EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes, PLoS One

Abstract Background: The genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution

Establishment of endolithic populations of extremophilic Cyanidiales (Rhodophyta

Abstract Background: Cyanidiales are unicellular extremophilic red algae that inhabit acidic and high temperature sites around hot springs and have also adapted to life in endolithic and interlithic habitats. Comparative genomic analysis of Cyanidioschyzon merolae and Galdieria sulphuraria predicts that the latter may be more broadly distributed in extreme environments because its genome contains membrane transporters involved in the uptake of reduced carbon compounds that are absent from C. merolae. Analysis of an endolithic site in the Phlegrean Fields near Naples, Italy is consistent with this prediction showing this population to be comprised solely of the newly described lineage Galdieria-B and C. merolae to be limited to humid habitats. Here, we conducted an environmental PCR survey of another extreme environment in Tuscany, Italy and contrasted Cyanidiales population structure at endolithic and interlithic habitats in Naples and Tuscany

EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes

Background: The genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution. Methodology/Principal Findings: Here we studied intron features and levels of expression in O. lucimarinus using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the O. lucimarinus Build 2.0 assembly using BLAST and the level of gene expression was inferred from the number of ESTs in each cluster. We find a positive correlation between expression levels and both intron number (R = +0.0893, p =,0.0005) and intron density (number of introns/kb of CDS; R = +0.0753, p =,0.005). Conclusions/Significance: In a species with a genome that has been recently subjected to a great reduction of non-coding DNA, these results imply the existence of selective/functional roles for introns that are principally detectable in highly expressed genes. In these cases, introns are likely maintained by balancing the selective forces favoring their maintenanc

Background selection as baseline for nucleotide variation across the Drosophila genome.

The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across the Drosophila melanogaster genome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms at 100-kb scale, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps between Drosophila species, suggest temporally variable recombination landscapes and, thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and selective events, future analyses should incorporate BGS predictions and capture local recombination variation across genomes and along lineages

Relationship between estimates of <i>B</i> and π_sil.

<p>(A) Relationship between estimates of <i>B</i> and π_sil for 100-kb autosomal regions. Spearman's <i>ρ = </i>0.770 (1,189 regions, <i>P</i><1×10⁻¹²). (B) Relationship between estimates of <i>B</i> and π_sil for 10-kb autosomal regions. Spearman's <i>ρ = </i>0.678 (8,883 regions, <i>P</i><1×10⁻¹²). Dark blue and red diamonds indicate regions with π_sil significantly different (higher or lower) than predicted based on residual analysis: dark blue (<i>P</i><0.01), red (FDR-corrected <i>q</i><0.10). Results shown for the default model M_{LN,StdMut,CO+GC}.</p

Estimates of <i>α</i> due to temporally fluctuating recombination rates and variable BGS effects.

<p>Results based on forward population genetic simulations of 10,000 diploid individuals (<i>N</i>), a chromosome segment of 1 Mb containing 100 genes, and two types of mutations: neutral and deleterious (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004434#s4" target="_blank">Materials and Methods</a> for details). Cycles of fluctuating recombination followed phases of moderately high recombination for 1<i>N</i> generations (<i>H</i>_rec phase) and moderately low recombination for 3<i>N</i> generations (<i>L</i>_rec phase). Estimates of <i>α</i> at negatively selected sites obtained following the models proposed by Eyre-Walker and Keightley <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004434#pgen.1004434-EyreWalker2" target="_blank">[91]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004434#pgen.1004434-Keightley3" target="_blank">[95]</a> every 0.1<i>N</i> generations. Blue and red lines indicate estimates of <i>α</i> assuming constant population size and variable population sizes, respectively. Continuous and dashed lines indicate estimates of <i>α</i> with and without correction for the effect of polymorphism to divergence, respectively.</p

Correlation coefficients between estimates of <i>B</i> and rates of protein evolution (<i>ω</i>_R).

<p>Rates of protein evolution (<i>ω</i>_R) were obtained after controlling for selection on synonymous mutations based on residual analysis (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004434#s4" target="_blank">Materials and Methods</a> for details). Spearman's rank correlation coefficients (<i>ρ</i>) are shown between <i>B</i> and <i>ω</i>_R for individual genes and for the average <i>B</i> and <i>ω</i>_R for all genes within 100-kb non-overlapping regions.</p

Correlation coefficients between estimates of <i>B</i> and levels of polymorphism at noncoding sites (π_sil).

<p>Spearman's rank correlation coefficients (<i>ρ</i>) based on the analysis of 100-, 10- and 1-kb non-overlapping regions are shown above columns (<i>P</i><1×10⁻¹² in all cases) and the number of regions analyzed is shown within columns. Results shown for the default model M_{LN,StdMut,CO+GC}.</p

High-resolution distribution of BGS effects across the <i>D. melanogaster</i> genome.

<p>Estimates of BGS effects are measured as <i>B</i> and shown along each chromosome arm for 100-kb adjacent windows. Red and blue lines depict estimates of <i>B</i> based on models M_{LN,StdMut,CO+GC} (M_CO+GC) and M_LN,StdMut,CO (M_CO), respectively. Grey dashed lines show the distribution of crossover rates (<i>c</i>), measured as centimorgans (cM) per megabase (Mb) per female meiosis (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004434#pgen.1004434-Comeron1" target="_blank">[31]</a> for details).</p

Genome-wide estimates of BGS.

<p>(A) Boxplots of estimates of <i>B</i> for complete or trimmed chromosomes and for models M_{LN,StdMut,CO+GC} (M_CO+GC) and M_LN,StdMut,CO (M_CO). Results shown for the complete genome, and autosomes and the X chromosome separately. The median is identified by the line inside the box, the length of the box and whiskers indicate 50% and 90% CI, respectively. (B) Frequency distribution of <i>B</i> estimates for complete or trimmed chromosomes under model M_{LN,StdMut,CO+GC}. All results based on the analysis of 1-kb non-overlapping regions.</p