EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes

William Lanier; Ahmed Moustafa; Debashish Bhattacharya; Josep M Comeron

doi:10.1371/journal.pone.0002171

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EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes

Journal article

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EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes

William Lanier, Ahmed Moustafa, Debashish Bhattacharya and Josep M Comeron

PloS one, Vol.3(5), pp.e2171-e2171

05/14/2008

DOI: 10.1371/journal.pone.0002171

PMCID: PMC2367439

PMID: 18478122

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Abstract

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. 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). 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 maintenance with other mutational and/or selective forces acting on genome size.

Chlorophyta - genetics

Gene Expression

Exons

Genes, Plant

Introns

Expressed Sequence Tags

Details

Title: Subtitle: EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes
Creators: William Lanier - Interdisciplinary Program in Genetics, University of Iowa, Iowa, United States of America
Ahmed Moustafa
Debashish Bhattacharya
Josep M Comeron
Resource Type: Journal article
Publication Details: PloS one, Vol.3(5), pp.e2171-e2171
DOI: 10.1371/journal.pone.0002171
PMID: 18478122
PMCID: PMC2367439
NLM abbreviation: PLoS One
ISSN: 1932-6203
eISSN: 1932-6203
Publisher: United States
Grant note: T32 GM008629 / NIGMS NIH HHS R01 GM098629 / NIGMS NIH HHS T 32 GM98629 / NIGMS NIH HHS
Language: English
Date published: 05/14/2008
Academic Unit: Biology
Record Identifier: 9983992063502771

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