The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species

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Plant Biology

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Introduction

Materials and Methods

DNA extraction and chloroplast genome sequencing

Annotation and genome analysis

Repeat and SSR analysis

Intra-individual single nucleotide polymorphism

Synonymous (Ks) and non-synonymous (Ka) substitution rate analysis

Phylogenetic analysis

Results

Genome organization and content

Repeat sequences and SSRs

Intra-individual single nucleotide polymorphism

Synonymous and non-synonymous substitution rate analysis

C. apetalus vs members of the Caryophyllaceae family

C. apetalus vs. C. quitensis

A comparative analysis of the organization of C. apetalus and C. quitensis chloroplast genomes

Phylogenetic analysis

Discussion

Conclusions

Supplemental Information

List of repeated sequences in the chloroplast genome of Colobanthus apetalus.

DOI: 10.7717/peerj.4723/supp-1

List of repeated sequences in the chloroplast genome of Colobanthus quitensis.

DOI: 10.7717/peerj.4723/supp-2

Distribution of SSR in the Colobanthus apetalus cp genome

DOI: 10.7717/peerj.4723/supp-3

Distribution of SSR in the Colobanthus quitensis cp genome

DOI: 10.7717/peerj.4723/supp-4

SNPs within cp genome of C. apetalus

DOI: 10.7717/peerj.4723/supp-5

Ks and Ka values of C. apetalus chloroplast genome vs. selected representatives of Caryophyllaceae

DOI: 10.7717/peerj.4723/supp-6

Ks and Ka values of C. apetalus chloroplast genome vs. C. quitensis cp genome

DOI: 10.7717/peerj.4723/supp-7

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Piotr Androsiuk conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper approved the final draft.

Jan Paweł Jastrzębski analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Łukasz Paukszto analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Adam Okorski and Agnieszka Pszczółkowska performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Katarzyna Joanna Chwedorzewska, Ryszard Górecki and Irena Giełwanowska contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Justyna Koc performed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Data Availability

The following information was supplied regarding data availability:

Our raw data (complete chloroplast genome sequence for Colobanthus apetalus) is available on GenBank, accession number MF687919.

Funding

This work was supported by internal funding of the Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, and the Polish National Science Centre grant NN303796240. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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