Publications by authors named "Erwan Corre"

86 Publications

High-throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally.

Ecol Evol 2021 May 23;11(10):5533-5546. Epub 2021 Mar 23.

Sorbonne université CNRS UMR 7144 Station Biologique de Roscoff Roscoff France.

High-throughput sequencing of amplicons (HTSA) has been proposed as an effective approach to evaluate taxonomic and genetic diversity at the same time. However, there are still uncertainties as to how the results produced by different bioinformatics treatments impact the conclusions drawn on biodiversity and population genetics indices.We evaluated the ability of six bioinformatics pipelines to recover taxonomic and genetic diversity from HTSA data obtained from controlled assemblages. To that end, 20 assemblages were produced using 354 colonies of spp., sampled in the wild in ten marinas around Brittany (France). We used DNA extracted from preservative ethanol (ebDNA) after various time of storage (3, 6, and 12 months), and from a bulk of preserved specimens (bulkDNA). DNA was amplified with primers designed for targeting this ascidian genus. Results obtained from HTSA data were compared with Sanger sequencing on individual zooids (i.e., individual barcoding).Species identification and relative abundance determined with HTSA data from either ebDNA or bulkDNA were similar to those obtained with traditional individual barcoding. However, after 12 months of storage, the correlation between HTSA and individual-based data was lower than after shorter durations. The six bioinformatics pipelines were able to depict accurately the genetic diversity using standard population genetics indices (H and F), despite producing false positives and missing rare haplotypes. However, they did not perform equally and dada2 was the only pipeline able to retrieve all expected haplotypes.This study showed that ebDNA is a nondestructive alternative for both species identification and haplotype recovery, providing storage does not last more than 6 months before DNA extraction. Choosing the bioinformatics pipeline is a matter of compromise, aiming to retrieve all true haplotypes while avoiding false positives. We here recommend to process HTSA data using dada2, including a chimera-removal step. Even if the possibility to use multiplexed primer sets deserves further investigation to expand the taxonomic coverage in future similar studies, we showed that primers targeting a particular genus allowed to reliably analyze this genus within a complex community.
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http://dx.doi.org/10.1002/ece3.7453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131761PMC
May 2021

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines.

PeerJ 2021 6;9:e11344. Epub 2021 May 6.

UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France.

Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
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http://dx.doi.org/10.7717/peerj.11344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106915PMC
May 2021

Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams.

Sci Rep 2021 Mar 12;11(1):5876. Epub 2021 Mar 12.

Normandie Univ, UNICAEN, UNIROUEN, ABTE-EA4651, ToxEMAC, Cancer Centre François Baclesse, 14000, Caen, France.

Proton therapy allows to avoid excess radiation dose on normal tissues. However, there are some limitations. Indeed, passive delivery of proton beams results in an increase in the lateral dose upstream of the tumor and active scanning leads to strong differences in dose delivery. This study aims to assess possible differences in the transcriptomic response of skin in C57BL/6 mice after TBI irradiation by active or passive proton beams at the dose of 6 Gy compared to unirradiated mice. In that purpose, total RNA was extracted from skin samples 3 months after irradiation and RNA-Seq was performed. Results showed that active and passive delivery lead to completely different transcription profiles. Indeed, 140 and 167 genes were differentially expressed after active and passive scanning compared to unirradiated, respectively, with only one common gene corresponding to RIKEN cDNA 9930021J03. Moreover, protein-protein interactions performed by STRING analysis showed that 31 and 25 genes are functionally related after active and passive delivery, respectively, with no common gene between both types of proton delivery. Analysis showed that active scanning led to the regulation of genes involved in skin development which was not the case with passive delivery. Moreover, 14 ncRNA were differentially regulated after active scanning against none for passive delivery. Active scanning led to 49 potential mRNA-ncRNA pairs with one ncRNA mainly involved, Gm44383 which is a miRNA. The 43 genes potentially regulated by the miRNA Gm44393 confirmed an important role of active scanning on skin keratin pathway. Our results demonstrated that there are differences in skin gene expression still 3 months after proton irradiation versus unirradiated mouse skin. And strong differences do exist in late skin gene expression between scattered or scanned proton beams. Further investigations are strongly needed to understand this discrepancy and to improve treatments by proton therapy.
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http://dx.doi.org/10.1038/s41598-021-85394-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7955113PMC
March 2021

High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox.

Elife 2021 Feb 18;10. Epub 2021 Feb 18.

Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.

In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox () and the aardwolf (), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status ( and ) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
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http://dx.doi.org/10.7554/eLife.63167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7963486PMC
February 2021

Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Infection.

Front Microbiol 2020 18;11:600823. Epub 2020 Dec 18.

UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France.

Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate (Dinophyceae) can be infected by the microeukaryotic parasitoids spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by . We report here a multi-approach monitoring study of organelles over a complete infection cycle by nucleus-targeting sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite sp. A120 and improve its fitness during the intracellular infective stage.
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http://dx.doi.org/10.3389/fmicb.2020.600823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793755PMC
December 2020

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.

BMC Biol 2021 01 6;19(1). Epub 2021 Jan 6.

Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.

Background: Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization.

Results: We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions.

Conclusion: These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
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http://dx.doi.org/10.1186/s12915-020-00927-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7789003PMC
January 2021

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.

Nucleic Acids Res 2021 01;49(D1):D667-D676

Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.
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http://dx.doi.org/10.1093/nar/gkaa958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779031PMC
January 2021

Diversity of Light Sensing Molecules and Their Expression During the Embryogenesis of the Cuttlefish ().

Front Physiol 2020 29;11:521989. Epub 2020 Sep 29.

Laboratoire Biologie des Organismes et Ecosystèmes Aquatiques, Muséum National d'Histoire Naturelle, Sorbonne Université, Centre National de la Recherche Française (FRE2030), Université de Caen Normandie, Institut de Recherche pour le Développement (IRD 207), Université des Antilles, Paris, France.

Eyes morphologies may differ but those differences are not reflected at the molecular level. Indeed, the ability to perceive light is thought to come from the same conserved gene families: opsins and cryptochromes. Even though cuttlefish (Cephalopoda) are known for their visually guided behaviors, there is a lack of data about the different opsins and cryptochromes orthologs represented in the genome and their expressions. Here we studied the evolutionary history of opsins, cryptochromes but also visual arrestins in molluscs with an emphasis on cephalopods. We identified 6 opsins, 2 cryptochromes and 1 visual arrestin in and we showed these families undergo several duplication events in Mollusca: one duplication in the arrestin family and two in the opsin family. In cuttlefish, we studied the temporal expression of these genes in the eyes of embryos from stage 23 to hatching and their expression in two extraocular tissues, skin and central nervous system (CNS = brain + optic lobes). We showed in embryos that some of these genes (Sof_CRY, Sof_reti-1, Sof_reti-2, Sof_r-opsin1 and Sof_v-arr) are expressed in the eyes and not in the skin or CNS. By looking at a juvenile and an adult , it seems that some of these genes (Sof_r-opsin1 and Sof_reti1) are used for light detection in these extraocular tissues but that they set-up later in development than in the eyes. We also showed that their expression (except for Sof_CRY) undergoes an increase in the eyes from stage 25 to 28 thus confirming their role in the ability of the cuttlefish embryos to perceive light through the egg capsule. This study raises the question of the role of Sof_CRY in the developing eyes in cuttlefish embryos and the role and localization of xenopsins and r-opsin2. Consequently, the diversity of molecular actors involved in light detection both in the eyes and extraocular tissues is higher than previously known. These results open the way for studying new molecules such as those of the signal transduction cascade.
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http://dx.doi.org/10.3389/fphys.2020.521989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7553075PMC
September 2020

Deciphering the Infectious Process of in Lupin through Transcriptomic and Proteomic Analysis.

Microorganisms 2020 Oct 21;8(10). Epub 2020 Oct 21.

Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France.

The fungal phytopathogen is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of spp. during the onset of plant infection.
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http://dx.doi.org/10.3390/microorganisms8101621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589765PMC
October 2020

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.

Front Microbiol 2020 15;11:567431. Epub 2020 Sep 15.

Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France.

Marine picocyanobacteria of the genera and are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new , we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters ( clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.
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http://dx.doi.org/10.3389/fmicb.2020.567431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522525PMC
September 2020

Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed.

BMC Genomics 2020 Oct 2;21(1):687. Epub 2020 Oct 2.

ABiMS Bioinformatics Facility, CNRS, Sorbonne Université, FR2424, Station Biologique, 29680, Roscoff, France.

Background: Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from different species and comparison is challenging. The goal of this study was develop a relevant strategy for transcriptome analysis and comparison between different species.

Results: Transcriptomes were first assembled with a reference-based approach. Important mapping biases were observed when heterologous mapping were conducted on common duck reference genome, suggesting that this reference-based strategy was not suited to compare the four different genetic types. De novo transcriptome assemblies were then performed using Trinity and Oases. Assemblies of transcriptomes were not relevant when more than a single genetic type was considered. Finally, single genetic type transcriptomes were assembled with DRAP in a mega-transcriptome. No bias was observed when reads from the different genetic types were mapped on this mega-transcriptome and differences in gene expression between the four genetic types could be identified.

Conclusions: Analyses using both reference-based and de novo transcriptome assemblies point out a good performance of the de novo approach for the analysis of gene expression in different species. It also allowed the identification of differences in responses to overfeeding between Pekin and Muscovy ducks and hinny and mule hybrids.
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http://dx.doi.org/10.1186/s12864-020-07099-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531116PMC
October 2020

Response of Downy Oak Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics.

Plants (Basel) 2020 Sep 4;9(9). Epub 2020 Sep 4.

CNRS, Aix-Marseille University, Avignon University, IRD, IMBE, 13331 Marseille, France.

Global change scenarios in the Mediterranean basin predict a precipitation reduction within the coming hundred years. Therefore, increased drought will affect forests both in terms of adaptive ecology and ecosystemic services. However, how vegetation might adapt to drought is poorly understood. In this report, four years of climate change was simulated by excluding 35% of precipitation above a downy oak forest. RNASeq data allowed us to assemble a genome-guided transcriptome. This led to the identification of differentially expressed features, which was supported by the characterization of target metabolites using a metabolomics approach. We provided 2.5 Tb of RNASeq data and the assembly of the first genome guided transcriptome of . Up to 5724 differentially expressed transcripts were obtained; 42 involved in plant response to drought. Transcript set enrichment analysis showed that drought induces an increase in oxidative pressure that is mitigated by the upregulation of ubiquitin-like protein protease, ferrochelatase, oxaloacetate decarboxylase and oxo-acid-lyase activities. Furthermore, the downregulation of auxin biosynthesis and transport, carbohydrate storage metabolism were observed as well as the concomitant accumulation of metabolites, such as oxalic acid, malate and isocitrate. Our data suggest that early metabolic changes in the resistance of to drought involve a tricarboxylic acid (TCA) cycle shunt through the glyoxylate pathway, galactose metabolism by reducing carbohydrate storage and increased proteolytic activity.
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http://dx.doi.org/10.3390/plants9091149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7570186PMC
September 2020

Methanohalophilus profundi sp. nov., a methylotrophic halophilic piezophilic methanogen isolated from a deep hypersaline anoxic basin.

Syst Appl Microbiol 2020 Sep 27;43(5):126107. Epub 2020 Jun 27.

Univ Brest (UBO), Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France.

A novel anaerobic methylotrophic halophilic methanogen strain SLHTYRO was isolated from a deep hypersaline anoxic basin called "Tyro" located in the Eastern Mediterranean Sea. Cells of SLHTYRO were motile cocci. The strain SLHTYRO grew between 12 and 37 °C (optimum 30 °C), at pH between 6.5 and 8.2 (optimum pH 7.5) and salinity from 45 to 240 g L NaCl (optimum 135 g L). Strain SLHTYRO was methylotrophic methanogen able to use methylated compounds (trimethylamine, dimethylamine, monomethylamine and methanol). Strain SLHTYRO was able to grow at in situ hydrostatic pressure and temperature conditions (35 MPa, 14 °C). Phylogenetic analysis based on 16S rRNA gene and mcrA gene sequences indicated that strain SLHTYRO was affiliated to genus Methanohalophilus within the order Methanosarcinales. It shared >99.16% of the 16S rRNA gene sequence similarity with strains of other Methanohalophilus species. Based on ANIb, AAI and dDDH measurements, and the physiological properties of the novel isolate, we propose that strain SLHTYRO should be classified as a representative of a novel species, for which the name Methanohalophilus profundi sp. nov. is proposed; the type strain is SLHTYRO (=DSM 108854 = JCM 32768 = UBOCC-M-3308).
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http://dx.doi.org/10.1016/j.syapm.2020.126107DOI Listing
September 2020

In-Depth In Silico Search for Cuttlefish ( Antimicrobial Peptides Following Bacterial Challenge of Haemocytes.

Mar Drugs 2020 Aug 24;18(9). Epub 2020 Aug 24.

