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Type: Journal article
Title: Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree
Author: McPherson, H.
van der Merwe, M.
Delaney, S.
Edwards, M.
Henry, R.
McIntosh, E.
Rymer, P.
Milner, M.
Siow, J.
Rossetto, M.
Citation: BMC Ecology, 2013; 13(8):1-11
Publisher: BioMed Central Ltd.
Issue Date: 2013
ISSN: 1472-6785
Statement of
Hannah McPherson, Marlien van der Merwe, Sven K. Delaney, Mark A. Edwards, Robert J. Henry, Emma McIntosh, Paul D. Rymer, Melita L. Milner, Juelian Siow and Maurizio Rossetto
Abstract: BACKGROUND: With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. RESULTS: The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution. CONCLUSIONS: Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology.
Keywords: Illumina; shotgun sequencing; chloroplast genome; SNP; phylogeography
Description: Extent: 11 p.
Rights: © 2013 McPherson et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of theCreative Commons Attribution License (, which permits unrestricted use,distribution, and reproduction in any medium, provided the original work is properly cited.
RMID: 0020126548
DOI: 10.1186/1472-6785-13-8
Appears in Collections:Earth and Environmental Sciences publications
Environment Institute publications

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