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

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Abstract

The complete plastid genome sequence of the American cranberry (Vaccinium macrocarpon Ait.) 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 “HyRed” via homology comparisons with complete sequences from several species available at the National Center for Biotechnology Information database. Eleven cranberry plastid contigs were selected for the construction of the plastid genome-based homologies and on raw reads flowing through contigs and connection information. We assembled and annotated a cranberry plastid genome (82,284 reads; 185x coverage) with a length of 176 kb and the typical structure found in plants, but with several structural rearrangements in the large single-copy region when compared to other plastid asterid genomes. To evaluate the reliability of the sequence data, phylogenetic analysis of 30 species outside the order Ericales (with 54 genes) showed Vaccinium inside the clade Asteridae, 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.

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Acknowledgments

The authors thank PS100, Emily Gustin, P. Simon, and M. Iorizzo for their help with different aspects of this work. Eric Zeldin and Brent McCown provided the “HyRed” DNA. This research was supported by funds from the National Foundation Science (DBI-1228280), Wisconsin Cranberry Growers Association, and USDA-ARS (project no. 3655-21220-001-00), provided to J.E.Z., S.A.S., and R.H.

Data archiving statement

The accession number JQ_757046 was assigned to the complete cranberry plastid genome sequence after being submitted to NCBI.

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Authors and Affiliations

  1. USDA-ARS, Vegetable Crops Research Unit, USDA, 1575 Linden Drive, Madison, WI, 53706, USA

    Douglas Senalik, Shawn A. Steffan & Juan E. Zalapa

  2. Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    Diego Fajardo, Mercedes Ames, Huayu Zhu & Rebecca Harbut

  3. Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, Chatsworth, NJ, USA

    James Polashock

  4. Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ, USA

    Nicholi Vorsa

  5. Department of Biology, Marshall University, Huntington, WV, USA

    Emily Gillespie

  6. Department of Biology, Wake Forest University, Winston-Salem, NC, USA

    Kathy Kron

Authors
  1. Diego Fajardo
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  2. Douglas Senalik
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  3. Mercedes Ames
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  4. Huayu Zhu
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  5. Shawn A. Steffan
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  6. Rebecca Harbut
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  7. James Polashock
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  8. Nicholi Vorsa
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  9. Emily Gillespie
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  10. Kathy Kron
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  11. Juan E. Zalapa
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Corresponding author

Correspondence to Juan E. Zalapa.

Additional information

Communicated by W. Guo

Data archiving statement

The accession number JQ_757046 was assigned to the complete cranberry plastid genome sequence after being submitted to NCBI.

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Fajardo, D., Senalik, D., Ames, M. et al. Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing. Tree Genetics & Genomes 9, 489–498 (2013). https://doi.org/10.1007/s11295-012-0573-9

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  • DOI: https://doi.org/10.1007/s11295-012-0573-9

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