Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

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 polymorphi

SUBMITTER: Brozynska M 

PROVIDER: S-EPMC4201551 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature