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1.
Cell ; 179(5): 1084-1097.e21, 2019 11 14.
Artigo em Inglês | MEDLINE | ID: mdl-31730851

RESUMO

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. VIDEO ABSTRACT.


Assuntos
Biodiversidade , Plâncton/fisiologia , Água do Mar/microbiologia , Geografia , Modelos Teóricos , Oceanos e Mares , Filogenia
2.
Nature ; 616(7958): 783-789, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-37076623

RESUMO

DNA viruses have a major influence on the ecology and evolution of cellular organisms1-4, but their overall diversity and evolutionary trajectories remain elusive5. Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this large monophyletic clade is typical of viruses from the realm Duplodnaviria6, with multiple components strongly indicating a common ancestry with animal-infecting Herpesvirales. Yet, a substantial fraction of mirusvirus genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologues of giant eukaryotic DNA viruses from another viral realm, Varidnaviria. These remarkable chimaeric attributes connecting Mirusviricota to herpesviruses and giant eukaryotic viruses are supported by more than 100 environmental mirusvirus genomes, including a near-complete contiguous genome of 432 kilobases. Moreover, mirusviruses are among the most abundant and active eukaryotic viruses characterized in the sunlit oceans, encoding a diverse array of functions used during the infection of microbial eukaryotes from pole to pole. The prevalence, functional activity, diversification and atypical chimaeric attributes of mirusviruses point to a lasting role of Mirusviricota in the ecology of marine ecosystems and in the evolution of eukaryotic DNA viruses.


Assuntos
Organismos Aquáticos , Vírus Gigantes , Herpesviridae , Oceanos e Mares , Filogenia , Plâncton , Animais , Ecossistema , Eucariotos/virologia , Genoma Viral/genética , Vírus Gigantes/classificação , Vírus Gigantes/genética , Herpesviridae/classificação , Herpesviridae/genética , Plâncton/virologia , Metagenômica , Metagenoma , Luz Solar , Transcrição Gênica/genética , Organismos Aquáticos/virologia
4.
Proc Natl Acad Sci U S A ; 118(25)2021 06 22.
Artigo em Inglês | MEDLINE | ID: mdl-34155140

RESUMO

Unicellular eukaryotic predators play a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionarily diverse organisms have been combined into a single functional group (heterotrophic flagellates), overlooking their organismal differences. Here, we investigated four evolutionarily related species belonging to one cosmopolitan group of uncultured marine picoeukaryotic predators: marine stramenopiles (MAST)-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A and C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using single-cell genomics. Analyses of 69 single cells recovered 66 to 83% of the MAST-4A/B/C/E genomes, which displayed substantial interspecies divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition (A and C) coexcluded each other in the surface global ocean, while species with a different set of GHs (B and C) appeared to be able to coexist, suggesting further niche diversification associated with prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. We show that minute ocean predators from the same phylogenetic group may have different biogeography and genomic content, which needs to be accounted for to better comprehend marine food webs.


Assuntos
Adaptação Fisiológica , Evolução Biológica , Ecossistema , Oceanos e Mares , Comportamento Predatório/fisiologia , Animais , Geografia , Glicosídeo Hidrolases/metabolismo , Internacionalidade , Filogenia , Seleção Genética , Especificidade da Espécie , Estramenópilas/enzimologia , Estramenópilas/genética
5.
Mol Biol Evol ; 39(2)2022 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-35150280

RESUMO

The emergence of the eukaryotic cytoskeleton is a critical yet puzzling step of eukaryogenesis. Actin and actin-related proteins (ARPs) are ubiquitous components of this cytoskeleton. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) would have therefore harbored both actin and various ARPs. Here, we report the presence and expression of actin-related genes in viral genomes (viractins) of some Imitervirales, a viral order encompassing the giant Mimiviridae. Phylogenetic analyses suggest an early recruitment of an actin-related gene by viruses from ancient protoeukaryotic hosts before the emergence of modern eukaryotes, possibly followed by a back transfer that gave rise to eukaryotic actins. This supports a coevolutionary scenario between pre-LECA lineages and their viruses, which could have contributed to the emergence of the modern eukaryotic cytoskeleton.


