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The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species
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 C...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970550/ https://www.ncbi.nlm.nih.gov/pubmed/29844954 http://dx.doi.org/10.7717/peerj.4723 |
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author | Androsiuk, Piotr Jastrzębski, Jan Paweł Paukszto, Łukasz Okorski, Adam Pszczółkowska, Agnieszka Chwedorzewska, Katarzyna Joanna Koc, Justyna Górecki, Ryszard Giełwanowska, Irena |
author_facet | Androsiuk, Piotr Jastrzębski, Jan Paweł Paukszto, Łukasz Okorski, Adam Pszczółkowska, Agnieszka Chwedorzewska, Katarzyna Joanna Koc, Justyna Górecki, Ryszard Giełwanowska, Irena |
author_sort | Androsiuk, Piotr |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5970550 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-59705502018-05-29 The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species Androsiuk, Piotr Jastrzębski, Jan Paweł Paukszto, Łukasz Okorski, Adam Pszczółkowska, Agnieszka Chwedorzewska, Katarzyna Joanna Koc, Justyna Górecki, Ryszard Giełwanowska, Irena PeerJ Biodiversity 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. PeerJ Inc. 2018-05-23 /pmc/articles/PMC5970550/ /pubmed/29844954 http://dx.doi.org/10.7717/peerj.4723 Text en ©2018 Androsiuk et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Biodiversity Androsiuk, Piotr Jastrzębski, Jan Paweł Paukszto, Łukasz Okorski, Adam Pszczółkowska, Agnieszka Chwedorzewska, Katarzyna Joanna Koc, Justyna Górecki, Ryszard Giełwanowska, Irena The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species |
title | The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species |
title_full | The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species |
title_fullStr | The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species |
title_full_unstemmed | The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species |
title_short | The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species |
title_sort | complete chloroplast genome of colobanthus apetalus (labill.) druce: genome organization and comparison with related species |
topic | Biodiversity |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970550/ https://www.ncbi.nlm.nih.gov/pubmed/29844954 http://dx.doi.org/10.7717/peerj.4723 |
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