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The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing
Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we rep...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332240/ https://www.ncbi.nlm.nih.gov/pubmed/26205052 http://dx.doi.org/10.3390/molecules200713080 |
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author | Raveendar, Sebastin Na, Young-Wang Lee, Jung-Ro Shim, Donghwan Ma, Kyung-Ho Lee, Sok-Young Chung, Jong-Wook |
author_facet | Raveendar, Sebastin Na, Young-Wang Lee, Jung-Ro Shim, Donghwan Ma, Kyung-Ho Lee, Sok-Young Chung, Jong-Wook |
author_sort | Raveendar, Sebastin |
collection | PubMed |
description | Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC; SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants. |
format | Online Article Text |
id | pubmed-6332240 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-63322402019-01-24 The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing Raveendar, Sebastin Na, Young-Wang Lee, Jung-Ro Shim, Donghwan Ma, Kyung-Ho Lee, Sok-Young Chung, Jong-Wook Molecules Communication Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC; SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants. MDPI 2015-07-20 /pmc/articles/PMC6332240/ /pubmed/26205052 http://dx.doi.org/10.3390/molecules200713080 Text en © 2015 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Communication Raveendar, Sebastin Na, Young-Wang Lee, Jung-Ro Shim, Donghwan Ma, Kyung-Ho Lee, Sok-Young Chung, Jong-Wook The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing |
title | The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing |
title_full | The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing |
title_fullStr | The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing |
title_full_unstemmed | The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing |
title_short | The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing |
title_sort | complete chloroplast genome of capsicum annuum var. glabriusculum using illumina sequencing |
topic | Communication |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332240/ https://www.ncbi.nlm.nih.gov/pubmed/26205052 http://dx.doi.org/10.3390/molecules200713080 |
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