Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/springer-journals/strong-heterogeneity-in-nucleotidic-composition-and-codon-bias-in-the-VNInorgFbV
References (49)
-
C. Rispe, Jean-Sébastien Pierre (1998)
Coexistence between cyclical parthenogens, obligate parthenogens, and intermediates in a fluctuating environmentJournal of theoretical biology, 195 1
-
David Carlini, Ying Chen, Wolfgang Stephan (2001)
The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr.Genetics, 159 2
-
(2006)
No evidence for tissue-specific -
B. Sabater-Muñoz, F. Legeai, C. Rispe, J. Bonhomme, P. Dearden, C. Dossat, A. Duclert, J. Gauthier, D. Ducray, W. Hunter, P. Dang, S. Kambhampati, D. Martínez-Torres, T. Cortés, A. Moya, A. Nakabachi, Cathy Philippe, N. Prunier-Leterme, Y. Rahbé, J. Simon, D. Stern, P. Wincker, D. Tagu (2006)
Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)Genome Biology, 7
-
H. Akashi (2003)
Translational selection and yeast proteome evolution.Genetics, 164 4
-
Dc Shields, P. Sharp, Dg Higgins, F. Wright (1988)
"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons.Molecular biology and evolution, 5 6
-
A. Cutter, J. Wasmuth, M. Blaxter (2006)
The evolution of biased codon and amino acid usage in nematode genomes.Molecular biology and evolution, 23 12
-
(1999)
A comparison of homologous -
G. Perrière, J. Thioulouse (2002)
Use and misuse of correspondence analysis in codon usage studies.Nucleic acids research, 30 20
-
(2006)
Phylogenomic analysis -
Marie Sémon, J. Lobry, L. Duret (2006)
No evidence for tissue-specific adaptation of synonymous codon usage in humans.Molecular biology and evolution, 23 3
-
A. Wada, A. Suyama (1986)
Local stability of DNA and RNA secondary structure and its relation to biological functions.Progress in biophysics and molecular biology, 47 2
-
K. Jabbari, G. Bernardi (2004)
Comparative genomics of Anopheles gambiae and Drosophila melanogaster.Gene, 333
-
G. Marais, G. Piganeau (2002)
Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes.Molecular biology and evolution, 19 9
-
M. Reis, R. Savva, L. Wernisch (2004)
Solving the riddle of codon usage preferences: a test for translational selection.Nucleic acids research, 32 17
-
F Wright (1990)
The ‘effective number of codons’ in a geneGene, 87
-
Jeffrey Powell, Etsuko Moriyama (1997)
Evolution of codon usage bias in Drosophila.Proceedings of the National Academy of Sciences of the United States of America, 94 15
-
P. Sharp, T. Tuohy, K. Mosurski (1986)
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genesNucleic acids research, 14 13
-
(1999)
Compositional correlations in the -
Araxi Urrutia, L. Hurst (2003)
The signature of selection mediated by expression on human genes.Genome research, 13 10
-
(2002)
Accounting for background nucleotide -
N. Besansky (1993)
Codon usage patterns in chromosomal and retrotransposon genes of the mosquito Anopheles gambiaeInsect Molecular Biology, 1
-
(1986)
Codon usage in yeast -
(1998)
Coexistence between cyclical partheno -
P. Sharp, E. Bailes, R. Grocock, J. Peden, R. Sockett (2005)
Variation in the strength of selected codon usage bias among bacteriaNucleic Acids Research, 33
-
(1990)
The ‘effective number of codons -
L. Duret, D. Mouchiroud (1999)
Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.Proceedings of the National Academy of Sciences of the United States of America, 96 8
-
A. Fuglsang (2006)
Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice.Molecular biology and evolution, 23 7
-
(2002)
Use and misuse of correspondance -
(2004)
Solving the riddle of codon -
M. Mitreva, M. Blaxter, D. Bird, J. McCarter (2005)
Comparative genomics of nematodes.Trends in genetics : TIG, 21 10
-
J. Garel (1974)
Functional adaptation of tRNA population.Journal of theoretical biology, 43 1
-
Joël Savard, D. Tautz, S. Richards, G. Weinstock, R. Gibbs, J. Werren, H. Tettelin, M. Lercher (2006)
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects.Genome research, 16 11
