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Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes
INRA, UMR 0320, UMR Genet Quantitat & Evolut Le Moulon 8120, Gif Sur Yvette, France..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Montpellier, CNRS IRD EPHE, UMR 5554, Inst Sci Evolut ISEM, Montpellier, France..
INRA, UMR 0320, UMR Genet Quantitat & Evolut Le Moulon 8120, Gif Sur Yvette, France..
Ctr Rech Angers Nantes, INRA, UMR IRHS Inst Rech Hort & Semences 1345, Beaucouse, France..
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2015 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 7, no 10, 2913-2928 p.Article in journal (Refereed) Published
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Abstract [en]

Plant genomes present a continuous range of variation in nucleotide composition (G+C content). In coding regions, G+C-poor species tend to have unimodal distributions of G+C content among genes within genomes and slight 50-30 gradients along genes. In contrast, G+C-rich species display bimodal distributions of G+C content among genes and steep 50-30 decreasing gradients along genes. The causes of these peculiar patterns are still poorly understood. Within two species (Arabidopsis thaliana and rice), each representative of one side of the continuum, we studied the consequences of intron presence on coding region and intron G+C content at different scales. By properly taking intron structure into account, we showed that, in both species, intron presence is associated with step changes in nucleotide, codon, and amino acid composition. This suggests that introns have a barrier effect structuring G+C content along genes and that previous continuous characterizations of the 50-30 gradients were artifactual. In external gene regions (located upstream first or downstream last introns), species-specific factors, such as GC-biased gene conversion, are shaping G+C contentwhereas in internal gene regions (surrounded by introns), G+C content is likely constrained to remain within a range common to both species.

Place, publisher, year, edition, pages
2015. Vol. 7, no 10, 2913-2928 p.
Keyword [en]
intron, nucleotide composition, protein-coding genes, Arabidopsis thaliana, Oryza sativa
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-270640DOI: 10.1093/gbe/evv189ISI: 000364951100009PubMedID: 26450849OAI: oai:DiVA.org:uu-270640DiVA: diva2:890215
Available from: 2016-01-01 Created: 2016-01-01 Last updated: 2017-12-01Bibliographically approved

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Glemin, Sylvain

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