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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...

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Autores principales: Raveendar, Sebastin, Na, Young-Wang, Lee, Jung-Ro, Shim, Donghwan, Ma, Kyung-Ho, Lee, Sok-Young, Chung, Jong-Wook
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2015
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.
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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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