Normandy University, Unicaen, CNRS, BOREA, 14000 CAEN, France.

Cuttlefish () haemocytes are potential sources of antimicrobial peptides (AMPs). To study the immune response to and identify new AMPs, an original approach was developed based on a differential transcriptomic study and an in-depth in silico analysis using multiple tools. Two de novo transcriptomes were retrieved from cuttlefish haemocytes following challenge by . or not. A first analysis of the annotated transcripts revealed the presence of Toll/NF-κB pathway members, including newly identified factors such as -TLR-h, -IKK-h and -Rel/NF-κB-h. Out of the eight Toll/NF-κB pathway members, seven were found up-regulated following . challenge. Besides, immune factors involved in the immune response were also identified and up-regulated. However, no AMP was identified based on annotation or conserved pattern searches. We therefore performed an in-depth in silico analysis of unannotated transcripts based on differential expression and sequence characteristics, using several tools available like PepTraq, a homemade software program. Finally, five AMP candidates were synthesized. Among them, NF19, AV19 and GK28 displayed antibacterial activity against Gram-negative bacteria. Each peptide had a different spectrum of activity, notably against species. GK28-the most active peptide-was not haemolytic, whereas NF19 and AV19 were haemolytic at concentrations between 50 and 100 µM, 5 to 10 times higher than their minimum inhibitory concentration.
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http://dx.doi.org/10.3390/md18090439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551771PMC
August 2020

Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Strain WH7803.

Front Microbiol 2020 24;11:1707. Epub 2020 Jul 24.

CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France.

Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.
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http://dx.doi.org/10.3389/fmicb.2020.01707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393227PMC
July 2020

Seascape genomics reveals population isolation in the reef-building honeycomb worm, Sabellaria alveolata (L.).

BMC Evol Biol 2020 08 10;20(1):100. Epub 2020 Aug 10.

Laboratoire des Sciences de l'Environnement Marin, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, Université de Brest (UBO), Université Européenne de Bretagne (UEB), Institut Universitaire Européen de la Mer (IUEM), 29280, Plouzané, France.

Background: Under the threat of climate change populations can disperse, acclimatise or evolve in order to avoid fitness loss. In light of this, it is important to understand neutral gene flow patterns as a measure of dispersal potential, but also adaptive genetic variation as a measure of evolutionary potential. In order to assess genetic variation and how this relates to environment in the honeycomb worm (Sabellaria alveolata (L.)), a reef-building polychaete that supports high biodiversity, we carried out RAD sequencing using individuals from along its complete latitudinal range. Patterns of neutral population genetic structure were compared to larval dispersal as predicted by ocean circulation modelling, and outlier analyses and genotype-environment association tests were used to attempt to identify loci under selection in relation to local temperature data.

Results: We genotyped 482 filtered SNPs, from 68 individuals across nine sites, 27 of which were identified as outliers using BAYESCAN and ARLEQUIN. All outlier loci were potentially under balancing selection, despite previous evidence of local adaptation in the system. Limited gene flow was observed among reef-sites (F = 0.28 ± 0.10), in line with the low dispersal potential identified by the larval dispersal models. The North Atlantic reef emerged as a distinct population and this was linked to high local larval retention and the effect of the North Atlantic Current on dispersal.

Conclusions: As an isolated population, with limited potential for natural genetic or demographic augmentation from other reefs, the North Atlantic site warrants conservation attention in order to preserve not only this species, but above all the crucial functional ecological roles that are associated with their bioconstructions. Our study highlights the utility of using seascape genomics to identify populations of conservation concern.
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http://dx.doi.org/10.1186/s12862-020-01658-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418442PMC
August 2020

Alterocin, an Antibiofilm Protein Secreted by sp. Strain 3J6.

Appl Environ Microbiol 2020 10 1;86(20). Epub 2020 Oct 1.

