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Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae)
Costaria costata is a commercially and industrially important brown alga. In this study, we used next-generation sequencing to determine the complete plastid genome of C. costata. The genome consists of a 129,947 bp circular DNA molecule with an A+T content of 69.13% encoding a standard set of six r...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596871/ https://www.ncbi.nlm.nih.gov/pubmed/26444909 http://dx.doi.org/10.1371/journal.pone.0140144 |
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author | Zhang, Lei Wang, Xumin Liu, Tao Wang, Haiyang Wang, Guoliang Chi, Shan Liu, Cui |
author_facet | Zhang, Lei Wang, Xumin Liu, Tao Wang, Haiyang Wang, Guoliang Chi, Shan Liu, Cui |
author_sort | Zhang, Lei |
collection | PubMed |
description | Costaria costata is a commercially and industrially important brown alga. In this study, we used next-generation sequencing to determine the complete plastid genome of C. costata. The genome consists of a 129,947 bp circular DNA molecule with an A+T content of 69.13% encoding a standard set of six ribosomal RNA genes, 27 transfer RNA genes, and 137 protein-coding genes with two conserved open reading frames (ORFs). The overall genome structure of C. costata is nearly the same as those of Saccharina japonica and Undaria pinnatifida. The plastid genomes of these three algal species retain a strong conservation of the GTG start codon while infrequently using TGA as a stop codon. In this regard, they differ substantially from the plastid genomes of Ectocarpus siliculosus and Fucus vesiculosus. Analysis of the nucleic acid substitution rates of the Laminariales plastid genes revealed that the petF gene has the highest substitution rate and the petN gene contains no substitution over its complete length. The variation in plastid genes between C. costata and S. japonica is lower than that between C. costata and U. pinnatifida as well as that between U. pinnatifida and S. japonica. Phylogenetic analyses demonstrated that C. costata and U. pinnatifida have a closer genetic relationship. We also identified two gene length mutations caused by the insertion or deletion of repeated sequences, which suggest a mechanism of gene length mutation that may be one of the key explanations for the genetic variation in plastid genomes. |
format | Online Article Text |
id | pubmed-4596871 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-45968712015-10-20 Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae) Zhang, Lei Wang, Xumin Liu, Tao Wang, Haiyang Wang, Guoliang Chi, Shan Liu, Cui PLoS One Research Article Costaria costata is a commercially and industrially important brown alga. In this study, we used next-generation sequencing to determine the complete plastid genome of C. costata. The genome consists of a 129,947 bp circular DNA molecule with an A+T content of 69.13% encoding a standard set of six ribosomal RNA genes, 27 transfer RNA genes, and 137 protein-coding genes with two conserved open reading frames (ORFs). The overall genome structure of C. costata is nearly the same as those of Saccharina japonica and Undaria pinnatifida. The plastid genomes of these three algal species retain a strong conservation of the GTG start codon while infrequently using TGA as a stop codon. In this regard, they differ substantially from the plastid genomes of Ectocarpus siliculosus and Fucus vesiculosus. Analysis of the nucleic acid substitution rates of the Laminariales plastid genes revealed that the petF gene has the highest substitution rate and the petN gene contains no substitution over its complete length. The variation in plastid genes between C. costata and S. japonica is lower than that between C. costata and U. pinnatifida as well as that between U. pinnatifida and S. japonica. Phylogenetic analyses demonstrated that C. costata and U. pinnatifida have a closer genetic relationship. We also identified two gene length mutations caused by the insertion or deletion of repeated sequences, which suggest a mechanism of gene length mutation that may be one of the key explanations for the genetic variation in plastid genomes. Public Library of Science 2015-10-07 /pmc/articles/PMC4596871/ /pubmed/26444909 http://dx.doi.org/10.1371/journal.pone.0140144 Text en © 2015 Zhang 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Zhang, Lei Wang, Xumin Liu, Tao Wang, Haiyang Wang, Guoliang Chi, Shan Liu, Cui Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae) |
title | Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae) |
title_full | Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae) |
title_fullStr | Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae) |
title_full_unstemmed | Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae) |
title_short | Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae) |
title_sort | complete plastid genome of the brown alga costaria costata (laminariales, phaeophyceae) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596871/ https://www.ncbi.nlm.nih.gov/pubmed/26444909 http://dx.doi.org/10.1371/journal.pone.0140144 |
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