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

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

doi:10.7717/peerj.4723

Irena Giełwanowska, Agnieszka Pszczółkowska + Show 7 more

Open Access

https://doi.org/10.7717/peerj.4723

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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.

Highlights

Chloroplasts are organelles whose main function is the photosynthetic fixation of carbon
The Illumina MiSeq platform generated around 4,004,432 high-quality reads (∼150 bp in length each, 144.2 bp on average, SD = 19.1; PHRED >30 for 96% of reads) for the C. apetalus cp genome, which were assembled into a complete sequence based on the reference of C. quitensis cp genome
The entire C. apetalus cp genome contained 131 genes, including 112 unique genes and 19 genes which were duplicated in the inverted repeats (IRs) regions

Summary

Introduction

Chloroplasts are organelles whose main function is the photosynthetic fixation of carbon. The variations in size can be attributed mostly to the expansion, contraction or even loss of IRs as well as changes in the length of intergenic spacers (Palmer et al, 1988). Due to their compact size, highly conserved status, uniparental inheritance and haploid nature, cp genomes can be effectively used in studies of plant taxonomy and evolution and in species identification (Kress et al, 2005; Chase et al, 2007; Parks, Cronn & Liston, 2009; Yang et al, 2013)

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