Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes

Genome Biology and Evolution
Adrienne RessayreJohann Joets


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 int...Continue Reading


Jun 1, 1997·The Plant Journal : for Cell and Molecular Biology·J C Carle-UriosteV Walbot
Feb 7, 2001·Current Opinion in Biotechnology·P Hedden, A L Phillips
Apr 5, 2002·Nature·Tom Maniatis, Robin Reed
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Michael Lynch
Jun 5, 2002·Genome Research·Gane Ka-Shu WongJun Yu
Nov 5, 2003·Molecular Biology and Evolution·Huai-chun WangDonal A Hickey
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Aug 27, 2005·Molecular Biology and Evolution·Josep M Comeron, Theodore B Guthrie
Feb 15, 2007·PLoS Biology·Joanna L ParmleyLaurence D Hurst
Nov 3, 2007·BMC Evolutionary Biology·Xingyi GuoLongjiang Fan
Jan 22, 2008·Genome Research·Shengdong KeLawrence A Chasin
Feb 6, 2008·Trends in Genetics : TIG·Amanda M LarracuenteAndrew G Clark
Feb 26, 2009·Cell·Melissa J Moore, Nick J Proudfoot
Jul 21, 2009·Biochemical Society Transactions·Tobias WarneckeLaurence D Hurst
Jul 28, 2009·Annual Review of Genomics and Human Genetics·L Duret, Nicolas Galtier
Aug 18, 2009·Nature Structural & Molecular Biology·Hagen TilgnerRoderic Guigó
Aug 18, 2009·Nature Structural & Molecular Biology·Schraga SchwartzGil Ast
Aug 19, 2009·Genome Research·Robin AnderssonJan Komorowski
Dec 24, 2009·BMC Bioinformatics·Desiree Tillo, Timothy R Hughes
Jan 5, 2010·BMC Genomics·Tim van ZutphenIda J van der Klei
Jun 1, 2010·Nature·Ramakrishna K ChodavarapuMatteo Pellegrini
Jan 5, 2011·PLoS Computational Biology·Ephraim KenigsbergAmos Tanay
Apr 12, 2012·The Plant Cell·Laurana Serres-GiardiSylvain Glémin
Jul 12, 2012·Frontiers in Genetics·Andreas G Bader
Jan 8, 2013·Nucleic Acids Research·Svetlana A ShabalinaAnna Kashina
Jan 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Shohei Takuno, Brandon S Gaut
Nov 15, 2013·Proceedings of the National Academy of Sciences of the United States of America·Uffe HellstenDaniel S Rokhsar
Dec 18, 2013·Science·Robert J Weatheritt, M Madan Babu
Apr 3, 2014·Nucleic Acids Research·Alessia FalangaMarco Baralle
Jun 12, 2014·Trends in Genetics : TIG·Sylvain GléminAdrienne Ressayre
Jun 27, 2014·Genome Biology and Evolution·Stepan V DenisovAlexey S Kondrashov
Sep 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Hugo K Dooner, Limei He
Dec 21, 2014·Genome Biology and Evolution·Yves ClémentSylvain Glémin


Feb 6, 2014·PloS One·Eng-Ti L LowRajinder Singh
May 23, 2017·PLoS Genetics·Yves ClémentSylvain Glémin
Sep 16, 2016·Genetics·Megan G Behringer, David W Hall
Nov 21, 2017·Annals of Botany·Purabi MazumdarJennifer Ann Harikrishna
May 24, 2017·G3 : Genes - Genomes - Genetics·Salvatore CamioloAndrea Porceddu

Related Concepts

G+C Composition
Sense Codon
Plant Proteins
Rice (Dietary)
Unassigned Reading Frames
Arabidopsis thaliana <plant>

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