Chloroplast genomes contain large (≈25,000 bp) almost perfect inverted repeats (IR). During de novo assembly individual repeats cannot be resolved unless the paired-read insert size is larger than the repeat unit. This means a complete circular plastome cannot be resolved during assembly if using only short-read data.
However, the use of paired-read data, combined with identification of the repeat and truncated repeat boundaries, can allow reconstruction of the complete circular plastome.
In this application note we take a short-read NGS data set and describe how to use Geneious Prime to reconstruct a complete, circular, annotated chloroplast genome.