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Vacant S, Benites LF, Salmeron C, Intertaglia L, Norest M, Cadoudal A, Sanchez F, Caceres C, Piganeau G. Long-Term Stability of Bacterial Associations in a Microcosm of Ostreococcus tauri (Chlorophyta, Mamiellophyceae). FRONTIERS IN PLANT SCIENCE 2022; 13:814386. [PMID: 35463414 PMCID: PMC9024300 DOI: 10.3389/fpls.2022.814386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Phytoplankton-bacteria interactions rule over carbon fixation in the sunlit ocean, yet only a handful of phytoplanktonic-bacteria interactions have been experimentally characterized. In this study, we investigated the effect of three bacterial strains isolated from a long-term microcosm experiment with one Ostreococcus strain (Chlorophyta, Mamiellophyceae). We provided evidence that two Roseovarius strains (Alphaproteobacteria) had a beneficial effect on the long-term survival of the microalgae whereas one Winogradskyella strain (Flavobacteriia) led to the collapse of the microalga culture. Co-cultivation of the beneficial and the antagonistic strains also led to the loss of the microalga cells. Metagenomic analysis of the microcosm is consistent with vitamin B12 synthesis by the Roseovarius strains and unveiled two additional species affiliated to Balneola (Balneolia) and Muricauda (Flavobacteriia), which represent less than 4% of the reads, whereas Roseovarius and Winogradskyella recruit 57 and 39% of the reads, respectively. These results suggest that the low-frequency bacterial species may antagonize the algicidal effect of Winogradskyella in the microbiome of Ostreococcus tauri and thus stabilize the microalga persistence in the microcosm. Altogether, these results open novel perspectives into long-term stability of phytoplankton cultures.
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Affiliation(s)
- Sophie Vacant
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - L. Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Christophe Salmeron
- Sorbonne Université, Centre National de la Recherche Scientifique, Observatoire Océanologique de Banyuls, FR3724, Banyuls-sur-Mer, France
| | - Laurent Intertaglia
- Sorbonne Université, Centre National de la Recherche Scientifique, Observatoire Océanologique de Banyuls, FR3724, Banyuls-sur-Mer, France
| | - Manon Norest
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Adrien Cadoudal
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Frederic Sanchez
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Carlos Caceres
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
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Sex-linked deubiquitinase establishes uniparental transmission of chloroplast DNA. Nat Commun 2022; 13:1133. [PMID: 35241655 PMCID: PMC8894339 DOI: 10.1038/s41467-022-28807-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/09/2022] [Indexed: 12/26/2022] Open
Abstract
Most sexual organisms inherit organelles from one parent, commonly by excluding organelles from the smaller gametes. However, post-mating elimination of organelles derived from one gamete ensures uniparental inheritance, where the underlying mechanisms to distinguish organelles by their origin remain obscure. Mating in Chlamydomonas reinhardtii combines isomorphic plus and minus gametes, but chloroplast DNA from minus gametes is selectively degraded in zygotes. Here, we identify OTU2p (otubain protein 2), encoded in the plus mating-type locus MT+, as the protector of plus chloroplast. Otu2p is an otubain-like deubiquitinase, which prevents proteasome-mediated degradation of the preprotein translocase of the outer chloroplast membrane (TOC) during gametogenesis. Using OTU2p-knockouts and proteasome inhibitor treatment, we successfully redirect selective DNA degradation in chloroplasts with reduced TOC levels regardless of mating type, demonstrating that plus-specific Otu2p establishes uniparental chloroplast DNA inheritance. Our work documents that a sex-linked organelle quality control mechanism drives the uniparental organelle inheritance without dimorphic gametes. Most sexual organisms ensure that organelles are inherited from a single parent. Here, the authors describe OTU2p, a Chlamydomonas deubiquitinase that drives uniparental organelle inheritance without gametic dimorphism by preventing proteasome-mediated degradation exclusively in gametes of the plus mating type.
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Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.
