![]() ĭNA sequencing platforms differ in their throughput and accuracy. Reference-guided mapping of sequence reads and de novo assembly have been used to generate these whole chloroplast barcodes. This method relies on successful extraction of chloroplast genome sequence reads from total genomic DNA reads and their assembly to form a consensus sequence for the sample that can be used as a barcode. Recently a simple approach involving NGS of a total genomic DNA preparation was proposed. However, the universal amplification of chloroplast sequences from all species has proven difficult and chloroplast purification is laborious and not perfect. These tools will also support protection of biosecurity and management of wild plant populations of rare or threatened plants.Įarly analysis relied on either specific amplification of the chloroplast genome or separation of chloroplasts from nuclear and mitochondrial DNA before chloroplast DNA isolation and sequencing the amplified or cloned product derived from PCR amplification. Protection of intellectual property rights associated with plant varieties will also be simplified by a standard approach to plant identification. This will complement the use of next generation sequencing to screen for the presence of pathogenic microbes. ![]() Industrial applications will include the identification of plant components in whole and processed foods and the management of food processing to ensure food safety and authenticity of labelling. ![]() Ī generic method for rapid and cost effective DNA-based identification of plants at this level (species or sub-species) will find wide application in industry and research. Analysis of complex mixtures of plants has applications in many ecological studies. The chloroplast has unique features found in all green plants, conserved sufficiently to be readily aligned for comparison of different samples and large enough to contain variation, which allow species or sub species distinction across the seed plants. The emergence of next generation sequencing (NGS) technology allowing whole chloroplast genomic DNA sequencing has provided the opportunity to use the whole chloroplast genome sequence as a barcode. Analysis of different plant groups has required the use of different genetic loci. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.Ī universal plant barcoding method based upon sequencing a specific gene or combination of specific genes has proven elusive. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. 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. 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. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. 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.
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