@article{nokey,

title = {Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems},

author = {France Denoeud and Olivier Godfroy and Corinne Cruaud and Svenja Heesch and Zofia Nehr and Nachida Tadrent and Arnaud Couloux and Loraine Brillet-Guéguen and Ludovic Delage and Dean Mckeown and Taizo Motomura and Duncan Sussfeld and Xiao Fan 0and Lisa Mazéas and Nicolas Terrapon and Josué Barrera-Redondo and Romy Petroll and Lauric Reynes and Seok-Wan Choi and Jihoon Jo and Kavitha Uthanumallian and Kenny Bogaert and Céline Duc and Pélagie Ratchinski and Agnieszka Lipinska and Benjamin Noel and Eleanor A Murphy and Martin Lohr 0and Ananya Khatei and Pauline Hamon-Giraud and Christophe Vieira and Komlan Avia and Svea Sanja Akerfors 0and Shingo Akita and Yacine Badis and Tristan Barbeyron and Arnaud Belcour and Wahiba Berrabah and Samuel Blanquart and Ahlem Bouguerba-Collin and Trevor Bringloe and Rose Ann Cattolico and Alexandre Cormier and Helena Cruz de Carvalho and Romain Dallet and Olivier De Clerck and Ahmed Debit and Erwan Denis and Christophe Destombe and Erica Dinatale and Simon Dittami and Elodie Drula and Sylvain Faugeron 0and Jeanne Got and Louis Graf and Agnès Groisillier and Marie-Laure Guillemin and Lars Harms and William John Hatchett and Bernard Henrissat and Galice Hoarau and Chloé Jollivet and Alexander Jueterbock and Ehsan Kayal and Andrew H Knoll and Kazuhiro Kogame and Arthur Le Bars and Catherine Leblanc and Line Le Gall and Ronja Ley 0and Xi Liu and Steven T LoDuca and Pascal Jean Lopez 0and Philippe Lopez and Eric Manirakiza and Karine Massau and Stéphane Mauger and Laetitia Mest and Gurvan Michel and Catia Monteiro and Chikako Nagasato and Delphine Nègre and Eric Pelletier and Naomi Phillips and Philippe Potin and Stefan A Rensing and Ellyn Rousselot and Sylvie Rousvoal and Declan Schroeder and Delphine Scornet and Anne Siegel and Leila Tirichine and Thierry Tonon and Klaus Valentin and Heroen Verbruggen and Florian Weinberger and Glen Wheeler and Hiroshi Kawai and Akira F Peters and Hwan Su Yoon and Cécile Hervé 0and Naihao Ye and Eric Bapteste and Myriam Valero and Gabriel V Markov and Erwan Corre and Susana M Coelho and Patrick Wincker and Jean-Marc Aury and J Mark Cock },

editor = {Cell Press},

url = {https://www.cell.com/cell/fulltext/S0092-8674(24)01272-8?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867424012728%3Fshowall%3Dtrue},

doi = {doi: 10.1016/j.cell.2024.10.049},

year  = {2024},

date = {2024-11-27},

journal = {Cell},

volume = {187},

issue = {24},

pages = {6943-6965},

abstract = {Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Genomic sequences and annotations of two Pseudomonas species isolated from marine and terrestrial habitats},

author = {Eric Manirakiza and Timothée Chaumier and Leïla Tirichine},

editor = {ASM Journals},

doi = { https://doi.org/10.1128/mra.00373-24},

year  = {2024},

date = {2024-08-27},

urldate = {2024-08-27},

journal = {Microbiol Resour Announc .},

pages = {e0037324},

abstract = {Here, we present the complete genome sequences and annotations of two species of the Pseudomonas genus isolated from marine and terrestrial environments. Both genomes and their annotations are available on BacBrowse (https://BacBrowse.univ-nantes.fr). This study will contribute to a better understanding of the diversity present within the Pseudomonas genus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {H3K27me3 and EZH Are Involved in the Control of the Heat-Stress-Elicited Morphological Changes in Diatoms},