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4
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Tanifuji G, Kamikawa R, Moore CE, Mills T, Onodera NT, Kashiyama Y, Archibald JM, Inagaki Y, Hashimoto T. Comparative Plastid Genomics of Cryptomonas Species Reveals Fine-Scale Genomic Responses to Loss of Photosynthesis. Genome Biol Evol 2020; 12:3926-3937. [PMID: 31922581 PMCID: PMC7058160 DOI: 10.1093/gbe/evaa001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2020] [Indexed: 01/20/2023] Open
Abstract
Loss of photosynthesis is a recurring theme in eukaryotic evolution. In organisms that have lost the ability to photosynthesize, nonphotosynthetic plastids are retained because they play essential roles in processes other than photosynthesis. The unicellular algal genus Cryptomonas contains both photosynthetic and nonphotosynthetic members, the latter having lost the ability to photosynthesize on at least three separate occasions. To elucidate the evolutionary processes underlying the loss of photosynthesis, we sequenced the plastid genomes of two nonphotosynthetic strains, Cryptomonas sp. CCAC1634B and SAG977-2f, as well as the genome of the phototroph Cryptomonas curvata CCAP979/52. These three genome sequences were compared with the previously sequenced plastid genome of the nonphotosynthetic species Cryptomonas paramecium CCAP977/2a as well as photosynthetic members of the Cryptomonadales, including C. curvata FBCC300012D. Intraspecies comparison between the two C. curvata strains showed that although their genome structures are stable, the substitution rates of their genes are relatively high. Although most photosynthesis-related genes, such as the psa and psb gene families, were found to have disappeared from the nonphotosynthetic strains, at least ten pseudogenes are retained in SAG977-2f. Although gene order is roughly shared among the plastid genomes of photosynthetic Cryptomonadales, genome rearrangements are seen more frequently in the smaller genomes of the nonphotosynthetic strains. Intriguingly, the light-independent protochlorophyllide reductase comprising chlB, L, and N is retained in nonphotosynthetic SAG977-2f and CCAC1634B. On the other hand, whereas CCAP977/2a retains ribulose-1,5-bisphosphate carboxylase/oxygenase-related genes, including rbcL, rbcS, and cbbX, the plastid genomes of the other two nonphotosynthetic strains have lost the ribulose-1,5-bisphosphate carboxylase/oxygenase protein-coding genes.
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Affiliation(s)
- Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Ibaraki, Japan
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Christa E Moore
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Tyler Mills
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Naoko T Onodera
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Yuichiro Kashiyama
- Department of Applied Chemistry and Food Science, Fukui University of Technology, Fukui, Japan
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Yuji Inagaki
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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Kariyawasam T, Joo S, Lee J, Toor D, Gao AF, Noh KC, Lee JH. TALE homeobox heterodimer GSM1/GSP1 is a molecular switch that prevents unwarranted genetic recombination in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:938-953. [PMID: 31368133 DOI: 10.1111/tpj.14486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Eukaryotic sexual life cycles alternate between haploid and diploid stages, the transitions between which are delineated by cell fusion and meiotic division. Transcription factors in the TALE-class homeobox family, GSM1 and GSP1, predominantly control gene expression for the haploid-to-diploid transition during sexual reproduction in the unicellular green alga, Chlamydomonas reinhardtii. To understand the roles that GSM1 and GSP1 play in zygote development, we used gsm1 and gsp1 mutants and examined fused gametes that normally undergo the multiple organellar fusions required for the genetic unity of the zygotes. In gsm1 and gsp1 zygotes, no fusion was observed for the nucleus and chloroplast. Surprisingly, mitochondria and endoplasmic reticulum, which undergo dynamic autologous fusion/fission, did not undergo heterologous fusions in gsm1 or gsp1 zygotes. Furthermore, the mutants failed to resorb their flagella, an event that normally renders the zygotes immotile. When gsm1 and gsp1 zygotes resumed the mitotic cycle, their two nuclei fused prior to mitosis, but neither chloroplastic nor mitochondrial fusion took place, suggesting that these fusions are specifically turned on by GSM1/GSP1. Taken together, this study shows that organellar restructuring during zygotic diploidization does not occur by default but is triggered by a combinatorial switch, the GSM1/GSP1 dyad. This switch may represent an ancient mechanism that evolved to restrict genetic recombination during sexual development.
