In silico analysis of 454 data yields the complete American cranberry (Vaccinium macrocarpon Ait.) plastid genome

The complete plastid genome sequence of the cranberry cultivar “HyRed” was reconstructed using next generation sequencing (NGS) data by in silico procedures. We used previously generated “HyRed” 454 shotgun sequence data to isolate plastid data via homology comparisons with complete sequences from several species available at the National Center for Biotechnology (NCBI) database. Initially, forty cranberry plastid contigs, spanning a total length of 137,475 were discovered. After further analysis, 11 cranberry plastids scaffolds were constructed based on similarities with other plastid sequences at NCBI.  From the cranberry plastid scaffolds, we reconstructed and annotation a putative cranberry plastid genome with an approximate length of 176kb. We aligned the putative plastid genome with previously published genomes from other species and observed numerous rearrangements. Comparisons of gene sequences obtained by Sanger and 454 showed few discrepancies between the two sequences. To evaluate the reliability of the sequence data, phylogenetic analysis including species outside the order Ericales with 28 genes showed Vaccinium inside the clade Asterids, as reported in other studies. The cranberry plastid genome sequence will allow the accumulation of critical data useful for breeding and a suite of other genetic studies.