Direct Chloroplast sequencing: Comparison of sequencing platforms and analysis tools for whole chloroplast barcoding

Brozynska, Marta, Furtado, Angelo and Henry, Robert James (2014) Direct Chloroplast sequencing: Comparison of sequencing platforms and analysis tools for whole chloroplast barcoding. PLoS One, 9 10: e110387.1-e110387.10. doi:10.1371/journal.pone.0110387


Author Brozynska, Marta
Furtado, Angelo
Henry, Robert James
Title Direct Chloroplast sequencing: Comparison of sequencing platforms and analysis tools for whole chloroplast barcoding
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2014-10-17
Year available 2014
Sub-type Article (original research)
DOI 10.1371/journal.pone.0110387
Open Access Status DOI
Volume 9
Issue 10
Start page e110387.1
End page e110387.10
Total pages 10
Place of publication San Francisco, CA United States
Publisher Public Library of Science
Collection year 2015
Language eng
Formatted abstract
Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina) and Ion Torrent (Life Technology) sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare). Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2015 Collection
 
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Citation counts: TR Web of Science Citation Count  Cited 3 times in Thomson Reuters Web of Science Article | Citations
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