Premature stop codon in a cavefish sequence.

<p>A: Alignment of surface fish and Pachón cavefish nucleotide sequences of the si:ch211–210c8.6 transcript. B: Alignment of surface, Pachón and zebrafish translated protein sequences.</p

Types of polymorphism uncovered in the surface fish and cavefish transcriptomes.

<p>A: Number of polymorphic positions in the nucleotidic sequences of the two Astyanax morphs. B: Number of fixed nucleotide differences, shared polymorphisms and divergent polymorphisms.</p

Analysis of expression patterns for transcripts with radical mutations.

<p>2 genes contain 2 mutations, one that occurred in cavefish lineage, the other in surface fish lineage: these two genes are thus counted twice in this table.</p

Overrepresented gene ontologies in Astyanax proteins with surface fish/cave fish substitutions (A), radical substitutions (B) or specifically with radical mutations in cavefish (C).

<p>GO terms are ordered by p-value. GO terms represented only once are not shown here.</p

Composition and quality of the Astyanax cDNA libraries.

<p>A: Composition of the 8 Astyanax developmental cDNA libraries. Biological process (B) and molecular function (C) gene ontology pie charts of the 17,152 contigs annotated for GO term.</p

Ln-transformed expression levels of poplar transcripts.

<p>(A) Venn-diagram of expressed poplar transcripts measured by whole-genome oligoarray and RNA-Seq. Numbers in brackets correspond to the percentage of the coding genome; numbers in parentheses correspond to the highly expressed (HE) transcripts and numbers in parentheses and in bold correspond to HE transcripts validated by oligoarrays (i.e. VHE transcripts). (B) RNA-Seq and oligoarrays average expression levels correlation. The black rectangle indicates the area containing the 1,794 VHE transcripts discussed in the text.</p

Similarity between <i>B. prasinos</i> RCC1105 genome and T142 and T149 assemblies for the three larger chromosomes.

<p>Only regions with coverage in excess 10× for both samples were considered. Total genome and non-CDS regions were analyzed separately (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039648#s4" target="_blank">Material and Methods</a> for details).</p

Summary of 454-pyrosequencing transcriptome data from poplar leaves infected by <i>M. larici-populina.</i>

a<p>Number of poplar transcripts expressed in all conditions.</p>b<p>Number of poplar transcripts with an average number of 10 reads (i.e. a total of 60 reads in the 6 conditions).</p>c<p>Normalised number of reads per conditions used for quantitative analysis is 102,813 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044408#pone.0044408.s011" target="_blank">Table S1</a>).</p

Chromosomal location of genes differentially expressed between reproductive morphs.

<p>Frequency of X-linkage for genes with different rate of expression among males, sexual females and asexual females. Genes were classified according to their pattern of expression (M, F and A stand for male, sexual female and asexual female, respectively, and the sign represents relative expression in each morph) considering different minimal fold-change in expression between reproductive morphs (2-, 5- and 10-fold). The black line shows the expected frequency of X-linkage (based on genes supported by at least 5 reads over the eight libraries). Significance for deviation from the random expectation was calculated with Chi2-tests (* : <i>p</i><0.05, **: p<0.01, *** : <i>p</i><0.001). Theoretical predictions for the preferred genomic location of these different classes of genes (derived under the hypothesis that the evolution of sex-biased gene expression to restrict the product of a sexually antagonistic allele to the sex it benefits might solve intra-locus sexual conflicts) are shown on the top of the figure.</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