PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum

Abstract

Motivation: Recent advances in DNA sequencing technologies in particular of long reads type greatly improved genomes assembly leading to discrepancies between both published annotations and epigenome tracks which did not keep pace with new assemblies. This comprises the availability of accurate resources which penalizes the progress in research. Results: Here, we used the latest improved telomere to telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genome annotation including genes and transposable elements to map the epigenome landscape, namely DNA methylation and post translational modifications of histones providing the community with PhaeoEpiView, a browser that allows the visualization of epigenome data as well as transcripts on an updated reference genome to better understand the biological significance of the mapped data on contiguous genome rather than a fragmented one. We updated previously published histone marks with a more accurate mapping using monoclonal antibodies instead of polyclonal and deeper sequencing. PhaeoEpiView will be continuously updated with the newly published epigenomic data making it the largest and richest epigenome browser of any stramenopile. We expect that PhaeoEpiView will be a standard tool for the coming era of molecular environmental studies where epigenetics holds a place of choice. Availability: PhaeoEpiView is available at: https://PhaeoEpiView.univ-nantes.fr .

Genome wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatomPhaeodactylum tricornutum

“…By incorporating recently sampled accessions, we have further confirmed a persistent long-term balancing selection and the high level of heterozygosity in P. tricornutum through population genetic analyses, suggesting that this characteristic arises from a heterozygous advantage. Our findings establish a crucial groundwork for future research that utilizes sequencing data from various P. tricornutum accessions which we made available via PhaeoEpiView platform (https://PhaeoEpiView.univ-nantes.fr) [10] for easy and comprehensive use. This will enhance our understanding of diatom biology, foster advancements in biotechnology applications, and optimize trait selection.…”

“…tricornutum, a marine pennate diatom is commonly found in coastal waters, including tidal areas, estuaries, rock pools and shallow waters exposing the species to important fluctuations in light intensity and salinity. The diatom is a well-established model with a genome that has been fully assembled and well annotated, along with an expanding molecular toolbox using the reference strain Pt1 8.6 [6][7][8][9][10]. Genome wide sequencing of ten accessions of P. tricornutum (Pt1 to Pt10) using Illumina, identified throughout the genome diverse variations, including single nucleotide and insertion deletion polymorphisms (SNPs, INDEls) and copy number variations [11].…”

“…Furthermore, our study identified novel transcripts among which various non-coding RNA species and provides insights into the regulation of genes mediated by genetic and transcript diversity. Our study offers easy and valuable access to these novel genetic resources, particularly focusing on a model species, through the PhaeoEpiView platform (https://PhaeoEpiView.univ-nantes.fr) [10]. This unprecedented accessibility provides a multitude of opportunities for exploring diverse ecological functions by leveraging the genetic diversity of this model organism, thereby expanding our understanding of the biology and ecology of microalgae.…”

Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates

“…hPTMs are used in a variety of ways to regulate the expression of genes 15,16 . PTMs have generally conserved genomic distributions across eukaryotes, e.g., Histone H3 lysine 4 tri-methylation and lysine 27 acetylation (H3K4me3 and H3K27ac) are found at active genomic regions like promoters or active enhancers in diverse organisms [17][18][19][20][21][22] . Other modifications like H3K4me1 have varying distributions.…”

Chromosome-Wide Distribution and Characterization of H3K36me3 and H3K27Ac in the Marine Model Diatom Phaeodactylum tricornutum

“…Additionally, we sought to broaden our understanding of the H3K36me3 diversity in diatoms by analyzing the occurrence and evolution of H3K36me3-specific methyltransferase from other species using the Marine Microbial Eukaryote Transcriptome Sequencing Project database (MMETSP) [42]. Furthermore, we undertook a re-examination of the epigenetic code that was previously established in P. tricornutum [19,43,44] and analyzed the mapping profiles of H3K27ac and H3K36me3 in relation to other histone marks. Our aim was to determine their co-occurrence pattern and effect on transcriptional regulation of genes and transposable elements in this unicellular organism.…”