaeodactylum tricornutum.The New phytologist · 2026Article
- PHYCUT: Scalable Multiplex CRISPR/Cas9 Editing for Genome Engineering in the DiatomACS synthetic biology · 2026Article
- Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.Journal of phycology · 2025Article
- A new tool for engineering Phaeodactylum tricornutum: the METE promoter drives both high expression and BThe Plant journal : for cell and molecular biology · 2025Article
- A Comprehensive Review on Nutritional Traits, Extraction Methods, Oxidative Stability, Encapsulation Technologies, Food Applications and Health Benefits of Omega Fatty Acids.Food science & nutrition · 2025Review
- Multiblock Metabolomics Responses of the DiatomMarine drugs · 2025Article
- Prevalence and environmental abundance of the TSET complex in cosmopolitan algal groups.iScience · 2025Article
- Glutamate Methylation, a Novel Histone Mark in Diatoms: Mass Spectrometry Identification and Structural Characterization.Plant direct · 2025Article
- Characterization of the VOC Promoter That Is Active Under Low-Salinity Conditions in the DiatomMarine drugs · 2025Article
- Three reference genomes for freshwater diatom ecology and evolution.Journal of phycology · 2025Article
- DiatOmicBase: a versatile gene-centered platform for mining functional omics data in diatom research.The Plant journal : for cell and molecular biology · 2025Article
- Localization of heme biosynthesis in the diatomFrontiers in plant science · 2025Article
- Metabolic response to a heterologous poly-3-hydroxybutyrate (PHB) pathway in Phaeodactylum tricornutum.Applied microbiology and biotechnology · 2024Article
- No two clones are alike: characterization of heterologous subpopulations in a transgenic cell line of the model diatom Phaeodactylum tricornutum.Microbial cell factories · 2024Article
- Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid.The Plant cell · 2024Article
- Comparative RNA-Seq of TenMarine drugs · 2024Article
- Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatomISME communications · 2024Article
- Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering.ACS synthetic biology · 2023Article
- Alkaline Phosphatase PhoD Mutation Induces Fatty Acid and Long-Chain Polyunsaturated Fatty Acid (LC-PUFA)-Bound Phospholipid Production in the Model DiatomMarine drugs · 2023Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery of extensive alternative splicing in diatoms, including intron retention and exon skipping, which increase the diversity of transcripts generated in changing environments. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genes. We show that the P. tricornutum genome is enriched in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of transposable elements such as SINE, MITE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.
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