author = {Mhammad Zarif and Ellyn Rousselot and Bruno Jesus and Leïla Tirichine and Céline Duc},

editor = {MDPI},

url = {https://www.mdpi.com/1422-0067/25/15/8373},

doi = {doi.org/10.3390/ijms25158373},

year  = {2024},

date = {2024-07-31},

journal = {Int. J. Mol. Sci.},

volume = {25},

issue = {15},

pages = {8373},

abstract = {Marine water temperatures are increasing due to anthropogenic climate change, constituting a major threat to marine ecosystems. Diatoms are major marine primary producers, and as such, they are subjected to marine heat waves and rising ocean temperatures. Additionally, under low tide, diatoms are regularly exposed to high temperatures. However, physiological and epigenetic responses to long-term exposure to heat stress remain largely unknown in the diatom Phaeodactylum tricornutum. In this study, we investigated changes in cell morphology, photosynthesis, and H3K27me3 abundance (an epigenetic mark consisting of the tri-methylation of lysine 27 on histone H3) after moderate and elevated heat stresses. Mutants impaired in PtEZH—the enzyme depositing H3K27me3—presented reduced growth and moderate changes in their PSII quantum capacities. We observed shape changes for the three morphotypes of P. tricornutum (fusiform, oval, and triradiate) in response to heat stress. These changes were found to be under the control of PtEZH. Additionally, both moderate and elevated heat stresses modulated the expression of genes encoding proteins involved in photosynthesis. Finally, heat stress elicited a reduction of genome-wide H3K27me3 levels in the various morphotypes. Hence, we provided direct evidence of epigenetic control of the H3K27me3 mark in the responses of Phaeodactylum tricornutum to heat stress.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Timothée2024,

title = {Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum},

author = {Chaumier Timothée and Feng Yang and Eric Manirakiza and Ouardia Ait-Mohamed and Yue Wu and Udita Chandola and Bruno Jesus and Gwenael Piganeau and Agnès Groisillier and Leila Tirichine},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833087/},

doi = {10.1093/ismeco/ycad008},

year  = {2024},

date = {2024-01-10},

urldate = {2024-01-10},

journal = {ISME Communications},

volume = {4},

issue = {1},

pages = {ycad008},

abstract = {Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lin2023,

title = {The dynamic duo: how DNA methylation and gene transcription help diatoms thrive in modern oceans},

author = {Xin Lin and Leïla Tirichine and Xu Zhang},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10400112/

 hal-04284583v1 },

doi = {10.1093/jxb/erad205},

issn = {00220957},

year  = {2023},

date = {2023-08-03},

urldate = {2023-08-03},

journal = {Journal of Experimental Botany},

volume = {74},

issue = {14},

pages = {3879–3882},

abstract = {DNA methylation is essential for maintaining genome stability, mediating gene expression, and aiding species in adapting to their environment. Wan et al. (2023) measured the changes in phenotypic traits of the model diatom Phaeodactylum tricornutum in response to a 2-year exposure to ocean acidification, warming, or both, and analysed the concomitant changes in DNA methylation and transcriptomic patterns. Their study revealed that DNA methylation and gene transcription work in concert to enable unicellular phytoplankton to adapt to dynamic environmental changes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wu2023b,

title = {Chromosome-Wide Distribution and Characterization of H3K36me3 and H3K27Ac in the Marine Model Diatom Phaeodactylum tricornutum},

author = {Yue Wu and Leila Tirichine },

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10421102/

hal-04284555v1 },

doi = { 10.3390/plants12152852},

year  = {2023},

date = {2023-08-02},

urldate = {2023-08-02},

journal = {Plants (Basel)},

volume = {12},

issue = {15},

pages = {2852},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hisanaga2023,

title = {The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes},

author = {Tetsuya Hisanaga and Facundo Romani and Shuangyang Wu and Teresa Kowar and Yue Wu and Ruth Lintermann and Arie Fridrich and Chung Hyun Cho and Timothée Chaumier and Bhagyshree Jamge and Sean A Montgomery and Elin Axelsson and Svetlana Akimcheva and Tom Dierschke and John L Bowman and Takayuki Fujiwara and Shunsuke Hirooka and Shin-Ya Miyagishima and Liam Dolan and Leila Tirichine and Daniel Schubert and Frédéric Berger},