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Affiliation(s)
| | - Sunjoo Joo
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jenny Lee
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Deepak Toor
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Ally F Gao
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Kyung-Chul Noh
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, Vancouver, Canada
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6
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Benites LF, Poulton N, Labadie K, Sieracki ME, Grimsley N, Piganeau G. Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190089. [PMID: 31587637 DOI: 10.1098/rstb.2019.0089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and Micromonas, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their in situ ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four Ostreococcus SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- L Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique, université Paris Saclay, 9105 Evry, France
| | | | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
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7
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Turmel M, Lopes Dos Santos A, Otis C, Sergerie R, Lemieux C. Tracing the Evolution of the Plastome and Mitogenome in the Chloropicophyceae Uncovered Convergent tRNA Gene Losses and a Variant Plastid Genetic Code. Genome Biol Evol 2019; 11:1275-1292. [PMID: 30937436 PMCID: PMC6486808 DOI: 10.1093/gbe/evz074] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2019] [Indexed: 01/06/2023] Open
Abstract
The tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (Chloropicon and Chloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with the trnI(cau) and trnL(uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance of trnI(cau) from the plastome in the Chloroparvula lineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine in Chloroparvula. This noncanonical genetic code has not previously been uncovered in plastids.
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Affiliation(s)
- Monique Turmel
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | - Adriana Lopes Dos Santos
- Asian School of the Environment, Nanyang Technological University, Singapore.,CNRS, Sorbonne Université, UMR 7144 Station Biologique de Roscoff, Roscoff, France
| | - Christian Otis
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | - Roxanne Sergerie
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | - Claude Lemieux
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
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8
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Blanc-Mathieu R, Krasovec M, Hebrard M, Yau S, Desgranges E, Martin J, Schackwitz W, Kuo A, Salin G, Donnadieu C, Desdevises Y, Sanchez-Ferandin S, Moreau H, Rivals E, Grigoriev IV, Grimsley N, Eyre-Walker A, Piganeau G. Population genomics of picophytoplankton unveils novel chromosome hypervariability. SCIENCE ADVANCES 2017; 3:e1700239. [PMID: 28695208 PMCID: PMC5498103 DOI: 10.1126/sciadv.1700239] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/25/2017] [Indexed: 05/18/2023]
Abstract
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 107) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes.
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Affiliation(s)
- Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marc Krasovec
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Maxime Hebrard
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, CNRS, and Université de Montpellier, 161 rue Ada, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, CNRS, and Université de Montpellier, 860 rue Saint Priest, 34095 Montpellier Cedex 5, France
| | - Sheree Yau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Elodie Desgranges
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Joel Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wendy Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerald Salin
- INRA, plateforme Génome et Transcriptome (GeT-PlaGe), GenoToul, Castanet-Tolosan, France
| | - Cecile Donnadieu
- INRA, plateforme Génome et Transcriptome (GeT-PlaGe), GenoToul, Castanet-Tolosan, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Sophie Sanchez-Ferandin
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Hervé Moreau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Eric Rivals
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, CNRS, and Université de Montpellier, 161 rue Ada, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, CNRS, and Université de Montpellier, 860 rue Saint Priest, 34095 Montpellier Cedex 5, France
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - Nigel Grimsley
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Gwenael Piganeau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
- Corresponding author.
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9
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Satjarak A, Burns JA, Kim E, Graham LE. Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis. JOURNAL OF PHYCOLOGY 2017; 53:601-615. [PMID: 28191642 DOI: 10.1111/jpy.12521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Mitochondria are archetypal eukaryotic organelles that were acquired by endosymbiosis of an ancient species of alpha-proteobacteria by the last eukaryotic common ancestor. The genetic information contained within the mitochondrial genome has been an important source of information for resolving relationships among eukaryotic taxa. In this study, we utilized mitochondrial and chloroplast genomes to explore relationships among prasinophytes. Prasinophytes are represented by diverse early-diverging green algae whose physical structures and genomes have the potential to elucidate the traits of the last common ancestor of the Viridiplantae (or Chloroplastida). We constructed de novo mitochondrial genomes for two prasinophyte algal species, Pyramimonas parkeae and Cymbomonas tetramitiformis, representing the prasinophyte clade. Comparisons of genome structure and gene order between these species and to those of other prasinophytes revealed that the mitochondrial genomes of P. parkeae and C. tetramitiformis are more similar to each other than to other prasinophytes, consistent with other molecular inferences of the close relationship between these two species. Phylogenetic analyses using the inferred amino acid sequences of mitochondrial and chloroplast protein-coding genes resolved a clade consisting of P. parkeae and C. tetramitiformis; and this group (representing the prasinophyte clade I) branched with the clade II, consistent with previous studies based on the use of nuclear gene markers.
