Chloroplast genetics

Oil palm chloroplast is maternally inherited, making investigation of the chloroplast diversity an interesting endeavor. This paper describes a method for extracting enriched oil palm chloroplast DNA (cpDNA) done on six palms of different origins from Angola, Nigeria, Ghana, Madagascar and Suriname. Restriction enzyme digestion was used to evaluate the successful extraction of the oil palm cpDNA. The use of a mitochondrial DNA specific- universal primer revealed that most of the cpDNA were free from mitochondrial DNA contamination. Three chloroplast- specific universal primers were also used to evaluate the cpDNA. Their amplicons were cloned and sequenced to confirm that the cpDNA was indeed amplified. A search against the public databases further confirmed that the primers amplied sequences of the Elaeis guineensis Jacq. chloroplast genome. Two of them gave consistent amplifications when tested on cpDNA from the Angolan, Nigerian, Ghanian, Madagascan and Suriname palms.

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. How to cite this article Androsiuk et al. (2018), The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species. PeerJ 6:e4723; DOI 10.7717/peerj.4723