url = {https://www.sciencedirect.com/science/article/pii/S0960982223011533?via%3Dihub

hal-04284522v1},

doi = {10.1016/j.cub.2023.08.073},

year  = {2023},

date = {2023-08-02},

urldate = {2023-08-02},

journal = {Current Biology},

volume = {33},

issue = {20},

pages = {4367-4380.e9},

abstract = {The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wu2023,

title = {PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum},

author = {Yue Wu and Timothée Chaumier and Eric Manirakiza and Alaguraj Veluchamy and Leila Tirichine},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10206091/

hal-04284562v1 },

doi = { 10.1038/s41598-023-35403-1},

issn = {2045-2322},

year  = {2023},

date = {2023-05-23},

urldate = {2023-05-23},

journal = {Scientific Reports },

volume = {13},

pages = {8320},

abstract = {Recent advances in DNA sequencing technologies particularly long-read sequencing, greatly improved genomes assembly. However, this has created discrepancies between published annotations and epigenome tracks, which have not been updated to keep pace with the new assemblies. 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 genes annotation and newly published transposable elements to map the epigenome landscape, namely DNA methylation and post-translational modifications of histones. This provides the community with PhaeoEpiView, a browser that allows the visualization of epigenome data and transcripts on an updated and contiguous reference genome, to better understand the biological significance of the mapped data. We updated previously published histone marks with a more accurate peak calling using mono instead of poly(clonal) antibodies and deeper sequencing. PhaeoEpiView (https://PhaeoEpiView.univ-nantes.fr) will be continuously updated with the newly published epigenomic data, making it the largest and richest epigenome browser of any stramenopile. In the upcoming era of molecular environmental studies, where epigenetics plays a significant role, we anticipate that PhaeoEpiView will become a widely used tool.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hoguin2023,

title = {The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases},

author = {Antoine Hoguin and Feng Yang and Agnès Groisillier and Chris Bowler and Auguste Genovesio and Ouardia Ait-Mohamed and Fabio Rocha Jimenez Vieira and Leila Tirichine},

editor = {Nature},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9998398/

hal-04024906v1 },

doi = {10.1038/s42003-023-04629-0 },

issn = {23993642},

year  = {2023},

date = {2023-03-09},

urldate = {2023-03-09},

journal = {Communications Biology},

volume = {6},

number = {1},

issue = {1},

pages = {253},

abstract = {Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Editorial: Algal symbiotic relationships in freshwater and marine environments},

author = {Leila Tirichine and Gwenael Piganeau},

url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1155759/full

hal-04284580v1 },

doi = {doi: 10.3389/fpls.2023.1155759},

year  = {2023},

date = {2023-02-20},

urldate = {2023-02-20},

journal = {Front. Plant Sci.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches. },

author = {Zhanru Shao and Osei Ampomah andFabio Vieira and Richard Dorrell and Shaoxuan Li and Leila Tirichine and Vincent Bulone and Delin Duan and Chris Bowler},

doi = {doi: 10.1128/msystems.01131-22},

year  = {2023},

date = {2023-02-15},

urldate = {2023-02-15},

journal = {mSystems},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chandola2022.08.25.505241,

title = {Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic nitrogen fixing interactions between non-cyanobacterial diazotrophs and microalgae},

author = {Udita Chandola and Camille Trottier and Marinna Gaudin and Erik Manirakiza and Samuel Menicot and Isabelle Louvet and Thomas Lacour and Timothée Chaumier and Atsuko Tanaka and Samuel Chaffron and Leila Tirichine},