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Affiliation(s)
- Anchittha Satjarak
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln drive, Madison, Wisconsin, USA
| | - John A Burns
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York, USA
| | - Eunsoo Kim
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York, USA
| | - Linda E Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln drive, Madison, Wisconsin, USA
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10
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Satjarak A, Graham LE. Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes. JOURNAL OF PHYCOLOGY 2017; 53:415-424. [PMID: 28130930 DOI: 10.1111/jpy.12515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/13/2016] [Indexed: 06/06/2023]
Abstract
Prasinophytes form a paraphyletic assemblage of early diverging green algae, which have the potential to reveal the traits of the last common ancestor of the main two green lineages: (i) chlorophyte algae and (ii) streptophyte algae. Understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary processes that may have occurred in both green lineages. In this study, we sequenced the chloroplast genome of Pyramimonas parkeae NIES254 and compared it with that of P. parkeae CCMP726, the only other fully sequenced P. parkeae chloroplast genome. The results revealed that P. parkeae chloroplast genomes are surprisingly variable. The chloroplast genome of NIES254 was larger than that of CCMP726 by 3,204 bp, the NIES254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and the IR was 1,086 bp shorter than that of CCMP726. Similarity values of the two strains were almost zero in four large hot spot regions. Finally, the strains differed in copy number for three protein-coding genes: ycf20, psaC, and ndhE. Phylogenetic analyses using 16S and 18S rDNA and rbcL sequences resolved a clade consisting of these two P. parkeae strains and a clade consisting of these plus other Pyramimonas isolates. These results are consistent with past studies indicating that prasinophyte chloroplast genomes display a higher level of variation than is commonly found among land plants. Consequently, prasinophyte chloroplast genomes may be less useful for inferring the early history of Viridiplantae than has been the case for land plant diversification.
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Affiliation(s)
- Anchittha Satjarak
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA
| | - Linda E Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA
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11
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Hirth M, Liverani S, Mahlow S, Bouget FY, Pohnert G, Sasso S. Metabolic profiling identifies trehalose as an abundant and diurnally fluctuating metabolite in the microalga Ostreococcus tauri. Metabolomics 2017; 13:68. [PMID: 28473745 PMCID: PMC5392535 DOI: 10.1007/s11306-017-1203-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The picoeukaryotic alga Ostreococcus tauri (Chlorophyta) belongs to the widespread group of marine prasinophytes. Despite its ecological importance, little is known about the metabolism of this alga. OBJECTIVES In this work, changes in the metabolome were quantified when O. tauri was grown under alternating cycles of 12 h light and 12 h darkness. METHODS Algal metabolism was analyzed by gas chromatography-mass spectrometry. Using fluorescence-activated cell sorting, the bacteria associated with O. tauri were depleted to below 0.1% of total cells at the time of metabolic profiling. RESULTS Of 111 metabolites quantified over light-dark cycles, 20 (18%) showed clear diurnal variations. The strongest fluctuations were found for trehalose. With an intracellular concentration of 1.6 mM in the dark, this disaccharide was six times more abundant at night than during the day. This fluctuation pattern of trehalose may be a consequence of starch degradation or of the synchronized cell cycle. On the other hand, maltose (and also sucrose) was below the detection limit (~10 μM). Accumulation of glycine in the light is in agreement with the presence of a classical glycolate pathway of photorespiration. We also provide evidence for the presence of fatty acid methyl and ethyl esters in O. tauri. CONCLUSIONS This study shows how the metabolism of O. tauri adapts to day and night and gives new insights into the configuration of the carbon metabolism. In addition, several less common metabolites were identified.
