We have shown (Kane et al., 2012) that low pass whole genome sequencing using Illumina NGS technology can be used to assemble whole plastid genomes and complete rDNA sequences and spacers. We call this approach ultrabarcoding (UBC), as it allows unique identification (barcoding) of maternal lineages within a species, using the maximum amount of data.
From the paper:
Variation in single nucleotide polymorphisms (SNPs) within Theobroma cacao (column 2) and fixed SNP differences between T. cacao and T. grandiflorum (column 3) in four plastid regions.
| Region | Within T. cacao | Between Theobroma species |
|---|---|---|
| psbA-trnH | 0 | 7 |
| rbcL | 1 | 4 |
| matK | 0 | 1 |
| ccsA | 4 | 2 |
| Entire plastid genome | 78 | 415 |
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Paper: Kane NC, Sveinsson S, Dempewolf H, Yang JY, Zhang D, Engels JMM, Cronk QCB (2012) Ultra-barcoding in cacao (Theobroma spp.) using whole chloroplast genomes and nuclear ribosomal DNA. American Journal of Botany 99: 320–329 (Special issue on next generation sequencing)
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