url = {https://www.biorxiv.org/content/early/2022/08/25/2022.08.25.505241},

doi = {10.1101/2022.08.25.505241},

year  = {2022},

date = {2022-08-25},

urldate = {2022-08-25},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Non-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance and raising fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented finding in the widely used model diatom Phaeodactylum triconrnutum (Pt) of NCDs sustaining diatom cells in the absence of bioavailable nitrogen. We identified PtNCDs using metagenomics sequencing and detected nitrogenase gene in silico and/or by PCR. We demonstrated nitrogen fixation in PtNCDs and their close genetic affiliation with NCDs from the environment. We showed the wide occurrence of this type of symbiosis with the isolation of NCDs from other microalgae and their identification in the environment and in co-occurrence with photosynthetic microalgae. Overall, this study provides evidence for a previously overlooked symbiosis using a multidisciplinary model-based approach which will consequently help understand the different players driving global marine nitrogen fixation.Competing Interest StatementThe authors have declared no competing interest.},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Wu2022.07.29.502047,

title = {PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum},

author = {Yue Wu and Chaumier Timothée and Eric Manirakiza and Alaguraj Veluchamy and Leila Tirichine},

url = {https://www.biorxiv.org/content/early/2022/08/01/2022.07.29.502047},

doi = {10.1101/2022.07.29.502047},

year  = {2022},

date = {2022-08-01},

urldate = {2022-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

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.frCompeting Interest StatementThe authors have declared no competing interest.},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{nokey,

title = {An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus},

author = {Simon Bourdareau and Olivier Godfroy and Josselin Gueno and Delphine Scornet and Susana M. Coelho and Leila Tirichine and Jean Mark Cock},

url = {hal-03658367v1 },

doi = {doi: 10.3390/mps5030036},

year  = {2022},

date = {2022-04-25},

urldate = {2022-04-25},

journal = {Methods Protoc. },

volume = {36},

issue = {3},

pages = {36},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35253891,

title = {Chromatin landscape associated with sexual differentiation in a UV sex determination system},

author = {Josselin Gueno and Michael Borg and Simon Bourdareau and Guillaume Cossard and Olivier Godfroy and Agnieszka Lipinska and Leila Tirichine and J Mark Cock and Susana M Coelho},

doi = {doi: 10.1093/nar/gkac145},

issn = {1362-4962},

year  = {2022},

date = {2022-03-01},

urldate = {2022-03-01},

journal = {Nucleic Acids Res},

volume = {50},

issue = {6},

pages = {3307-3322},

abstract = {In many eukaryotes, such as dioicous mosses and many algae, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. In these species, the male and female developmental programs are initiated by the presence of the U- or V-specific regions of the sex chromosomes but, as in XY and ZW systems, sexual differentiation is largely driven by autosomal sex-biased gene expression. The mechanisms underlying the regulation of sex-biased expression of genes during sexual differentiation remain elusive. Here, we investigated the extent and nature of epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, a model UV system. Six histone modifications were quantified in near-isogenic lines, leading to the identification of 16 chromatin signatures across the genome. Chromatin signatures correlated with levels of gene expression and histone PTMs changes in males versus females occurred preferentially at genes involved in sex-specific pathways. Despite the absence of chromosome scale dosage compensation and the fact that UV sex chromosomes recombine across most of their length, the chromatin landscape of these chromosomes was remarkably different to that of autosomes. Hotspots of evolutionary young genes in the pseudoautosomal regions appear to drive the exceptional chromatin features of UV sex chromosomes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bourdareau2021,

title = {Histone modifications during the life cycle of the brown alga Ectocarpus},

author = {Simon Bourdareau and Leila Tirichine and Bérangère Lombard and Damarys Loew and Delphine Scornet and Yue Wu and Susana M Coelho and Mark J Cock},

url = {https://pubmed.ncbi.nlm.nih.gov/33397407/},

doi = {10.1186/s13059-020-02216-8},

issn = {1474760X},

year  = {2021},

date = {2021-12-01},

journal = {Genome Biology},

volume = {22},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. Results: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. Conclusions: The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hoguin2021,

title = {Genome ‑ wide analysis of allele ‑ specific expression of genes in the model diatom Phaeodactylum tricornutum},

author = {Antoine Hoguin and Achal Rastogi and Chris Bowler and Leila Tirichine},