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Affiliation(s)
- Matthias Hirth
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - Silvia Liverani
- 0000 0001 0724 6933grid.7728.aDepartment of Mathematics, Brunel University London, Uxbridge, UK
| | - Sebastian Mahlow
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - François-Yves Bouget
- 0000 0001 2369 4306grid.463752.1Sorbonne Universités, UPMC Univ Paris 06 & Centre National pour la Recherche Scientifique CNRS, UMR 7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Georg Pohnert
- 0000 0001 1939 2794grid.9613.dInstitute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- 0000 0004 0491 7131grid.418160.aMax Planck Institute for Chemical Ecology, Jena, Germany
| | - Severin Sasso
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
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12
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Smith DR. The mutational hazard hypothesis of organelle genome evolution: 10 years on. Mol Ecol 2016; 25:3769-75. [PMID: 27357487 DOI: 10.1111/mec.13742] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/14/2016] [Accepted: 06/22/2016] [Indexed: 12/12/2022]
Abstract
Why is there such a large variation in size and noncoding DNA content among organelle genomes? One explanation is that this genomic variation results from differences in the rates of organelle mutation and random genetic drift, as opposed to being the direct product of natural selection. Along these lines, the mutational hazard hypothesis (MHH) holds that 'excess' DNA is a mutational liability (because it increases the potential for harmful mutations) and, thus, has a greater tendency to accumulate in an organelle system with a low mutation rate as opposed to one with a high rate of mutation. Various studies have explored this hypothesis and, more generally, the relationship between organelle genome architecture and the mode and efficiency of organelle DNA repair. Although some of these investigations are in agreement with the MHH, others have contradicted it; nevertheless, they support a central role of mutation, DNA maintenance pathways and random genetic drift in fashioning organelle chromosomes. Arguably, one of the most important contributions of the MHH is that it has sparked crucial, widespread discussions about the importance of nonadaptive processes in genome evolution.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
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13
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Gao Y, Li MY, Zhao J, Zhang YC, Xie QJ, Chen DH. Genome-wide analysis of RING finger proteins in the smallest free-living photosynthetic eukaryote Ostreococus tauri. Mar Genomics 2015; 26:51-61. [PMID: 26751716 DOI: 10.1016/j.margen.2015.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022]
Abstract
RING finger proteins and ubiquitination marks are widely involved in diverse aspects of growth and development, biological processes, and stress or environmental responses. As the smallest free-living photosynthetic eukaryote known so far, the green alga Ostreococus tauri has become an excellent model for investigating the origin of different gene families in the green lineage. Here, 65 RING domains in 65 predicted proteins were identified from O. tauri and on the basis of one or more substitutions at the metal ligand positions and spacing between them they were divided into eight canonical or modified types (RING-CH, -H2, -v, -C2, -C3HCHC2, -C2HC5, -C3GC3S, and -C2SHC4), in which the latter four were newly identified and might represent the intermediate states between RING domain and other similar domains, respectively. RING finger proteins were classified into eight classes based on the presence of additional domains, including RING-Only, -Plus, -C3H1, -PHD, -WD40, -PEX, -TM, and -DEXDc classes. These RING family genes usually lack introns and are distributed over 17 chromosomes. In addition, 29 RING-finger proteins in O. tauri share different degrees of homology with those in the model flowering plant Arabidopsis, indicating they might be necessary for the basic survival of free-living eukaryotes. Therefore, our results provide new insight into the general classification and evolutionary conservation of RING domain-containing proteins in O. tauri.
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Affiliation(s)
- Yan Gao
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Ming-Yi Li
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Jing Zhao
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Yan-Cui Zhang
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Qiu-Jiao Xie
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Dong-Hong Chen
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China; College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, Changsha 410128, China.
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14
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D'Alelio D, Ruggiero MV. Interspecific plastidial recombination in the diatom genus Pseudo-nitzschia. JOURNAL OF PHYCOLOGY 2015; 51:1024-1028. [PMID: 26986997 DOI: 10.1111/jpy.12350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Abstract
Plastids are usually uni-parentally inherited and genetic recombination between these organelles is seldom observed. The genus Pseudo-nitzschia, a globally relevant marine diatom, features bi-parental plastid inheritance in the course of sexual reproduction. This observation inspired the recombination detection we pursued in this paper over a ~1,400-nucleotide-long region of the plastidial rbcL, a marker used in both molecular taxonomy and phylogenetic studies in diatoms. Among all the rbcL-sequences available in web-databases for Pseudo-nitzschia, 42 haplotypes were identified and grouped in five clusters by Bayesian phylogeny. Signs of hybridization were evident in four of five clusters, at both intra- and interspecific levels, suggesting that, in diatoms, (i) plastidial recombination is not absent and (ii) hybridization can play a role in speciation of Pseudo-nitzschia spp.
