Abstract
BackgroundThe 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 FindingsHere 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/SignificanceIn 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 maintenance with other mutational and/or selective forces acting on genome size.
Highlights
The genus Ostreococcus encompasses a group of globally distributed photosynthetic, unicellular green algae in the anciently diverged class Prasinophyta [1]
Attempts to model the evolution of genome size typically involve a tendency for the mutational process of small insertions and deletions to be biased towards deletions that progressively eliminate nonessential portions of the genome
Differences in deletion bias alone cannot account for the ratios of genome sizes and retention of non-coding sequence in all instances because these phenomena have been shown to not always correlate with observed patterns in genome size. This in turn suggests that genome sizes evolve out of a combination of mutational biases, neutral drift, and selection [21,22,23]
Summary
The genus Ostreococcus encompasses a group of globally distributed photosynthetic, unicellular green algae in the anciently diverged class Prasinophyta [1]. In comparison to the compact genome of Saccharomyces cerevisiae (12.1 Mbp) that contains ,6000 open reading frames, with one gene every 2.0 kb, O. tauri and O. lucimarinus have genomes sizes of 12.6 and 13.2 Mbp with a gene occurring every 1.6 and 1.7 kb, respectively [3,4,5] This degree of genome miniaturization is unparalleled among free-living eukaryotes and has led to the contraction of intergenic regions to an average of less than 200 bp in O. tauri, which is the smallest among eukaryotes [6,7]. 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. Patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution
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