title: Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes.
abstract: 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 5'-3' gradients along genes. In contrast, G + C-rich species display bimodal distributions of G + C content among genes and steep 5'-3' 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 5'-3' 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 content whereas in internal gene regions (surrounded by introns), G + C content is likely constrained to remain within a range common to both species.
authors.affiliation: UMR 0320/UMR 8120 Génétique Quantitative et Evolution-Le Moulon, INRA, Gif-sur-Yvette, France ressayre@moulon.inra.fr.
authors.forename: Adrienne
authors.initials: A
authors.lastname: Ressayre
authors.affiliation: Institut des Sciences de l'Evolution (ISEM), UMR 5554, Université de Montpellier, CNRS-IRD-EPHE, France Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Glémin
authors.affiliation: UMR 0320/UMR 8120 Génétique Quantitative et Evolution-Le Moulon, INRA, Gif-sur-Yvette, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Montalent
authors.affiliation: UMR 1345 IRHS Institut de Recherche en Horticulture et Semences, INRA, Centre de Recherche Angers-Nantes, Beaucousé, France.
authors.forename: Laurana
authors.initials: L
authors.lastname: Serre-Giardi
authors.affiliation: UMR 0320/UMR 8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Sud, Gif-sur-Yvette, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Dillmann
authors.affiliation: UMR 0320/UMR 8120 Génétique Quantitative et Evolution-Le Moulon, INRA, Gif-sur-Yvette, France.
authors.forename: Johann
authors.initials: J
authors.lastname: Joets
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D001482:Base Composition; D003062:Codon; D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D005091:Exons; D005785:Gene Conversion; D018745:Genome, Plant; D007438:Introns; D009711:Nucleotides / Q000235:genetics* / Q000378:metabolism; D016366:Open Reading Frames; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D013045:Species Specificity
chemical_list: D003062:Codon; D018076:DNA, Complementary; D009711:Nucleotides; D010940:Plant Proteins
keywords: Arabidopsis thaliana; Oryza sativa; intron; nucleotide composition; protein-coding genes