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Affiliation(s)
- Domenico D'Alelio
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, I-80121, Italy
| | - Maria Valeria Ruggiero
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, I-80121, Italy
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15
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Raven JA. Implications of mutation of organelle genomes for organelle function and evolution. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5639-50. [PMID: 26077836 DOI: 10.1093/jxb/erv298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK †School of Plant Biology, University of Western Australia, M048, 35 Stirling Highway, Crawley, WA 6009, Australia
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16
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Speijer D, Lukeš J, Eliáš M. Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life. Proc Natl Acad Sci U S A 2015; 112:8827-34. [PMID: 26195746 PMCID: PMC4517231 DOI: 10.1073/pnas.1501725112] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to protists. We present results of phylogenetically extended searches for homologs of two proteins functioning in cell and nuclear fusion, respectively (HAP2 and GEX1), providing indirect evidence for these processes in several eukaryotic lineages where sex has not been observed yet. We argue that (i) the debate on the relative significance of sex and clonality in eukaryotes is confounded by not appropriately distinguishing multicellular and unicellular organisms; (ii) eukaryotic sex is extremely widespread and already present in the last eukaryotic common ancestor; and (iii) the general mode of existence of eukaryotes is best described by clonally propagating cell lines with episodic sex triggered by external or internal clues. However, important questions concern the relative longevity of true clonal species (i.e., species not able to return to sexual procreation anymore). Long-lived clonal species seem strikingly rare. We analyze their properties in the light of meiotic sex development from existing prokaryotic repair mechanisms. Based on these considerations, we speculate that eukaryotic sex likely developed as a cellular survival strategy, possibly in the context of internal reactive oxygen species stress generated by a (proto) mitochondrion. Thus, in the context of the symbiogenic model of eukaryotic origin, sex might directly result from the very evolutionary mode by which eukaryotic cells arose.
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Affiliation(s)
- Dave Speijer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands;
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice, Czech Republic; Canadian Institute for Advanced Research, Toronto, ON, Canada M5G 1Z8
| | - Marek Eliáš
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
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17
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Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carré I, Château A, Eyre-Walker A, Grimsley N, Moreau H, Piégu B, Rivals E, Schackwitz W, Van de Peer Y, Piganeau G. An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics 2014; 15:1103. [PMID: 25494611 PMCID: PMC4378021 DOI: 10.1186/1471-2164-15-1103] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/19/2014] [Indexed: 12/17/2022] Open
Abstract
Background Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gwenaël Piganeau
- CNRS, UMR 7232, Observatoire Océanologique, Avenue du Fontaulé, BP44, 66650 Banyuls-sur-Mer, France.
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Abby SS, Touchon M, De Jode A, Grimsley N, Piganeau G. Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers? Front Microbiol 2014; 5:505. [PMID: 25426102 PMCID: PMC4224133 DOI: 10.3389/fmicb.2014.00505] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/08/2014] [Indexed: 11/13/2022] Open
Abstract
Marine phytoplankton produce half of the oxygen we breathe and their astounding diversity is just starting to be unraveled. Many microbial phytoplankton are thought to be phototrophic, depending solely on inorganic sources of carbon and minerals for growth rather than preying on other planktonic cells. However, there is increasing evidence that symbiotic associations, to a large extent with bacteria, are required for vitamin or nutrient uptake for many eukaryotic microalgae. Here, we use in silico approaches to look for putative symbiotic interactions by analysing the gene content of microbial communities associated with 13 different Ostreococcus tauri (Chlorophyta, Mamilleophyceae) cultures sampled from the Mediterranean Sea. While we find evidence for bacteria in all cultures, there is no ubiquitous bacterial group, and the most prevalent group, Flavobacteria, is present in 10 out of 13 cultures. Among seven of the microbiomes, we detected genes predicted to encode type 3 secretion systems (T3SS, in 6/7 microbiomes) and/or putative type 6 secretion systems (T6SS, in 4/7 microbiomes). Phylogenetic analyses show that the corresponding genes are closely related to genes of systems identified in bacterial-plant interactions, suggesting that these T3SS might be involved in cell-to-cell interactions with O. tauri.
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Affiliation(s)
- Sophie S Abby
- Institut Pasteur, Microbial Evolutionary Genomics Paris, France ; CNRS, UMR 3525 Paris, France
| | - Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics Paris, France ; CNRS, UMR 3525 Paris, France
| | - Aurelien De Jode
- CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique Banyuls-sur-Mer, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Nigel Grimsley
- CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique Banyuls-sur-Mer, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique Banyuls-sur-Mer, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
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