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Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content and rearrangements revealed by next generation sequencing

Fajardo, Diego, Senalik, Douglas, Ames, Mercedes, Zhu, Huayu, Steffan, Shawn A., Harbut, Rebecca, Polashock, James, Vorsa, Nicholi, Gillespie, Emily, Kron, Kathy, Zalapa, Juan E.
Tree genetics & genomes 2013 v.9 no.2 pp. 489
Vaccinium macrocarpon, breeding, cranberries, cultivars, gene banks, genes, genetic recombination, nucleotide sequences, phylogeny, plastid DNA, sequence alignment
The complete plastid genome sequence of the American cranberry was reconstructed using next-generation sequencing data by in silico procedures. We used Roche 454 shotgun sequence data to isolate cranberry plastid-specific sequences of the cultivar ?HyRed? via homology comparisons with complete sequences from several species available at the National Center for Biotechnology (NCBI) database. Initially, 40 cranberry plastid contigs, spanning a total length of 137,475 bases were discovered based on similarities with other plastid sequences. After further analysis, 11 cranberry plastid scaffolds were selected for the construction of the plastid genome based on connection and reads flowing through contigs information. From the selected scaffolds, we reconstructed and annotated 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 30 species outside the order Ericales (with 54 genes) showed Vaccinium inside the clade asterids, as reported in other studies using single genes. The cranberry plastid genome sequence will allow the accumulation of critical data useful for breeding and a suite of other genetic studies.