Assuntos
Vírus Gigantes , Actinas/genética , Eucariotos/genética , Células Eucarióticas , Evolução Molecular , Vírus Gigantes/genética , Filogenia
6.
Glob Chang Biol ; 29(21): 5999-6001, 2023 11.
Artigo em Inglês | MEDLINE | ID: mdl-37665245

RESUMO

Geoscientists and ecologists alike must confront the impact of climate change on ecosystems and the services they provide. In the marine realm, major changes are projected in net primary and export production, with significant repercussions on food security, carbon storage, and climate system feedbacks. However, these projections do not include the potential for rapid linear evolution to facilitate adaptation to environmental change. Climate genomics confronts this challenge by assessing the vulnerability of ecosystem services to climate change. Because DNA is the primary biological repository of detectable environmentally selected mutations (showing evidence of change before impacts arise in morphological or metabolic patterns), genomics provides a window into selection in response to climate change, while also recording neutral processes deriving from stochastic mechanisms (Lowe et al., Trends in Ecology & Evolution, 2017; 32:141-152). Due to the revolution afforded by sequencing technology developments, genomics can now meet ecologists and climate scientists in a cross-disciplinary space fertile for collaborations. Collaboration between geoscientists, ecologists, and geneticists must be reinforced in order to combine modeling and genomics approaches at every scale to improve our understanding and the management of ecosystems under climate change. To this end, we present advances in climate genomics from plankton to larger vertebrates, stressing the interactions between modeling and genomics, and identifying future work needed to develop and expand the field of climate genomics.


Assuntos
Mudança Climática , Ecossistema , Animais , Ecologia , Plâncton , Genômica
7.
Mol Biol Evol ; 36(10): 2328-2339, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31220870

RESUMO

Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being "synonymous," these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutational drift, is the major determinant of variation across species. Here, we find that in addition to GC content, interspecies codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding and show that domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain of life with high accuracy. We then wondered whether the inclusion of codon usage codon autocorrelation patterns, which reflects the nonrandom distribution of codon occurrences throughout a transcript, might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to previous reports. Instead, our results suggest that codon autocorrelation patterns are a by-product of codon optimality throughout a sequence, where highly expressed genes display autocorrelated "optimal" codons, whereas lowly expressed genes display autocorrelated "nonoptimal" codons.


Assuntos
Archaea/genética , Bactérias/genética , Uso do Códon , Eucariotos/genética , Arginina/genética , Composição de Bases , Humanos , Anotação de Sequência Molecular , RNA de Transferência/metabolismo
8.
Mol Ecol ; 28(18): 4272-4289, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31448836

RESUMO

Viruses are the most abundant biological entities on Earth and have fundamental ecological roles in controlling microbial communities. Yet, although their diversity is being increasingly explored, little is known about the extent of viral interactions with their protist hosts as most studies are limited to a few cultivated species. Here, we exploit the potential of single-cell genomics to unveil viral associations in 65 individual cells of 11 essentially uncultured stramenopiles lineages sampled during the Tara Oceans expedition. We identified viral signals in 57% of the cells, covering nearly every lineage and with narrow host specificity signal. Only seven out of the 64 detected viruses displayed homologies to known viral sequences. A search for our viral sequences in global ocean metagenomes showed that they were preferentially found at the DCM and within the 0.2-3 µm size fraction. Some of the viral signals were widely distributed, while others geographically constrained. Among the viral signals we detected an endogenous mavirus virophage potentially integrated within the nuclear genome of two distant uncultured stramenopiles. Virophages have been previously reported as a cell's defence mechanism against other viruses, and may therefore play an important ecological role in regulating protist populations. Our results point to single-cell genomics as a powerful tool to investigate viral associations in uncultured protists, suggesting a wide distribution of these relationships, and providing new insights into the global viral diversity.