url = {https://doi.org/10.1038/s41598-021-82529-1},

doi = {10.1038/s41598-021-82529-1},

issn = {2045-2322},

year  = {2021},

date = {2021-01-01},

journal = {Scientific Reports},

pages = {1--10},

publisher = {Nature Publishing Group UK},

abstract = {Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hoguin2021.06.11.447926,

title = {Evolutionary analysis of DNA methyltransferases in microeukaryotes: Insights from the model diatom Phaeodactylum tricornutum},

author = {Antoine Hoguin and Ouardia Ait Mohamed and Chris Bowler and Auguste Genovesio and Fabio Rocha Jimenez Vieira and Leila Tirichine},

url = {https://www.biorxiv.org/content/early/2021/06/11/2021.06.11.447926},

doi = {10.1101/2021.06.11.447926},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Cytosine DNA methylation is an important epigenetic mark in eukaryotes that is involved in the transcriptional control of mainly transposable elements in mammals, plants, and fungi. Eukaryotes encode a diverse set of DNA methyltransferases that were iteratively acquired and lost during evolution. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes that include the main phytoplankton classes such as diatoms and dinoflagellates. However, little is known about the diversity of DNA methyltransferases and their role in the deposition and maintenance of DNA methylation in microalgae. We performed a phylogenetic analysis of DNA methyltransferase families found in marine microeukaryotes and show that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes family revisiting previously established phylogenies. Furthermore, we reveal a novel group of DNMTs with three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrate that the loss of the DNMT5 gene correlates with a global depletion of DNA methylation and overexpression of transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a pioneering view of the structure and function of a DNMT family in the SAR supergroup.Competing Interest StatementThe authors have declared no competing interest.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhao2020b,

title = {Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum},

author = {Xue Zhao and Achal Rastogi and Anne Flore {Deton Cabanillas} and Ouardia {Ait Mohamed} and Catherine Cantrel and Berangère Lombard and Omer Murik and Auguste Genovesio and Chris Bowler and Daniel Bouyer and Damarys Loew and Xin Lin and Alaguraj Veluchamy and Fabio Rocha Jimenez Vieira and Leila Tirichine},

url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17129},

doi = {10.1111/nph.17129},

issn = {0028-646X},

year  = {2021},

date = {2021-01-01},

urldate = {2020-12-01},

journal = {New Phytologist},

pages = {nph.17129},

publisher = {Blackwell Publishing Ltd},

abstract = {In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{armbrecht2021paleo,

title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics},

author = {Linda Armbrecht and Raphael Eisenhofer and José Utge and Elizabeth C Sibert and Fabio Rocha and Ryan Ward and Juan José Pierella Karlusich and Leila Tirichine and Richard Norris and Mindi Summers and Chris Bowler},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {ISME Communications},

volume = {1},

number = {1},

pages = {1--10},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ait-Mohamed2020,

title = {PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum},

author = {Ouardia Ait-Mohamed and Anna M G {Novák Vanclová} and Nathalie Joli and Yue Liang and Xue Zhao and Auguste Genovesio and Leila Tirichine and Chris Bowler and Richard G Dorrell},

url = {https://pubmed.ncbi.nlm.nih.gov/33178253/},

doi = {10.3389/fpls.2020.590949},

issn = {1664462X},

year  = {2020},

date = {2020-10-01},

journal = {Frontiers in Plant Science},

volume = {11},

publisher = {Frontiers Media S.A.},

abstract = {Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sato2020,

title = {Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal},

author = {Shinya Sato and Deepak Nanjappa and Richard G Dorrell and Fabio Rocha Jimenez Vieira and Elena Kazamia and Leila Tirichine and Alaguraj Veluchamy and Roland Heilig and Jean Marc Aury and Olivier Jaillon and Patrick Wincker and Zoltan Fussy and Miroslav Obornik and Sergio A Mu{ñ}oz-Gómez and David G Mann and Chris Bowler and Adriana Zingone},

