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

Piotr Androsiuk; Jan Paweł Jastrzębski; Łukasz Paukszto; Adam Okorski; Agnieszka Pszczółkowska; Katarzyna Joanna Chwedorzewska; Justyna Koc; Ryszard Górecki; Irena Giełwanowska

doi:10.7717/peerj.4723

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

PeerJ. 2018 May 23:6:e4723. doi: 10.7717/peerj.4723. eCollection 2018.

Authors

Piotr Androsiuk¹, Jan Paweł Jastrzębski¹, Łukasz Paukszto¹, Adam Okorski², Agnieszka Pszczółkowska², Katarzyna Joanna Chwedorzewska³, Justyna Koc¹, Ryszard Górecki¹, Irena Giełwanowska¹

Affiliations

¹ Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
² Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
³ Department of Antarctic Biology, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warszawa, Poland.

Abstract

Colobanthus apetalus is a member of the genus Colobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genus Colobanthus consists of 25 species, including Colobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome of C. apetalus. The complete cp genome of C. apetalus has the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison of C. apetalus and C. quitensis cp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae and C. apetalus, and it revealed that C. apetalus and C. quitensis form a clade that is closely related to Silene species and Agrostemma githago. Moreover, the genus Silene appeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae.

Keywords: Caryophyllaceae; Colobanthus apetalus; Genome features; Next-generation sequencing; Phylogenetics; plastid genome.

Grants and 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.