Title |
Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform
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Published in |
Plant Methods, September 2010
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DOI | 10.1186/1746-4811-6-22 |
Pubmed ID | |
Authors |
Robin A Atherton, Bennet J McComish, Lara D Shepherd, Lorraine A Berry, Nick W Albert, Peter J Lockhart |
Abstract |
Complete chloroplast genome sequences provide a valuable source of molecular markers for studies in molecular ecology and evolution of plants. To obtain complete genome sequences, recent studies have made use of the polymerase chain reaction to amplify overlapping fragments from conserved gene loci. However, this approach is time consuming and can be more difficult to implement where gene organisation differs among plants. An alternative approach is to first isolate chloroplasts and then use the capacity of high-throughput sequencing to obtain complete genome sequences. We report our findings from studies of the latter approach, which used a simple chloroplast isolation procedure, multiply-primed rolling circle amplification of chloroplast DNA, Illumina Genome Analyzer II sequencing, and de novo assembly of paired-end sequence reads. |
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Geographical breakdown
Country | Count | As % |
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Brazil | 7 | 4% |
Germany | 2 | 1% |
Indonesia | 2 | 1% |
Pakistan | 2 | 1% |
Switzerland | 1 | <1% |
France | 1 | <1% |
Hungary | 1 | <1% |
Netherlands | 1 | <1% |
Australia | 1 | <1% |
Other | 3 | 2% |
Unknown | 153 | 88% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 46 | 26% |
Student > Ph. D. Student | 37 | 21% |
Student > Master | 21 | 12% |
Professor | 13 | 7% |
Student > Bachelor | 12 | 7% |
Other | 29 | 17% |
Unknown | 16 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 121 | 70% |
Biochemistry, Genetics and Molecular Biology | 18 | 10% |
Chemistry | 3 | 2% |
Social Sciences | 2 | 1% |
Environmental Science | 2 | 1% |
Other | 9 | 5% |
Unknown | 19 | 11% |