Santec, France


Santec, France
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Lipinska A.P.,Paris-Sorbonne University | Toda N.R.T.,Paris-Sorbonne University | Heesch S.,Paris-Sorbonne University | Peters A.F.,Bezhin Rosko | And 2 more authors.
Genome Biology | Year: 2017

Background: Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out for haploid phase UV sex chromosomes. Here, we explore sex-specific sequences of seven brown algal species to understand the dynamics of the sex-determining region (SDR) gene content across 100 million years of evolution. Results: A core set of sex-linked genes is conserved across all the species investigated, but we also identify modifications of both the U and the V SDRs that occurred in a lineage-specific fashion. These modifications involve gene loss, gene gain and relocation of genes from the SDR to autosomes. Evolutionary analyses suggest that the SDR genes are evolving rapidly and that this is due to relaxed purifying selection. Expression analysis indicates that genes that were acquired from the autosomes have been retained in the SDR because they confer a sex-specific role in reproduction. By examining retroposed genes in Saccharina japonica, we demonstrate that UV sex chromosomes have generated a disproportionate number of functional orphan retrogenes compared with autosomes. Movement of genes out of the UV sex chromosome could be a means to compensate for gene loss from the non-recombining region, as has been suggested for Y-derived retrogenes in XY sexual systems. Conclusion: This study provides the first analysis of gene traffic in a haploid UV system and identifies several features of general relevance to the evolution of sex chromosomes. © 2017 The Author(s).

Dittami S.M.,CNRS Integrative Biology of Marine Models | Dittami S.M.,University of Oslo | Gravot A.,University of Rennes 1 | Gravot A.,European University of Brittany | And 8 more authors.
Plant Journal | Year: 2012

Colonizations of freshwater by marine species are rare events, and little information is known about the underlying mechanisms. Brown algae are an independent lineage of photosynthetic and multicellular organisms from which few species inhabit freshwater. As a marine alga that is also found in freshwater, Ectocarpus is of particular interest for studying the transition between these habitats. To gain insights into mechanisms of the transition, we examined salinity tolerance and adaptations to low salinities in a freshwater strain of Ectocarpus on physiological and molecular levels. We show that this isolate belongs to a widely distributed and highly stress-resistant clade, and differed from the genome-sequenced marine strain in its tolerance of low salinities. It also exhibited profound, but reversible, morphological, physiological, and transcriptomic changes when transferred to seawater. Although gene expression profiles were similar in both strains under identical conditions, metabolite and ion profiles differed strongly, the freshwater strain exhibiting e.g. higher cellular contents of amino acids and nitrate, higher contents of n-3 fatty acids, and lower intracellular mannitol and sodium concentrations. Moreover, several stress markers were noted in the freshwater isolate in seawater. This finding suggests that, while high stress tolerance and plasticity may be prerequisites for the colonization of freshwater, genomic alterations have occurred that produced permanent changes in the metabolite profiles to stabilize the transition. © 2012 The Authors.

Dittami S.M.,CNRS Integrative Biology of Marine Models | Dittami S.M.,University of Oslo | Proux C.,Institute Pasteur Paris | Rousvoal S.,CNRS Integrative Biology of Marine Models | And 6 more authors.
BMC Molecular Biology | Year: 2011

Background: Brown algae of the genus Ectocarpus exhibit high levels of genetic diversity and variability in morphological and physiological characteristics. With the establishment of E. siliculosus as a model and the availability of a complete genome sequence, it is now of interest to analyze variability among different species, ecotypes, and strains of the genus Ectocarpus both at the genome and the transcriptome level.Results: We used an E. siliculosus gene expression microarray based on EST sequences from the genome-sequenced strain (reference strain) to carry out comparative genome hybridizations for five Ectocarpus strains: four E. siliculosus isolates (the male genome strain, a female strain used for outcrosses with the genome strain, a strain isolated from freshwater, and a highly copper-tolerant strain), as well as one strain of the sister species E. fasciculatus. Our results revealed significant genomic differences between ecotypes of the same species, and enable the selection of conserved probes for future microarray experiments with these strains. In the two closely related strains (a male and a female strain used for crosses), genomic differences were also detected, but concentrated in two smaller genomic regions, one of which corresponds to a viral insertion site.Conclusion: The high variability between strains supports the concept of E. siliculosus as a complex of cryptic species. Moreover, our data suggest that several parts of the Ectocarpus genome may have evolved at different rates: high variability was detected particularly in transposable elements and fucoxanthin chlorophyll a/c binding proteins. © 2011 Dittami et al; licensee BioMed Central Ltd.