doi = {10.1038/s41598-020-65941-x},

issn = {20452322},

year  = {2020},

date = {2020-01-01},

journal = {Scientific Reports},

volume = {10},

number = {1},

pages = {1--12},

abstract = {Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fan2020,

title = {Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants},

author = {Xiao Fan and Wentao Han and Linhong Teng and Peng Jiang and Xiaowen Zhang and Dong Xu and Chang Li and Matteo Pellegrini and Chunhui Wu and Yitao Wang and Michelle Joyce Slade Kaczurowski and Xin Lin and Leila Tirichine and Thomas Mock and Naihao Ye},

doi = {10.1111/nph.16125},

issn = {14698137},

year  = {2020},

date = {2020-01-01},

journal = {New Phytologist},

volume = {225},

number = {1},

pages = {234--249},

abstract = {Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fmars.2020.00189,

title = {Probing the Diversity of Polycomb and Trithorax Proteins in Cultured and Environmentally Sampled Microalgae},

author = {Xue Zhao and Anne Flore {Deton Cabanillas} and Alaguraj Veluchamy and Chris Bowler and Fabio Rocha Jimenez Vieira and Leila Tirichine},

url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00189},

doi = {10.3389/fmars.2020.00189},

issn = {2296-7745},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Marine Science},

volume = {7},

pages = {189},

abstract = {Polycomb (PcG) and Trithorax (TrxG) complexes are two evolutionarily conserved epigenetic regulatory components that act antagonistically to regulate the expression of genes involved in cell differentiation and development in multicellular organisms. The absence of PcG in both yeast models Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that polycomb proteins might have evolved together with the emergence of multicellular organisms. However, high throughput sequencing of several microalgal genomes and transcriptomes reveals an unprecedented abundance and diversity of genes encoding the components of these complexes. We report here the diversity of genes encoding PcG and TrxG proteins in microalgae from the Marine Microbial Eukaryote Transcriptome Sequencing Project database (MMETSP) and detected at broad scale in Tara Oceans genomics datasets using a highly sensitive method called eDAF (enhanced Domain Architecture Filtering). Further, we explored the correlation between environmental factors measured during the Tara Oceans expedition and transcript levels of PcG and TrxG components. PcG and TrxG are responsible for the deposition of a number of histone marks among which a TrxG associated mark, H3K4me3 which we profiled genome wide in the model diatom Phaeodactylum tricornutum to understand its role in microalgae and revisited the previously published histone code and co-occurrence with other histone marks including the antagonizing Polycomb deposited mark H3K27me3.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Murik2019,

title = {Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom},

author = {Omer Murik and Leila Tirichine and Judit Prihoda and Yann Thomas and Wagner L Ara{ú}jo and Andrew E Allen and Alisdair R Fernie and Chris Bowler},

doi = {10.1111/nph.15479},

issn = {14698137},

year  = {2019},

date = {2019-01-01},

journal = {New Phytologist},

volume = {221},

number = {3},

pages = {1303--1316},

abstract = {Diatom dominance in contemporary aquatic environments indicates that they have developed unique and effective mechanisms to cope with the rapid and considerable fluctuations that characterize these environments. In view of their evolutionary history from a secondary endosymbiosis, inter-organellar regulation of biochemical activities may be of particular relevance. Diatom mitochondrial alternative oxidase (AOX) is believed to play a significant role in supplying chloroplasts with ATP produced in the mitochondria. Using the model diatom Phaeodactylum tricornutum we generated AOX knockdown lines, and followed sensitivity to stressors, photosynthesis and transcriptome and metabolome profiles of wild-type and knockdown lines. We show here that expression of the AOX gene is upregulated by various stresses including H 2 O 2 , heat, high light illumination, and iron or nitrogen limitation. AOX knockdown results in hypersensitivity to stress. Knockdown lines also show significantly reduced photosynthetic rates and their chloroplasts are more oxidized. Comparisons of transcriptome and metabolome profiles suggest a strong impact of AOX activity on gene expression, which is carried through to the level of the metabolome. Our data provide evidence for the involvement of mitochondrial AOX in processes central to the cell biology of diatoms, revealing that cross-talk between mitochondria and chloroplasts is crucial for maintaining sensitivity to changing environments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fmicb.2018.03342,