-
M. Antezana, M. Kreitman (1999)
The Nonrandom Location of Synonymous Codons Suggests That Reading Frame-Independent Forces Have Patterned Codon PreferencesJournal of Molecular Evolution, 49
-
T. Schiex, J. Gouzy, A. Moisan, Yannick Oliveira (2003)
FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequencesNucleic acids research, 31 13
-
M. Bulmer (1991)
The selection-mutation-drift theory of synonymous codon usage.Genetics, 129 3
-
T. Ikemura (1981)
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes.Journal of molecular biology, 146 1
-
J. Bennetzen, B. Hall (1982)
Codon selection in yeast.The Journal of biological chemistry, 257 6
-
(1999)
A (1999) CAP3: a DNA sequence assembly -
F. Wright (1990)
The 'effective number of codons' used in a gene.Gene, 87 1
-
Hiroshi Akashi (1996)
Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster.Genetics, 144 3
-
Xiaoqiu Huang, A. Madan (1999)
CAP3: A DNA sequence assembly program.Genome research, 9 9
-
Liliana Florea, G. Hartzell, Zheng Zhang, G. Rubin, W. Miller (1998)
A computer program for aligning a cDNA sequence with a genomic DNA sequence.Genome research, 8 9
-
(1982)
Correlation between the abundance of yeast transfer RNAs and the occurence of the respective codons in protein genes -
(1988)
SAS/STAT user’s guide, release 6.03 edition -
J. Novembre (2002)
Accounting for background nucleotide composition when measuring codon usage bias.Molecular biology and evolution, 19 8
-
K. Schmid, D. Tautz (1999)
A Comparison of Homologous Developmental Genes from Drosophila and Tribolium Reveals Major Differences in Length and Trinucleotide Repeat ContentJournal of Molecular Evolution, 49
-
H. Musto, H. Romero, A. Zavala, G. Bernardi (1999)
Compositional Correlations in the Chicken GenomeJournal of Molecular Evolution, 49
-
T. Ikemura (1982)
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.Journal of molecular biology, 158 4
- Publisher
- Springer Journals
- Copyright
- Copyright © 2007 by Springer Science+Business Media, LLC
- Subject
- Life Sciences; Plant Sciences ; Microbiology ; Cell Biology
- ISSN
- 0022-2844
- eISSN
- 1432-1432
- DOI
- 10.1007/s00239-007-9023-y
- pmid
- 17928936
- Publisher site
- See Article on Publisher Site
Abstract
The aim of this study was to analyze patterns of nucleotidic composition and codon usage in the pea aphid genome (Acyrthosiphon pisum). A collection of 60,000 expressed sequence tags (ESTs) in the pea aphid has been used to automatically reconstruct 5809 coding sequences (CDSs), based on similarity with known proteins and on coding style recognition. Reconstructions were manually checked for ribosomal proteins, leading to tentatively reconstruct the nea-complete set of this category. Pea aphid coding sequences showed a shift toward AT (especially at the third codon position) compared to drosophila homologues. Genes with a putative high level of expression (ribosomal and other genes with high EST support) remained more GC3-rich and had a distinct codon usage from bulk sequences: they exhibited a preference for C-ending codons and CGT (for arginine), which thus appeared optimal for translation. However, the discrimination was not as strong as in drosophila, suggesting a reduced degree of translational selection. The space of variation in codon usage for A. pisum appeared to be larger than in drosophila, with a substantial fraction of genes that remained GC3-rich. Some of those (in particular some structural proteins) also showed high levels of codon bias and a very strong preference for C-ending codons, which could be explained either by strong translational selection or by other mechanisms. Finally, genomic traces were analyzed to build 206 fragments containing a full CDS, which allowed studying the correlations between GC contents of coding and those of noncoding (flanking and introns) sequences.
Journal
Journal of Molecular Evolution – Springer Journals
Published: Oct 10, 2007