Bothwell J.H.,Queen's University of Belfast | Bothwell J.H.,CNRS Integrative Biology of Marine Models | Bothwell J.H.,Marine Biological Association of The United Kingdom | Marie D.,French National Center for Scientific Research | And 3 more authors.
New Phytologist | Year: 2010

•The filamentous brown alga Ectocarpus has a complex life cycle, involving alternation between independent and morphologically distinct sporophyte and gametophyte generations. In addition to this basic haploid-diploid life cycle, gametes can germinate parthenogenetically to produce parthenosporophytes. This article addresses the question of how parthenosporophytes, which are derived from a haploid progenitor cell, are able to produce meiospores in unilocular sporangia, a process that normally involves a reductive meiotic division.•We used flow cytometry, multiphoton imaging, culture studies and a bioinformatics survey of the recently sequenced Ectocarpus genome to describe its life cycle under laboratory conditions and the nuclear DNA changes which accompany key developmental transitions.•Endoreduplication occurs during the first cell cycle in about one-third of parthenosporophytes. The production of meiospores by these diploid parthenosporophytes involves a meiotic division similar to that observed in zygote-derived sporophytes. By contrast, meiospore production in parthenosporophytes that fail to endoreduplicate occurs via a nonreductive apomeiotic event.•Our results highlight Ectocarpus's reproductive and developmental plasticity and are consistent with previous work showing that its life cycle transitions are controlled by genetic mechanisms and are independent of ploidy. © CNRS (2010). Journal compilation © New Phytologist Trust (2010).

Heesch S.,CNRS Integrative Biology of Marine Models | Cho G.Y.,CNRS Integrative Biology of Marine Models | Peters A.F.,Bezhin Rosko | Le Corguille G.,Computer and Genomics Resource Center | And 8 more authors.
New Phytologist | Year: 2010

•Ectocarpus siliculosus has been proposed as a genetic and genomic model for the brown algae and the 214 Mbp genome of this organism has been sequenced. The aim of this project was to obtain a chromosome-scale view of the genome by constructing a genetic map using microsatellite markers that were designed based on the sequence supercontigs.•To map genetic markers, a segregating F2 population was generated from a cross between the sequenced strain (Ec 32) and a compatible strain from northern Chile. Amplified fragment length polymorphism (AFLP) analysis indicated a significant degree of polymorphism (41%) between the genomes of these two parental strains. Of 1,152 microsatellite markers that were selected for analysis based on their location on long supercontigs, their potential as markers and their predicted ability to amplify a single genomic locus, 407 were found to be polymorphic.•A genetic map was constructed using 406 markers, resulting in 34 linkage groups. The 406 markers anchor 325 of the longest supercontigs on to the map, representing 70.1% of the genome sequence.•The Ectocarpus genetic map described here not only provides a large-scale assembly of the genome sequence, but also represents an important tool for future genetic analysis using this organism. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

Peters A.F.,Bezhin Rosko | Couceiro L.,French National Center for Scientific Research | Tsiamis K.,Hellenic Center for Marine Research | Kupper F.C.,University of Aberdeen | Valero M.,French National Center for Scientific Research
Cryptogamie, Algologie | Year: 2015

To identify cryptic stages of marine brown macroalgae present in the "bank of microscopic forms", we incubated natural substrata of different geographical origins and isolated emerging Phaeophyceae into clonal cultures. A total of 431 clones were subsequently identified by barcoding using 5'-COI. A proportion of 98% of the isolates belonged to the Ectocarpales. The distribution of pairwise genetic distances revealed a K2P divergence of 1.8% as species-level cut-off. Using this threshold, the samples were ascribed to 83 different species, 39 (47%) of which were identified through reference sequences or morphology. In the Ectocarpaceae, 16 lineages of Ectocarpus fulfilled the barcode criterion for different species, while three putative new species were detected. In the Chordariaceae, numerous microthalli were microstages of known macroscopic taxa. A separate cluster contained Hecatonema maculans and other microscopic species. Taxa traditionally classified in Acinetosporaceae were split in two species-rich groups containing Pylaiella and Hincksia in one and Acinetospora in the other. Feldmannia species were present in both clusters. The present study shows that the germling emergence method is suited to reveal the diversity of hidden life-history stages, albeit with a bias towards early successional species. © 2015 Adac. Tous droits réservés.

