PMID: 9541540Apr 29, 1998Paper

Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages

Journal of Molecular Evolution
B R Morton

Abstract

In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons based on the nucleotide composition of noncoding regions of that genome. The codon bias of the actual gene is then compared to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is show...Continue Reading

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Citations

May 11, 2005·Journal of Molecular Evolution·Junko Kusumi, Hidenori Tachida
Jun 2, 2007·Journal of Molecular Evolution·Robert W Cutler, Panuwan Chantawannakul
Aug 13, 2008·Journal of Molecular Evolution·Robert W Cutler, Panuwan Chantawannakul
Sep 24, 2009·Plant Molecular Biology·David Roy Smith
Jan 23, 1999·Current Opinion in Genetics & Development·H Akashi, A Eyre-Walker
Dec 23, 1999·Current Opinion in Genetics & Development·M Kreitman, J M Comeron
Jul 20, 2002·Molecular Phylogenetics and Evolution·Brian R MortonMartin Fox
Jun 12, 2003·Nucleic Acids Research·Hedda A Meijer, Adri A M Thomas
Feb 22, 2003·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Angela E Douglas, John A Raven
Jan 31, 2008·BMC Bioinformatics·Pere PuigbòSantiago Garcia-Vallvé
Dec 20, 2012·Bioinformation·Rahul R NairDoss Ganesh
Apr 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·B R Morton
Dec 23, 2004·Letters in Applied Microbiology·A FadielF Naftolin
Jun 9, 2009·Plant Biotechnology Journal·Thomas ZiegelhofferSandra Austin-Phillips
May 1, 2007·Journal of Evolutionary Biology·H K Stenøien
Feb 22, 2011·Journal of Integrative Plant Biology·Bin WangJian-Qun Chen
May 7, 2015·BMC Genomics·Xian JiaJingchen Sun
Jul 6, 2016·Frontiers in Plant Science·Sajjad AsafIn-Jung Lee
May 20, 2016·PloS One·Haruo Suzuki, Brian R Morton
Jan 19, 2012·Evolutionary Bioinformatics Online·Chen XuAiling Ben
Jul 28, 2019·Biomolecules·Christen M Klinger, Elisabeth Richardson
Apr 28, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Jing MengJun He
Jun 22, 2019·Evolutionary Bioinformatics Online·Raju BiswasRajib Bandopadhyay
Nov 14, 2008·Molecular Biology Reports·Meng Zhou, Xia Li
Jan 27, 2017·G3 : Genes - Genomes - Genetics·Paweł BłażejPaweł Mackiewicz

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