Université de Bretagne-Sud, EA 3884, LBCM, IUEM, Lorient, France

We sought to identify and study the antibiofilm protein secreted by the marine bacterium sp. strain 3J6. The latter is active against marine and terrestrial bacteria, including clinical strains forming different biofilm types. Several amino acid sequences were obtained from the partially purified antibiofilm protein, named alterocin. The sp. 3J6 genome was sequenced, and a candidate gene was identified by comparing the genome-encoded proteins to the sequences from purified alterocin. Expressing the gene in another nonactive sp. strain, 3J3, demonstrated that it is responsible for the antibiofilm activity. Alterocin is a 139-residue protein that includes a predicted 20-residue signal sequence, which would be cleaved off upon export by the general secretion system. No sequence homology was found between alterocin and proteins of known functions. The gene is not part of an operon and adjacent genes do not seem related to alterocin production, immunity, or regulation, suggesting that these functions are not fulfilled by devoted proteins. During growth in liquid medium, the mRNA level peaked during the stationary phase. A single promoter was experimentally identified, and several inverted repeats could be binding sites for regulators. genes were found in about 30% of the genomes and in only a few instances of other marine bacteria of the and genera. Comparative genomics yielded the hypothesis that gene losses occurred within the genus. Overall, alterocin is a novel kind of antibiofilm protein of ecological and biotechnological interest. Biofilms are microbial communities that develop on solid surfaces or interfaces and are detrimental in a number of fields, including for example food industry, aquaculture, and medicine. In the latter, antibiotics are insufficient to clear biofilm infections, leading to chronic infections such as in the case of infection by of the lungs of cystic fibrosis patients. Antibiofilm molecules are thus urgently needed to be used in conjunction with conventional antibiotics, as well as in other fields of application, especially if they are environmentally friendly molecules. Here, we describe alterocin, a novel antibiofilm protein secreted by a marine bacterium belonging to the genus, and its gene. Alterocin homologs were found in about 30% of strains, indicating that this new family of antibiofilm proteins likely plays an important albeit nonessential function in the biology of these bacteria. This study opens up the possibility of a variety of applications.
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http://dx.doi.org/10.1128/AEM.00893-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531970PMC
October 2020

-Omic Analysis of the White Body: New Insights into Multifunctionality and Haematopoiesis Regulation.

J Proteome Res 2020 08 22;19(8):3072-3087. Epub 2020 Jul 22.

NORMANDIE UNIV, UNICAEN, CNRS, BOREA, 14000 Caen, France.

Cephalopods, like other protostomes, lack an adaptive immune system and only rely on an innate immune system. The main immune cells are haemocytes (Hcts), which are able to respond to pathogens and external attacks. First reports based on morphological observations revealed that the white body (WB) located in the optic sinuses of cuttlefish was the origin of Hcts. Combining transcriptomic and proteomic analyses, we identified several factors known to be involved in haematopoiesis in vertebrate species in cuttlefish WB. Among these factors, members of the JAK-STAT signaling pathway were identified, some of them for the first time in a molluscan transcriptome and proteome. Immune factors, such as members of the Toll/NF-κB signaling pathway, pattern recognition proteins and receptors, and members of the oxidative stress responses, were also identified, and support an immune role of the WB. Both transcriptome and proteome analyses revealed that the WB harbors an intense metabolism concurrent with the haematopoietic function. Finally, a comparative analysis of the WB and Hct proteomes revealed many proteins in common, confirming previous morphological studies on the origin of Hcts in cuttlefish. This molecular work demonstrates that the WB is multifunctional and provides bases for haematopoiesis regulation in cuttlefish.
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http://dx.doi.org/10.1021/acs.jproteome.0c00100DOI Listing
August 2020

Identification and structural characterization of the factors involved in vitellogenesis and its regulation in the African Osteoglossiforme of aquacultural interest Heterotis niloticus (Cuvier, 1829).

Gen Comp Endocrinol 2020 09 12;296:113532. Epub 2020 Jun 12.

NORMANDIE UNIV, UNICAEN, CNRS, BOREA, 14000 Caen, France; Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen-Normandie, MNHN, SU, UA, CNRS, IRD, Esplanade de la paix, 14032 Caen Cedex, France. Electronic address:

The African bonytongue (Heterotis niloticus) is an excellent candidate for fish farming because it has outstanding biological characteristics and zootechnical performances. However, the absence of sexual dimorphism does not favor its reproduction in captivity or the understanding of its reproductive behavior. Moreover, no molecular data related to its reproduction is yet available. This study therefore focuses on the structural identification of the different molecular actors of vitellogenesis expressed in the pituitary gland, the liver and the ovary of H. niloticus. A transcriptomic approach based on de novo RNA sequencing of the pituitary gland, ovary and liver of females in vitellogenesis led to the creation of three transcriptomes. In silico analysis of these transcriptomes identified the sequences of pituitary hormones such as prolactin (PRL), luteinizing hormone (LH) and follicle-stimulating hormone (FSH) and their ovarian receptors (PRLR, FSHR, LHR). In the liver and ovary, estrogen receptors (ER) beta and gamma, liver vitellogenins (VtgB and VtgC) and their ovarian receptors (VLDLR) were identified. Finally, the partial transcript of an ovarian Vtg weakly expressed compared to hepatic Vtg was identified based on structural criteria. Moreover, a proteomic approach carried out from mucus revealed the presence of one Vtg exclusively in females in vitellogenesis. In this teleost fish that does not exhibit sexual dimorphism, mucus Vtg could be used as a sexing biomarker based on a non-invasive technique compatible with the implementation of experimental protocols in vivo.
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http://dx.doi.org/10.1016/j.ygcen.2020.113532DOI Listing
September 2020

Author Correction: Chloropicophyceae, a new class of picophytoplanktonic prasinophytes.

Sci Rep 2020 Apr 17;10(1):6778. Epub 2020 Apr 17.

Norwegian Institute for Water Research, Gaustadalléen 21, 0349, Oslo, Norway.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41598-020-63703-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165170PMC
April 2020

Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift.

iScience 2020 Feb 17;23(2):100849. Epub 2020 Jan 17.

Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France. Electronic address:

Inferring genome-scale metabolic networks in emerging model organisms is challenged by incomplete biochemical knowledge and partial conservation of biochemical pathways during evolution. Therefore, specific bioinformatic tools are necessary to infer biochemical reactions and metabolic structures that can be checked experimentally. Using an integrative approach combining genomic and metabolomic data in the red algal model Chondrus crispus, we show that, even metabolic pathways considered as conserved, like sterols or mycosporine-like amino acid synthesis pathways, undergo substantial turnover. This phenomenon, here formally defined as "metabolic pathway drift," is consistent with findings from other areas of evolutionary biology, indicating that a given phenotype can be conserved even if the underlying molecular mechanisms are changing. We present a proof of concept with a methodological approach to formalize the logical reasoning necessary to infer reactions and molecular structures, abstracting molecular transformations based on previous biochemical knowledge.
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http://dx.doi.org/10.1016/j.isci.2020.100849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6997860PMC
February 2020

Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach.

Sci Rep 2020 02 13;10(1):2531. Epub 2020 Feb 13.

Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.

As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k-mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow to intermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton.
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http://dx.doi.org/10.1038/s41598-020-59524-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7018713PMC
February 2020

Comparative genomics applied to Mucor species with different lifestyles.

BMC Genomics 2020 Feb 10;21(1):135. Epub 2020 Feb 10.

Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.

Background: Despite a growing number of investigations on early diverging fungi, the corresponding lineages have not been as extensively characterized as Ascomycota or Basidiomycota ones. The Mucor genus, pertaining to one of these lineages is not an exception. To this date, a restricted number of Mucor annotated genomes is publicly available and mainly correspond to the reference species, Mucor circinelloides, and to medically relevant species. However, the Mucor genus is composed of a large number of ubiquitous species as well as few species that have been reported to specifically occur in certain habitats. The present study aimed to expand the range of Mucor genomes available and identify potential genomic imprints of adaptation to different environments and lifestyles in the Mucor genus.

Results: In this study, we report four newly sequenced genomes of Mucor isolates collected from non-clinical environments pertaining to species with contrasted lifestyles, namely Mucor fuscus and Mucor lanceolatus, two species used in cheese production (during ripening), Mucor racemosus, a recurrent cheese spoiler sometimes described as an opportunistic animal and human pathogen, and Mucor endophyticus, a plant endophyte. Comparison of these new genomes with those previously available for six Mucor and two Rhizopus (formerly identified as M. racemosus) isolates allowed global structural and functional description such as their TE content, core and species-specific genes and specialized genes. We proposed gene candidates involved in iron metabolism; some of these genes being known to be involved in pathogenicity; and described patterns such as a reduced number of CAZymes in the species used for cheese ripening as well as in the endophytic isolate that might be related to adaptation to different environments and lifestyles within the Mucor genus.

Conclusions: This study extended the descriptive data set for Mucor genomes, pointed out the complexity of obtaining a robust phylogeny even with multiple genes families and allowed identifying contrasting potentially lifestyle-associated gene repertoires. The obtained data will allow investigating further the link between genetic and its biological data, especially in terms of adaptation to a given habitat.
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http://dx.doi.org/10.1186/s12864-019-6256-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7011435PMC
February 2020

The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga.