Ahmed S.,CNRS Integrative Biology of Marine Models | Ahmed S.,Queen's University of Belfast | Cock J.M.,CNRS Integrative Biology of Marine Models | Pessia E.,CNRS Biometry and Evolutionary Biology Laboratory | And 16 more authors.
Current Biology | Year: 2014

Background: A common feature of most genetic sex-determination systems studied so far is that sex is determined by nonrecombining genomic regions, which can be of various sizes depending on the species. These regions have evolved independently and repeatedly across diverse groups. A number of such sex-determining regions (SDRs) have been studied in animals, plants, and fungi, but very little is known about the evolution of sexes in other eukaryotic lineages. Results: We report here the sequencing and genomic analysis of the SDR of Ectocarpus, a brown alga that has been evolving independently from plants, animals, and fungi for over one giga-annum. In Ectocarpus, sex is expressed during the haploid phase of the life cycle, and both the female (U) and the male (V) sex chromosomes contain nonrecombining regions. The U and V of this species have been diverging for more than 70 mega-annum, yet gene degeneration has been modest, and the SDR is relatively small, with no evidence for evolutionary strata. These features may be explained by the occurrence of strong purifying selection during the haploid phase of the life cycle and the low level of sexual dimorphism. V is dominant over U, suggesting that femaleness may be the default state, adopted when the male haplotype is absent. Conclusions: The Ectocarpus UV system has clearly had a distinct evolutionary trajectory not only to the well-studied XY and ZW systems but also to the UV systems described so far. Nonetheless, some striking similarities exist, indicating remarkable universality of the underlying processes shaping sex chromosome evolution across distant lineages. © 2014 Elsevier Ltd.

Luthringer R.,Paris-Sorbonne University | Lipinska A.P.,Paris-Sorbonne University | Roze D.,Sorbonne Universites | Cormier A.,Paris-Sorbonne University | And 4 more authors.
Molecular Biology and Evolution | Year: 2015

The recombining regions of sex chromosomes (pseudoautosomal regions, PARs) are predicted to exhibit unusual features due to their being genetically linked to the nonrecombining, sex-determining region. This phenomenon is expected to occur in both diploid (XY, ZW) and haploid (UV) sexual systems, with slightly different consequences for UV sexual systems because of the absence of masking during the haploid phase (when sex is expressed) and because there is no homozygous sex in these systems. Despite a considerable amount of theoretical work on PAR genetics and evolution, these genomic regions have remained poorly characterized empirically. We show here that although the PARs of the U/V sex chromosomes of the brown alga Ectocarpus recombine at a similar rate to autosomal regions of the genome, they exhibit many genomic features typical of nonrecombining regions. The PARs were enriched in clusters of genes that are preferentially, and often exclusively, expressed during the sporophyte generation of the life cycle, and many of these genes appear to have evolved since the Ectocarpales diverged from other brown algal lineages. A modeling-based approach was used to investigate possible evolutionary mechanisms underlying this enrichment in sporophyte-biased genes. Our results are consistent with the evolution of the PAR in haploid systems being influenced by differential selection pressures in males and females acting on alleles that are advantageous during the sporophyte generation of the life cycle. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

PubMed | Bezhin Rosko and Paris-Sorbonne University
Type: | Journal: Development (Cambridge, England) | Year: 2017

The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared to the majority of brown algae. The first cell division is symmetrical and the apical/basal axis is established late in development. In the IMMEDIATE UPRIGHT mutant the initial cell undergoes an asymmetric division to immediately establish the apical/basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function, containing a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles suggesting that the expansion of this family may have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.

Cock J.M.,CNRS Integrative Biology of Marine Models | Godfroy O.,CNRS Integrative Biology of Marine Models | Macaisne N.,CNRS Integrative Biology of Marine Models | Peters A.F.,Bezhin Rosko | Coelho S.M.,CNRS Integrative Biology of Marine Models
Current Opinion in Plant Biology | Year: 2014

The life cycle of an organism is one of its fundamental features, influencing many aspects of its biology. The brown algae exhibit a diverse range of life cycles indicating that transitions between life cycle types may have been key adaptive events in the evolution of this group. Life cycle mutants, identified in the model organism Ectocarpus, are providing information about how life cycle progression is regulated at the molecular level in brown algae. We explore some of the implications of the phenotypes of the life cycle mutants described to date and draw comparisons with recent insights into life cycle regulation in the green lineage. Given the importance of coordinating growth and development with life cycle progression, we suggest that the co-option of ancient life cycle regulators to control key developmental events may be a common feature in diverse groups of multicellular eukaryotes. © 2013 Elsevier Ltd.

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