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Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology

Sequencing of the chloroplast (cp) genome using traditional sequencing methods has been difficult because of its size (>120 kb) and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the cp genome using DNA extracted from whole cells and Solexa sequ...

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Autores principales: Wu, Jian, Liu, Bo, Cheng, Feng, Ramchiary, Nirala, Choi, Su Ryun, Lim, Yong Pyo, Wang, Xiao-Wu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3492724/
https://www.ncbi.nlm.nih.gov/pubmed/23162558
http://dx.doi.org/10.3389/fpls.2012.00243
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author Wu, Jian
Liu, Bo
Cheng, Feng
Ramchiary, Nirala
Choi, Su Ryun
Lim, Yong Pyo
Wang, Xiao-Wu
author_facet Wu, Jian
Liu, Bo
Cheng, Feng
Ramchiary, Nirala
Choi, Su Ryun
Lim, Yong Pyo
Wang, Xiao-Wu
author_sort Wu, Jian
collection PubMed
description Sequencing of the chloroplast (cp) genome using traditional sequencing methods has been difficult because of its size (>120 kb) and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the cp genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246, 362, and 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16, and FT, respectively. Micro-reads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8 or 95.5–99.7% of the B. rapa cp genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of cp genome.
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spelling pubmed-34927242012-11-16 Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology Wu, Jian Liu, Bo Cheng, Feng Ramchiary, Nirala Choi, Su Ryun Lim, Yong Pyo Wang, Xiao-Wu Front Plant Sci Plant Science Sequencing of the chloroplast (cp) genome using traditional sequencing methods has been difficult because of its size (>120 kb) and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the cp genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246, 362, and 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16, and FT, respectively. Micro-reads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8 or 95.5–99.7% of the B. rapa cp genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of cp genome. Frontiers Media S.A. 2012-11-08 /pmc/articles/PMC3492724/ /pubmed/23162558 http://dx.doi.org/10.3389/fpls.2012.00243 Text en Copyright © 2012 Wu, Liu, Cheng, Ramchiary, Choi, Lim and Wang. http://www.frontiersin.org/licenseagreement This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
spellingShingle Plant Science
Wu, Jian
Liu, Bo
Cheng, Feng
Ramchiary, Nirala
Choi, Su Ryun
Lim, Yong Pyo
Wang, Xiao-Wu
Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology
title Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology
title_full Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology
title_fullStr Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology
title_full_unstemmed Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology
title_short Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology
title_sort sequencing of chloroplast genome using whole cellular dna and solexa sequencing technology
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3492724/
https://www.ncbi.nlm.nih.gov/pubmed/23162558
http://dx.doi.org/10.3389/fpls.2012.00243
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