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

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

A Viral Immunity Chromosome in the Marine Picoeukaryote, <i>Ostreococcus tauri</i>

<div><p>Micro-algae of the genus <i>Ostreococcus</i> and related species of the order Mamiellales are globally distributed in the photic zone of world's oceans where they contribute to fixation of atmospheric carbon and production of oxygen, besides providing a primary source of nutrition in the food web. Their tiny size, simple cells, ease of culture, compact genomes and susceptibility to the most abundant large DNA viruses in the sea render them attractive as models for integrative marine biology. In culture, spontaneous resistance to viruses occurs frequently. Here, we show that virus-producing resistant cell lines arise in many independent cell lines during lytic infections, but over two years, more and more of these lines stop producing viruses. We observed sweeping over-expression of all genes in more than half of chromosome 19 in resistant lines, and karyotypic analyses showed physical rearrangements of this chromosome. Chromosome 19 has an unusual genetic structure whose equivalent is found in all of the sequenced genomes in this ecologically important group of green algae.</p></div

Experimental strategy for production of <i>Ostreococcus tauri</i> clonal lines susceptible or resistant to OtV5.

<p>A single colony of <i>O</i>. <i>tauri</i> was used to produce two 1-litre cultures of <i>O</i>. <i>tauri</i> cells, one used to prepare DNA for genome re-sequencing and to produce 46 independent clonal lines and another that was lysed by clonal OtV5. The viral lysate was subsequently used to inoculate 38 small flasks. Fresh medium (small blue flasks) was added to each lysate or control flask, and after ~1 week OtV5-resistant cells grew. A single colony from all lines was randomly chosen after plating and maintained in liquid culture for transcriptome sequencing and further analyses.</p

Proportion of resistant producer (RP) and resistant non-producer (RNP) lines over the course of the study.

<p>Percentage of RP and RNP in resistant lines on the ordinate and date when virus production test was performed on the abscissa.</p

Pulsed-field gel electrophoresis (PFGE) analysis of susceptible and resistant lines ethidium bromide stained (top) and corresponding hybridization (bottom) using a probe for a gene on chromosome 19.

<p>Chromosome number and size are indicated on the left. Symbols on the upper gel images show, at positions observed by the ethidium-bromide fluorescence: <b>−</b> : absence of a band that was present in controls, <b>+</b>: presence of a band that was not present in controls, <b>v</b>: presence of a band at the expected size of the OtV5 genome. To aid the comparison, symbols from the upper images of ethidium-stained gels are shown at the same positions on the bottom Southern blot autoradiograph images. Note that since the probe hybridizes to a specific part of chromosome 19, occasionally the band of differing mobility does not correspond to the band identified by radioactive labelling, witnessing fragmentation of chromosome 19 after deletions, insertions, or translocations that may have occurred.</p

Virus production in two <i>O</i>. <i>tauri</i> resistant strains.

<p>Very few cells (less than 0.5%) show visible viral particles in their cytoplasm. Morphology of lysing R^P cells is similar to that of susceptible cells. <b>(A)</b> Most of the cells of <i>O</i>. <i>tauri</i> R^P2 strain without visible viral particles. (<b>B)</b> Dividing <i>O</i>. <i>tauri</i> R^P2 strain cell. <b>(C)</b> Dividing <i>O</i>. <i>tauri</i> R^P3 strain cell with visible intracellular viral particles (vi). <b>(D)</b> <i>O</i>. <i>tauri</i> R^P3 strain cell with visible intracellular viral particles (vi). <b>E</b>. Lysis of an <i>O</i>. <i>tauri</i> R^P3 strain cell. <b>(F)</b> Lysis of an <i>O</i>. <i>tauri</i> R^P2 strain with visible viral particles (vi). The scale bar is 500 nm long.</p

Differential gene expression in OtV5-resistant compared to susceptible control <i>O</i>. <i>tauri</i>.

<p>Up (orange) and Down (purple) regulated genes in virus resistant lines. <b>(A)</b> Counts of differentially transcribed genes per chromosome. <b>(B)</b> Plot of the log₂ fold change values of differentially transcribed genes per chromosome. <b>(C)</b> Predicted glycosyltransferase gene counts per chromosome based on matches to InterPro domains and families associated with glycosyltransferases. Genes with no difference in regulation are shown in grey. <b>(D)</b> Counts of differentially transcribed genes grouped according to functional categories shown on the ordinate. Labels describe the genes in each category (full gene descriptions in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005965#ppat.1005965.s008" target="_blank">S2</a> and <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005965#ppat.1005965.s010" target="_blank">S4</a> Tables). Genes located on the large inverted duplicated region on chromosome 19 were only counted once.</p

Genotypes observed for <i>B. prasinos</i> RCC1105 gene Bathy02g01050 (pigment synthesis protein, BOGAS annotation code) for samples T142 (left) and T149 (right).

<p>At least two different sequences appear to be present in both samples, differing by one and three positions, respectively, from the reference <i>B.prasinos</i> RCC 1105 sequence. Only 23 representative reads are shown for each sample although more reads covered this region (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039648#pone.0039648.s010" target="_blank">Table S6</a>).</p

Assembly of metagenomic reads obtained from flow cytometry sorted picoeukaryote samples T142 and T149 from the Chile upwelling to <i>Bathycoccus prasinos</i> RCC1105 genome.

<p>(A) Relationship between average coverage fraction (expressed as % of the length of the chromosome covered by at least one read) and GC content for samples T142 and T149 for the 21 draft nuclear chromosomes of <i>B. prasinos</i> RCC1105 as well as the mitochondrion and plastid genomes. (B) Idem for average coverage depth (number of reads at each position).</p