Assuntos
Células Eucarióticas/virologia , Genômica , Oceanos e Mares , Análise de Célula Única , Vírus/genética , Sequência de Bases , Células Cultivadas , Mapeamento de Sequências Contíguas , Variação Genética , Genoma Viral , Filogeografia
9.
Nature ; 500(7463): 453-7, 2013 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-23873043

RESUMO

Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.


Assuntos
Evolução Biológica , Conversão Gênica/genética , Genoma/genética , Reprodução Assexuada/genética , Rotíferos/genética , Animais , Transferência Genética Horizontal/genética , Genômica , Meiose/genética , Modelos Biológicos , Tetraploidia
10.
Nature ; 488(7410): 213-7, 2012 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-22801500

RESUMO

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.


Assuntos
Evolução Molecular , Genoma de Planta/genética , Musa/genética , Sequência Conservada/genética , Elementos de DNA Transponíveis/genética , Duplicação Gênica/genética , Genes de Plantas/genética , Genótipo , Haploidia , Dados de Sequência Molecular , Musa/classificação , Filogenia
11.
Nature ; 464(7291): 1033-8, 2010 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-20348908

RESUMO

The Périgord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal Laccaria bicolor, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of T. melanosporum, which at approximately 125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for approximately 58% of the genome. In contrast, this genome only contains approximately 7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both L. bicolor and T. melanosporum, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis-'the symbiosis toolbox'-evolved along different ways in ascomycetes and basidiomycetes.


Assuntos
Ascomicetos/genética , Evolução Molecular , Genoma Fúngico/genética , Simbiose/genética , Carboidratos , Elementos de DNA Transponíveis/genética , Carpóforos/metabolismo , Genes Fúngicos/genética , Genômica , Haploidia , Dados de Sequência Molecular , Análise de Sequência de DNA , Enxofre/metabolismo
12.
Environ Microbiol ; 17(10): 4035-49, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26119494

RESUMO

Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.


Assuntos
Alveolados/genética , Sedimentos Geológicos/microbiologia , Plâncton/classificação , Plâncton/genética , Água do Mar/microbiologia , Estramenópilas/genética , Sequência de Bases , Biodiversidade , Ecossistema , Europa (Continente) , Fungos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , RNA Ribossômico 18S/genética , Análise de Sequência de DNA
13.
Environ Microbiol ; 16(9): 2659-71, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24102695

RESUMO

Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Here we show that 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes (mi tags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the Tara Oceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700 Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454 tags; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon (454 tags; ca. 0.075 Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mi tags may provide more realistic estimates of community richness and evenness than amplicon 454 tags. In addition, mi tags can capture expected beta diversity patterns. Using mi tags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.


Assuntos
DNA Ribossômico/genética , Metagenoma , Metagenômica/métodos , Análise de Sequência de DNA/métodos , Archaea/genética , Bactérias/genética , Primers do DNA/genética , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética
14.
PLoS Biol ; 9(10): e1001177, 2011 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-22028628

RESUMO

The structure, robustness, and dynamics of ocean plankton ecosystems remain poorly understood due to sampling, analysis, and computational limitations. The Tara Oceans consortium organizes expeditions to help fill this gap at the global level.


Assuntos
Ecossistema , Expedições , Biologia Marinha , Plâncton/crescimento & desenvolvimento , Animais , Oceanos e Mares
15.
Nature ; 451(7176): 359-62, 2008 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-18202663

RESUMO

Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs. Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood. In most organisms, short introns recognized by the intron definition mechanism cannot be efficiently predicted solely on the basis of sequence motifs. In multicellular eukaryotes, long introns are recognized through exon definition and most genes produce multiple mRNA variants through alternative splicing. The nonsense-mediated mRNA decay (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals. Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals. By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs. The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy.


