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United States Department of Agriculture

Agricultural Research Service

Research Project: CRANBERRY GENETIC IMPROVEMENT AND INSECT PEST MANAGEMENT

Location: Vegetable Crops Research Unit

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

Authors
item Fajardo, Diego -
item Senalik, Douglas
item Ames, Mercedes -
item Zhu, Huayu -
item Steffan, Shawn
item Harbut, Rebecca -
item Polashock, James
item Vorsa, Nicholi -
item Gillespie, Emily -
item Kron, Kathy -
item Zalapa, Juan

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 11, 2012
Publication Date: April 1, 2013
Repository URL: http://handle.nal.usda.gov/10113/56941
Citation: Fajardo, D., Senalik, D.A., Ames, M., Zhu, H., Steffan, S.A., Harbut, R., Polashock, J.J., Vorsa, N., Gillespie, E., Kron, K., Zalapa, J.E. 2013. Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content and rearrangements revealed by next generation sequencing. Tree Genetics and Genomes. 9(2):489-498.

Interpretive Summary: The American cranberry is an important fruit crop species. A fundamental requirement for breeding improved cranberries varieties is the accumulation of cranberry genetic information. The elucidation of complete genetic code of the cranberry chloroplasts (i.e., photosynthetic machinery) could help during breeding of new and high yielding varieties adapted cold and other environmental stresses. Additionally, cranberry chloroplast information will help understand evolutionary aspects of the species that could have important implications for breeding. We used new sequencing technologies and deciphered the cranberry chloroplast DNA code. The chloroplast DNA code of cranberry can be used as a model to study other closely related species such as blueberry.

Technical Abstract: 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.

Last Modified: 9/1/2014