title = {A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum},

author = {Ruiping Huang and Jiancheng Ding and Kunshan Gao and Maria Helena de Carvalho and Leila Tirichine and Chris Bowler and Xin Lin},

url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03342},

doi = {10.3389/fmicb.2018.03342},

issn = {1664-302X},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Microbiology},

volume = {9},

pages = {3342},

abstract = {Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shao2019,

title = {Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin-based metabolic processes in diatoms},

author = {Zhanru Shao and Yann Thomas and Lea Hembach and Xiaohui Xing and Delin Duan and Bruno M Moerschbacher and Vincent Bulone and Leila Tirichine and Chris Bowler},

doi = {10.1111/nph.15510},

issn = {14698137},

year  = {2019},

date = {2019-01-01},

journal = {New Phytologist},

volume = {221},

number = {4},

pages = {1890--1905},

abstract = {Chitin is generally considered to be present in centric diatoms but not in pennate species. Many aspects of chitin biosynthetic pathways have not been explored in diatoms. We retrieved chitin metabolic genes from pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom genomes. Chitin deacetylase (CDA) genes from each genome (PtCDA and TpCDA) were overexpressed in P. tricornutum. We performed comparative analysis of their sequence structure, phylogeny, transcriptional profiles, localization and enzymatic activities. The chitin relevant proteins show complex subcellular compartmentation. PtCDA was likely acquired by horizontal gene transfer from prokaryotes, whereas TpCDA has closer relationships with sequences in Opisthokonta. Using transgenic P. tricornutum lines expressing CDA-green fluorescent protein (GFP) fusion proteins, PtCDA predominantly localizes to Golgi apparatus whereas TpCDA localizes to endoplasmic reticulum/chloroplast endoplasmic reticulum membrane. CDA-GFP overexpression upregulated the transcription of chitin synthases and potentially enhanced the ability of chitin synthesis. Although both CDAs are active on GlcNAc 5 , TpCDA is more active on the highly acetylated chitin polymer DA60. We have addressed the ambiguous characters of CDAs from P. tricornutum and T. pseudonana. Differences in localization, evolution, expression and activities provide explanations underlying the greater potential of centric diatoms for chitin biosynthesis. This study paves the way for in vitro applications of novel CDAs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Caputi2019,

title = {Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems},

author = {L Caputi and Q Carradec and D Eveillard and A Kirilovsky and E Pelletier and J J Pierella Karlusich and F Rocha Jimenez Vieira and E Villar and S Chaffron and S Malviya and E Scalco and S G Acinas and A Alberti and J -M Aury and A -S Benoiston and A Bertrand and T Biard and L Bittner and M Boccara and J R Brum and C Brunet and G Busseni and A Carratalà and H Claustre and L P Coelho and S Colin and S Daniello and C Da Silva and M Del Core and H Doré and S Gasparini and F Kokoszka and J -L Jamet and C Lejeusne and C Lepoivre and M Lescot and G Lima-Mendez and F Lombard and J Lukeš and N Maillet and M -A Madoui and E Martinez and M G Mazzocchi and M B Néou and J Paz-Yepes and J Poulain and S Ramondenc and J -B Romagnan and S Roux and D Salvagio Manta and R Sanges and S Speich and M Sprovieri and S Sunagawa and V Taillandier and A Tanaka and Leila Tirichine and Camille Trottier and J Uitz and A Veluchamy and J Veselá and F Vincent and S Yau and S Kandels-Lewis and S Searson and C Dimier and M Picheral and P Bork and E Boss and C de Vargas and M J Follows and N Grimsley and L Guidi and P Hingamp and E Karsenti and P Sordino and L Stemmann and M B Sullivan and A Tagliabue and A Zingone and L Garczarek and F DÓrtenzio and P Testor and F Not and M R DÁlcalà and P Wincker and C Bowler and D Iudicone},

doi = {10.1029/2018GB006022},

issn = {19449224},

year  = {2019},

date = {2019-01-01},

journal = {Global Biogeochemical Cycles},

volume = {33},

number = {3},

abstract = {Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}