Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints - PubMed (original) (raw)

Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints

De-Long Guan et al. BMC Genomics. 2018.

Abstract

Background: Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data.

Results: We identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species.

Conclusions: Codon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection.

Keywords: Coding sequences; Codon usage bias; Evolutionary force; Genetic formation; Hirudinaria manillensis; Leech; Transcriptome analysis.

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Conflict of interest statement

Mature H. manillensis samples were collected from ponds in Hechi City, Guangxi Province, China. As prescribed by “Law of People’s Republic of China on the Protection of Wildlife” and “Regulations for the Implementation of the People’s Republic of China on the Protection of terrestrial Wildlife” (State Council Decree [1992] No. 13), the specimen collection did not ask for any ethical or institutional approvals, because H. manillensis is not endangered or protected by any current law. The care and treatment of animals in this study were performed according to the Guideline for the Care and Use of Laboratory Animals in China.

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1

Base composition of H. manillensis. a Distribution of CDSs with different GC content levels in of H. manillensis; (b) Box plot indicates GC content variation in different codon positions (1st, 2nd and 3rd represent the first, second and third codon position, respectively) and overall genome (All). c Dinucleotide frequency plot in different combination of different codon positions (1st&2nd, 2nd&3rd and 3rd&1st) and overall genome (All), unbiased frequency means the theoretical frequency when all dinucleotides were presented equal, the curve located at 0.0625 (1/16)

Fig. 2

Characterise of evolutionary forces in H. manillensis. a ENC-GC3 plot. The solid line represents the expected curve when codon usage bias is only affected by mutation pressure. b Frequency distribution of ENC. c PR2-bias plot. Using the values of A3/(A3 + U3) against G3/(G3 + C3). d Neutrality plot analysis of GC12 and GC3 contents

Fig. 3

GC content and codon usage bias variation among expressed unigenes. All CDSs with observed FPKM values above were taken and transformed using log10, respectively. Dots with different colors represent their different GC content, while red represent GC > 50.8%, green represent 41.8% < GC < 50.8%, purple represent GC > 50.8%

Fig. 4

Effects of different indices on codon usage bias. a Principal component analysis of RSCU values of unigenes, the color of purple, green and red show different GC content. b Principal component analysis on RSCU values of codons. Different ending bases were shown in red, blue, green and purple. c The relative first 20 factors from principle component analysis based on the amino acid proportions. d Plot of ENC value variation against different protein length

Fig. 5

Comparisons of GC12/GC3 ratio and ENC values between different functional categories. The average ENC and general GC12/GC3 values were used to illustrate the differences of these CDSs from the overall tendency, the average ENC value is obtained as 52.2 and general GC12/GC3 ratio is calculated to be 0.83

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Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints - PubMed (original) (raw)