Plant Molecular Biology Reporter

, Volume 32, Issue 4, pp 828–840

Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family

Original Paper

DOI: 10.1007/s11105-013-0691-z

Cite this article as:
Nie, X., Deng, P., Feng, K. et al. Plant Mol Biol Rep (2014) 32: 828. doi:10.1007/s11105-013-0691-z

Abstract

Codon usage bias (CUB) is an important evolutionary feature in a genome and has been widely documented from prokaryotes to eukaryotes. However, the significance of CUB in the Asteraceae family has not been well understood, with no Asteraceae species having been analyzed for this characteristic. Here, we use bioinformatics approaches to comparatively analyze the general patterns and influencing factors of CUB in five Asteraceae chloroplast (cp) genomes. The results indicated that the five genomes had similar codon usage patterns, showing a strong bias towards a high representation of NNA and NNT codons. Neutrality analysis showed that these cp genomes had a narrow GC distribution and no significant correlation was observed between GC12 and GC3. Parity Rule 2 (PR2) plot analysis revealed that purines were used more frequently than pyrimidines. Effective number of codons (ENc)-plot analysis showed that most genes followed the parabolic line of trajectory, but several genes with low ENc values lying below the expected curve were also observed. Furthermore, correspondence analysis of relative synonymous codon usage (RSCU) yielded a first axis that explained only a partial amount of variation of codon usage. These findings suggested that both natural selection and mutational bias contributed to codon bias, while selection was the major force to shape the codon usage in these Asteraceae cp genomes. Our study, which is the first to investigate codon usage patterns in Asteraceae plastomes, will provide helpful information about codon distribution and variation in these species, and also shed light on the genetic and evolutionary mechanisms of codon biology within this family.

Keyword

Chloroplast genome Codon usage bias Correspondence analysis Asteraceae 

Supplementary material

11105_2013_691_Fig6_ESM.jpg (100 kb)
Fig. S1

Correlation between synonymous codon usage order (SCUO) and GC composition (GC, GC1, GC2, GC3) of the five chloroplast (cp) genomes. (JPEG 99 kb)

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High resolution image (TIFF 877 kb)
11105_2013_691_Fig7_ESM.jpg (37 kb)
Fig. S2

GC content and CG skew across the five plastomes. a Local GC content across plastomes. Solid lines below each horizontal axis represent local GC content. b Local CG skew across plastomes. Histograms below each horizontal axis show local CG skew. Genomic regions in which the curve is colored as yellow-green are skewed toward higher G content, whereas genomic regions in which the curve is colored as purple are skewed toward higher C content. The height of the black/red curves represents the degree of CG skew. AA. adenophora, BG. abyssinica, CH. annuus, DJ. vulgari, EL. sativa (JPEG 36 kb)

11105_2013_691_MOESM2_ESM.tif (1.9 mb)
High resolution image (TIFF 1931 kb)
11105_2013_691_MOESM3_ESM.doc (61 kb)
Table S1SCUO value of the orthologous genes in five Asteraceae cp genomes (DOC 61 kb)
11105_2013_691_MOESM4_ESM.doc (33 kb)
Table S2Summary of the correlation between SCUO and other codon indices in five Asteraceae cp genomes. (DOC 33 kb)

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.College of Agronomy; State Key Laboratory of Crop Stress Biology in Arid Areas; Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingChina
  2. 2.Cereal Research Centre, Agriculture and Agri-Food CanadaWinnipegCanada

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