Skip to main content
SpringerLink
Log in

Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

Background

Synonymous codon usage bias is noticed in the genome of every organism, influenced by mutation pressure and natural selection. The analysis of codon usage pattern in Porphyra umbilicalis chloroplast genome are inferred while previous study focused on codon bias in nuclear genome.

Objective

To develop a better understanding of the factors affecting synonymous codon usage, codon usage patterns and nucleotide composition of 150 genes in P. umbilicalis cp genome, and provide a theoretical basis for genetic modification of chloroplast genome.

Methods

In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS and Microsoft Excel.

Results

It shows that codon usage models are mainly influenced by compositional constraints under mutational pressure and synonymous codon prefers to use codons ending with A/T, comparing to C/G. The ENC value is slight low which shows the weak codon bias. For all coding genes of P. umbilicalis chloroplast genome except Photosystem I genes, a weak correlation between GC3 and GC12 suggests natural selection might play a significant role in synonymous codon usage bias.

Conclusion

The codon usage bias in P. umbilicalis cp genome is low and in some way or other, influenced by natural selection, mutation pressure, nucleotide composition. Our results can provide a theoretical basis for codon modification of exogenous genes, accuracy of prediction about new members of chloroplast gene family and identification of unknown genome.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Bisalputra T, Bisalputra AA (1969) The ultrastructure of chloroplast of a brown alga Sphacelaria sp. I. Plastid DNA configuration—the chloroplast genophore. J Ultrastruct Res 29:151–170

    Article  CAS  Google Scholar 

  • Blunden G (1992) Seaweed resources in europe: uses and potential, vol 2. Wiley, Chichester, pp 178–198 (Issue 2)

    Google Scholar 

  • Brawley SH, Blouin NA, Fickoblean E, Wheeler GL (2017) Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). P Natl Acad Sci USA 114:E6361–E6370

    Article  CAS  Google Scholar 

  • Brodie JA, Irvine LM (2003) Seaweeds of the British Isles: Volume 1 Part 3b Bangiophycidae. Natural History Museum, London, ISBN 1-898298-87-4, XIII, pp 167

  • Cai MS, Cheng AC, Wang MS, Zhao LC (2009) Characterization of synonymous codon usage bias in the duck plague virus UL35 gene. Karger 52:266–278

    CAS  Google Scholar 

  • Chen X, Cai X, Chen Q, Zhou H (2011) Factors affecting synonymous codon usage bias in chloroplast genome of oncidium gower ramsey. Evol Bioinform 7:271–278

    Article  Google Scholar 

  • He S, Zhang SJ, Xiu LS, Xing ZB (2013) Codon usage analysis in squalene synthase gene. Genom Appl Biol 32:232–239

    CAS  Google Scholar 

  • He L, Qian J, Li X, Sun Z (2017) Complete chloroplast genome of medicinal plant lonicera japonica: genome rearrangement, intron gain and loss, and implications for phylogenetic studies. Molecules 22:249

    Article  Google Scholar 

  • Kh LVB, Kowallik KV (1992) Structural organization of the chloroplast genome of the chromophytic alga Vaucheria bursata. Plant Mol Biol 18:83–95

    Article  Google Scholar 

  • Li J, Shulian X, Jia F (2010) Progress in chloroplast genome of algae. J Northwest Bot 30:208–214

    Google Scholar 

  • Li ZZ, Saina JK, Gichira AW, Kyalo CM (2018) comparative genomics of the balsaminaceae sister genera Hydrocera triflora and Impatiens pinfanensis. Int J Mol Sci 19:319

    Article  Google Scholar 

  • Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res 41:W575–W581

    Article  Google Scholar 

  • Long S, Yao H, Wu Q, Li G (2018) Analysis of compositional bias and codon usage pattern of the coding sequence in Banna virus genome. Virus Res 258:68–72

    Article  CAS  Google Scholar 

  • Monisha N, Arif U, Supriyo C (2017) Codon usage bias and its influencing factors for Y-linked genes in human. Comput Biol Chem 69:77–86

    Article  Google Scholar 

  • Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7:84

    Article  Google Scholar 

  • Romero H, Zavala A, Musto H (2000) Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res 28:2084–2090

    Article  CAS  Google Scholar 

  • Sharp PM, Li WH (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 24:28–38

    Article  CAS  Google Scholar 

  • Shinozaki K, Ohme M, Tanaka M, Wakasugi T (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049

    Article  CAS  Google Scholar 

  • Snawar H, Sahibzada TR (2017) Analysis of synonymous codon usage in Zika virus. Acta Trop 173:136–146

    Article  Google Scholar 

  • Wang H, Meng T, Wei W (2018) Analysis of synonymous codon usage bias in helicase gene from Autographa californica multiple nucleopolyhedrovirus. Genes Genom 40:767–780

    Article  CAS  Google Scholar 

  • Wei L, He J, Jia X, Qi Q (2014) Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution. BMC Biol 14:262

    Google Scholar 

  • Wright F (1990) The ‘effective number of codons’ used in a gene. Gene 87:23

    Article  CAS  Google Scholar 

  • Yu T, Li J, Yang Y, Qi L (2012) Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus. Mol Phylogenet Evol 62:206–213

    Article  Google Scholar 

  • Zhang R, Zhang L, Wang W, Zhang Z (2018) Differences in codon usage bias between photosynthesis-related genes and genetic system-related genes of chloroplast genomes in cultivated and wild solanum species. Int J Mol Sci 19:3142

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the research grants from Discipline construction Double Support Project of Sichuan Agricultural University (Grant No. 00770114).

Author information

Authors and Affiliations

  1. College of Life Science, Sichuan Agricultural University, Ya’an, 625014, Sichuan, China

    Guoling Li, Zonglian Pan, Shichen Gao, Yuyang He, Qiaoyu Xia, Yan Jin & Huipeng Yao

Authors
  1. Guoling Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zonglian Pan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shichen Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yuyang He
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qiaoyu Xia
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yan Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Huipeng Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

GLL and HPY identified the research topic and designed the experiments. YYH, QYX and YJ collected the data. GLL and SCG performed the experiments and analyzed the data. GLL and ZLP wrote the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Huipeng Yao.

Ethics declarations

Conflict of interest

The authors have declared that no competing interest exists.

Ethical approval

This article does not contain any studies with human subjects or animals performed by any of the authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 14 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, G., Pan, Z., Gao, S. et al. Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis. Genes Genom 41, 1173–1181 (2019). https://doi.org/10.1007/s13258-019-00847-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-019-00847-1

Keywords

Search

Navigation