Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants

Liangjiang Wang, Marilyn J. Roossinck

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

Codon usage bias is a ubiquitous phenomenon, which may be caused by mutational bias, selection, or both. The patterns of codon usage in plants are not well understood. Datasets of expressed sequence tags (ESTs) available for many plant species provide the resources for large-scale comparative analysis of codon usage patterns. We developed a computational approach to translate EST or assembled contig sequences, and then used the coding information for comparative analysis of codon usage in 12 plant species, including 6 eudicots, 5 monocots and the green alga Chlamydomonas reinhardtii. While codon nucleotide composition is highly conserved within eudicots or monocots, there is a significant difference between these two major taxonomic groups of higher plants. The third nucleotide position of codons is AU-rich in the eudicot genomes (35-42% of G+C content), but GC-rich in the monocot genomes (59-61% of G+C content). To identify optimal codons in these species, we used EST counts to estimate gene transcript levels. It was demonstrated that codon usage bias is correlated positively with gene transcript levels. Interestingly, the use of optimal codons appears to be well conserved between eudicots and monocots, and to a lesser degree between the higher plants and C. reinhardtii. Most of the optimal codons end with a C or G base, regardless of the different nucleotide composition in these genomes. The results suggest that plant codon usage is affected by translational selection, and the selective pressure appears to be conserved in the plant kingdom.

Original languageEnglish (US)
Pages (from-to)699-710
Number of pages12
JournalPlant molecular biology
Volume61
Issue number4-5
DOIs
StatePublished - Jul 1 2006

Fingerprint

conserved sequences
codons
Codon
Sequence Analysis
Liliopsida
Expressed Sequence Tags
expressed sequence tags
Chlamydomonas reinhardtii
Nucleotides
nucleotides
Base Composition
Genome
genome
Chlorophyta
Selection Bias
Genes
genes

All Science Journal Classification (ASJC) codes

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

Cite this

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abstract = "Codon usage bias is a ubiquitous phenomenon, which may be caused by mutational bias, selection, or both. The patterns of codon usage in plants are not well understood. Datasets of expressed sequence tags (ESTs) available for many plant species provide the resources for large-scale comparative analysis of codon usage patterns. We developed a computational approach to translate EST or assembled contig sequences, and then used the coding information for comparative analysis of codon usage in 12 plant species, including 6 eudicots, 5 monocots and the green alga Chlamydomonas reinhardtii. While codon nucleotide composition is highly conserved within eudicots or monocots, there is a significant difference between these two major taxonomic groups of higher plants. The third nucleotide position of codons is AU-rich in the eudicot genomes (35-42{\%} of G+C content), but GC-rich in the monocot genomes (59-61{\%} of G+C content). To identify optimal codons in these species, we used EST counts to estimate gene transcript levels. It was demonstrated that codon usage bias is correlated positively with gene transcript levels. Interestingly, the use of optimal codons appears to be well conserved between eudicots and monocots, and to a lesser degree between the higher plants and C. reinhardtii. Most of the optimal codons end with a C or G base, regardless of the different nucleotide composition in these genomes. The results suggest that plant codon usage is affected by translational selection, and the selective pressure appears to be conserved in the plant kingdom.",
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Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants. / Wang, Liangjiang; Roossinck, Marilyn J.

In: Plant molecular biology, Vol. 61, No. 4-5, 01.07.2006, p. 699-710.

Research output: Contribution to journalArticle

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