Mar Genomics 2020 Aug 11;52:100740. Epub 2020 Jan 11.

Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France.

Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.
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http://dx.doi.org/10.1016/j.margen.2020.100740DOI Listing
August 2020

Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology.

Genome Biol Evol 2020 01;12(1):3647-3655

Sorbonne Université/CNRS, Station Biologique de Roscoff, UMR 8227, Integrative Biology of Marine Models, Roscoff, France.

Brown algae are important primary producers and ecosystem engineers in the ocean, and Ectocarpus has been established as a laboratory model for this lineage. Like most multicellular organisms, Ectocarpus is associated with a community of microorganisms, a partnership frequently referred to as holobiont due to the tight interconnections between the components. Although genomic resources for the algal host are well established, its associated microbiome is poorly characterized from a genomic point of view, limiting the possibilities of using these types of data to study host-microbe interactions. To address this gap in knowledge, we present the annotated draft genome sequences of seventy-two cultivable Ectocarpus-associated bacteria. A screening of gene clusters related to the production of secondary metabolites revealed terpene, bacteriocin, NRPS, PKS-t3, siderophore, PKS-t1, and homoserine lactone clusters to be abundant among the sequenced genomes. These compounds may be used by the bacteria to communicate with the host and other microbes. Moreover, detoxification and provision of vitamin B pathways have been observed in most sequenced genomes, highlighting potential contributions of the bacterial metabolism toward host fitness and survival. The genomes sequenced in this study form a valuable resource for comparative genomic analyses and evolutionary surveys of alga-associated bacteria. They help establish Ectocarpus as a model for brown algal holobionts and will enable the research community to produce testable hypotheses about the molecular interactions within this complex system.
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http://dx.doi.org/10.1093/gbe/evz278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6948157PMC
January 2020

Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima?

BMC Plant Biol 2019 Nov 21;19(1):513. Epub 2019 Nov 21.

Institute for Plant Science and Microbiology, University of Hamburg, Hamburg, Germany.

Background: Kelps (Laminariales, Phaeophyceae) are brown macroalgae of utmost ecological, and increasingly economic, importance on temperate to polar rocky shores. Omics approaches in brown algae are still scarce and knowledge of their acclimation mechanisms to the changing conditions experienced in coastal environments can benefit from the application of RNA-sequencing. Despite evidence of ecotypic differentiation, transcriptomic responses from distinct geographical locations have, to our knowledge, never been studied in the sugar kelp Saccharina latissima so far.

Results: In this study we investigated gene expression responses using RNA-sequencing of S. latissima from environments with contrasting temperature and salinity conditions - Roscoff, in temperate eastern Atlantic, and Spitsbergen in the Arctic. Juvenile sporophytes derived from uniparental stock cultures from both locations were pre-cultivated at 8 °C and S 30. Sporophytes acclimated to 0 °C, 8 °C and 15 °C were exposed to a low salinity treatment (S 20) for 24 h. Hyposalinity had a greater impact at the transcriptomic level than the temperature alone, and its effects were modulated by temperature. Namely, photosynthesis and pigment synthesis were extensively repressed by low salinity at low temperatures. Although some responses were shared among sporophytes from the different sites, marked differences were revealed by principal component analysis, differential expression and GO enrichment. The interaction between low temperature and low salinity drove the largest changes in gene expression in sporophytes from Roscoff while specimens from Spitsbergen required more metabolic adjustment at higher temperatures. Moreover, genes related to cell wall adjustment were differentially expressed between Spitsbergen and Roscoff control samples.

Conclusions: Our study reveals interactive effects of temperature and salinity on transcriptomic profiles in S. latissima. Moreover, our data suggest that under identical culture conditions sporophytes from different locations diverge in their transcriptomic responses. This is probably connected to variations in temperature and salinity in their respective environment of origin. The current transcriptomic results support the plastic response pattern in sugar kelp which is a species with several reported ecotypes. Our data provide the baseline for a better understanding of the underlying processes of physiological plasticity and may help in the future to identify strains adapted to specific environments and its genetic control.
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http://dx.doi.org/10.1186/s12870-019-2124-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6881991PMC
November 2019

Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae and .

Antioxidants (Basel) 2019 Nov 16;8(11). Epub 2019 Nov 16.

Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.