Assuntos
Processamento Alternativo , Células Eucarióticas/metabolismo , Íntrons/genética , Paramecium/genética , Biossíntese de Proteínas , Animais , Sequência de Bases , Códon de Terminação/genética , Biologia Computacional , Etiquetas de Sequências Expressas , Genes de Protozoários/genética , Dados de Sequência Molecular , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , Interferência de RNA , Estabilidade de RNA , RNA de Protozoário/genética , RNA de Protozoário/metabolismo
16.
Nature ; 449(7161): 463-7, 2007 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-17721507

RESUMO

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.


Assuntos
Evolução Molecular , Genoma de Planta/genética , Poliploidia , Vitis/classificação , Vitis/genética , Arabidopsis/genética , DNA Intergênico/genética , Éxons/genética , Genes de Plantas/genética , Íntrons/genética , Cariotipagem , MicroRNAs/genética , Dados de Sequência Molecular , Oryza/genética , Populus/genética , RNA de Plantas/genética , RNA de Transferência/genética , Análise de Sequência de DNA
17.
C R Biol ; 346: 13-24, 2023 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-37254792

RESUMO

This article summarizes recent advances in our knowledge of plankton biogeography obtained by genomic approaches and the impacts of global warming on it. Large-scale comparison of the genomic content of samples of different plankton size fractions revealed a partitioning of the oceans into genomic provinces and the impact of major oceanic currents on them. By defining ecological niches, these provinces are extrapolated to all oceans, with the exception of the Arctic Ocean. By the end of the 21st century, a major restructuring of these provinces is projected in response to a high emission greenhouse gas scenario over 50% of the surface of the studied oceans. Such a restructuring could lead to a decrease in export production by 4%. Finally, obtaining assembled sequences of a large number of plankton genomes defining this biogeography has allowed to better characterize the genomic content of the provinces and to identify the species structuring them. These genomes similarly enabled a better description of potential future changes of plankton communities under climate change.


Cet article résume des avancées récentes dans nos connaissances sur la biogéographie du plancton obtenues par des approches de génomiques ainsi que les impacts du réchauffement climatique sur celle-ci. La comparaison à large échelle du contenu génomique d'échantillons de différentes fractions de taille de plancton a révélé un partitionnement des océans en provinces génomiques ainsi que l'impact des principaux courants océaniques sur celles-ci. En définissant des niches écologiques, ces provinces sont extrapolées à l'ensemble des océans à l'exception de l'océan Arctique. D'ici la fin du XXI e siècle, une restructuration majeure de ces provinces est projetée en réponse à un scénario de fortes émissions de gaz à effet de serre sur 50 % de la surface des océans étudiés. Une telle restructuration pourrait engendrer une diminution de 4 % de la production exportée. L'obtention de séquences assemblées d'un grand nombre de génomes de plancton définissant cette biogéographie a permis de mieux caractériser le contenu génomique des provinces et d'identifier les espèces les structurant. Ces génomes ont aussi permis de mieux caractériser les futurs changements potentiels de communautés de plancton sous changement climatique.


Assuntos
Mudança Climática , Plâncton , Plâncton/genética , Ecossistema , Oceanos e Mares , Genômica
18.
ISME Commun ; 3(1): 83, 2023 Aug 18.
Artigo em Inglês | MEDLINE | ID: mdl-37596349

RESUMO

For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3- and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.

19.
Nature ; 444(7116): 171-8, 2006 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-17086204

RESUMO

The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.


Assuntos
Evolução Molecular , Duplicação Gênica , Genoma de Protozoário/genética , Genômica , Paramecium tetraurellia/genética , Animais , Células Eucarióticas/metabolismo , Genes Duplicados/genética , Genes de Protozoários/genética , Dados de Sequência Molecular , Filogenia
20.
Commun Biol ; 5(1): 983, 2022 09 16.
Artigo em Inglês | MEDLINE | ID: mdl-36114260

RESUMO

The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment.


Assuntos
Ferro , Estramenópilas , Aclimatação/genética , Cromossomos , Genômica , Ferro/metabolismo , Nitratos/metabolismo , Oceanos e Mares , Fitoplâncton/genética , Fitoplâncton/metabolismo , Estramenópilas/genética
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