Picoeukaryotic sequences in the Sargasso Sea metagenome

Many sequences from picoeukaryotes were found in DNA sequence data assembled from Sargasso seawater

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

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

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

Background: Bathycoccus prasinos is an extremely small cosmopolitan marine green alga whose cells are covered with intricate spider's web patterned scales that develop within the Golgi cisternae before their transport to the cell surface. The objective of this work is to sequence and analyze its genome, and to present a comparative analysis with other known genomes of the green lineage. Research: Its small genome of 15 Mb consists of 19 chromosomes and lacks transposons. Although 70% of all B. prasinos genes share similarities with other Viridiplantae genes, up to 428 genes were probably acquired by horizontal gene transfer, mainly from other eukaryotes. Two chromosomes, one big and one small, are atypical, an unusual synapomorphic feature within the Mamiellales. Genes on these atypical outlier chromosomes show lower GC content and a significant fraction of putative horizontal gene transfer genes. Whereas the small outlier chromosome lacks colinearity with other Mamiellales and contains many unknown genes without homologs in other species, the big outlier shows a higher intron content, increased expression levels and a unique clustering pattern of housekeeping functionalities. Four gene families are highly expanded in B. prasinos, including sialyltransferases, sialidases, ankyrin repeats and zinc ion-binding genes, and we hypothesize that these genes are associated with the process of scale biogenesis. Conclusion: The minimal genomes of the Mamiellophyceae provide a baseline for evolutionary and functional analyses of metabolic processes in green plants

Life-Cycle and Genome of OtV5, a Large DNA Virus of the Pelagic Marine Unicellular Green Alga Ostreococcus tauri

Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon

Systematic Deletion of Homeobox Genes in Podospora anserina Uncovers Their Roles in Shaping the Fruiting Body

Higher fungi, which comprise ascomycetes and basidiomycetes, play major roles in the biosphere. Their evolutionary success may be due to the extended dikaryotic stage of their life cycle, which is the basis for their scientific name: the Dikarya. Dikaryosis is maintained by similar structures, the clamp in basidiomycetes and the crozier in ascomycetes. Homeodomain transcription factors are required for clamp formation in all basidiomycetes studied. We identified all the homeobox genes in the filamentous ascomycete fungus Podospora anserina and constructed deletion mutants for each of these genes and for a number of gene combinations. Croziers developed normally in these mutants, including those with up to six deleted homeogenes. However, some mutants had defects in maturation of the fruiting body, an effect that could be rescued by providing wild-type maternal hyphae. Analysis of mutants deficient in multiple homeogenes revealed interactions between the genes, suggesting that they operate as a complex network. Similar to their role in animals and plants, homeodomain transcription factors in ascomycetes are involved in shaping multicellular structures

Etude des proteines specifiques de la reproduction chez le crustace decapode Macrobrachium rosenbergi a l'aide des anticorps monoclonaux

SIGLECNRS TD Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Evolution of a relationship: how Ostreococcus tauri viruses circumvent host resistance

Marine microeukaryotes battle every day with environmental pressures, predators and viruses to survive. To escape and survive certain threats they often have to change their life cycle stage for the cost of a lower growth rate. Marine viruses are ubiquitous in the oceans but they are unable to replicate without infecting host cells. Therefore they have to evolve as quickly as their host and change their infection strategy. Spontaneous resistance of the green microalgae Ostreococcus tauri occurs in culture once it is infected with the virus OtV5. Two newly isolated viruses were able to lyse these OtV5-resistant O. tauri cells. While o could only lyse OtV5-resistant cells, OtV15 was able to lyse both OtV5-susceptible and –resistant cells. Similar as the O. lucimarinus viruses, their genomes have a high level of synteny with 182 orthologous genes, reduced to 173 when including OtV1 and OtV2. We will discuss potential infection strategies based upon their specific genes. High-throughput sequencing projects like the Ocean Sampling Day and Tara Oceans Expedition enable us to monitor O. tauri and its viruses around the world

AT frequency distribution in the 128 eukaryotic SSD scaffolds retrieved (white bars) versus AT frequency distribution in the total SSD scaffolds (black bars)

<p><b>Copyright information:</b></p><p>Taken from "Picoeukaryotic sequences in the Sargasso Sea metagenome"</p><p>http://genomebiology.com/2008/9/1/R5</p><p>Genome Biology 2008;9(1):R5-R5.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2395239.</p><p></p

Phylogenetic position of the SSD -like sequence as inferred from the 18S rRNA sequences in 30

Outgroup sequence, ; OT95, (clade C); RCC356, RCC344 and MIC106, surface strains (clade A); RCC393 and RCC143, deep strains (clade B); RCC501, surface strain (clade D). Numbers on branches are support values (posterior probability).<p><b>Copyright information:</b></p><p>Taken from "Picoeukaryotic sequences in the Sargasso Sea metagenome"</p><p>http://genomebiology.com/2008/9/1/R5</p><p>Genome Biology 2008;9(1):R5-R5.</p><p>Published online 7 Jan 2008</p><p>PMCID:PMC2395239.</p><p></p