Understanding growth mechanisms in brown algae is a current scientific and economic challenge that can benefit from the modeling of their metabolic networks. The sequencing of the genomes of and has provided the necessary data for the reconstruction of Genome-Scale Metabolic Networks (GSMNs). The same in silico method deployed for the GSMN reconstruction of to investigate the metabolic capabilities of these two algae, was used. Integrating metabolic profiling data from the literature, we provided functional GSMNs composed of an average of 2230 metabolites and 3370 reactions. Based on these GSMNs and previously published work, we propose a model for the biosynthetic pathways of the main carotenoids in these two algae. We highlight, on the one hand, the reactions and enzymes that have been preserved through evolution and, on the other hand, the specificities related to brown algae. Our data further indicate that, if abscisic acid is produced by , its biosynthesis pathway seems to be different in its final steps from that described in land plants. Thus, our work illustrates the potential of GSMNs reconstructions for formalizing hypotheses that can be further tested using targeted biochemical approaches.
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http://dx.doi.org/10.3390/antiox8110564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6912245PMC
November 2019

Transcriptomic analysis of clam extrapallial fluids reveals immunity and cytoskeleton alterations in the first week of Brown Ring Disease development.

Fish Shellfish Immunol 2019 Oct 13;93:940-948. Epub 2019 Aug 13.

Univ Brest, CNRS, IRD, Ifremer, UMR 6539 LEMAR, F-29280, Plouzane, France. Electronic address:

The Brown Ring Disease is an infection caused by the bacterium Vibrio tapetis on the Manila clam Ruditapes philippinarum. The process of infection, in the extrapallial fluids (EPFs) of clams, involves alteration of immune functions, in particular on hemocytes which are the cells responsible of phagocytosis. Disorganization of the actin-cytoskeleton in infected clams is a part of what leads to this alteration. This study is the first transcriptomic approach based on collection of extrapallial fluids on living animals experimentally infected by V. tapetis. We performed differential gene expression analysis of EPFs in two experimental treatments (healthy-against infected-clams by V. tapetis), and showed the deregulation of 135 genes. In infected clams, a downregulation of transcripts implied in immune functions (lysosomal activity and complement- and lectin-dependent PRR pathways) was observed during infection. We also showed a deregulation of transcripts encoding proteins involved in the actin cytoskeleton organization such as an overexpression of β12-Thymosin (which is an actin sequestration protein) or a downregulation of proteins that closely interact with capping proteins such as Coactosin, that counteract action of capping proteins, or Profilin. We validated these transcriptomic results by cellular physiological analyses that showed a decrease of the lysosome amounts and the disorganization of actin cytoskeleton in infected hemocytes.
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http://dx.doi.org/10.1016/j.fsi.2019.08.025DOI Listing
October 2019

Responses of the kelp Saccharina latissima (Phaeophyceae) to the warming Arctic: from physiology to transcriptomics.

Physiol Plant 2020 Jan 7;168(1):5-26. Epub 2019 Aug 7.

Marine Botany, Faculty Biology/Chemistry, University of Bremen, Bremen, 28359, Germany.

The Arctic region is currently facing substantial environmental changes due to global warming. Melting glaciers cause reduced salinity environments in coastal Arctic habitats, which may be stressful for kelp beds. To investigate the responses of the kelp Saccharina latissima to the warming Arctic, we studied the transcriptomic changes of S. latissima from Kongsfjorden (Svalbard, Norway) over a 24-hour exposure to two salinities (Absolute Salinity [S ] 20 and 30) after a 7-day pre-acclimation at three temperatures (0, 8 and 15°C). In addition, corresponding physiological data were assessed during an 11-days salinity/temperature experiment. Growth and maximal quantum yield for photosystem II fluorescence were positively affected by increased temperature during acclimation, whereas hyposalinity caused negative effects at the last day of treatment. In contrast, hyposalinity induced marked changes on the transcriptomic level. Compared to the control (8°C - S 30), the 8°C - S 20 exhibited the highest number of differentially expressed genes (DEGs), followed by the 0°C - S 20. Comparisons indicate that S. latissima tends to convert its energy from primary metabolism (e.g. photosynthesis) to antioxidant activity under hyposaline stress. The increase in physiological performance at 15°C shows that S. latissima in the Arctic region can adjust and might even benefit from increased temperatures. However, in Arctic fjord environments its performance might become impaired by decreased salinity as a result of ice melting.
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http://dx.doi.org/10.1111/ppl.13009DOI Listing
January 2020