Discovery of nuclear and plastid microsatellites, and other key genomic information, in the rare endemic plant (Caulanthus amplexicaulis var. barbarae) using minimal 454 pyrosequencing

Abstract

Next-generation Roche 454 pyrosequencing was used to rapidly identify 149 novel nuclear microsatellite loci and five plastid microsatellites from non-enriched genomic DNA of the rare endemic Santa Barbara Jewelflower (Caulanthus amplexicaulis var. barbarae). Analysis of this dataset showed a high level of orthology to annotated genes of the model plant Arabidopsis thaliana, as well as low levels of repetitive DNA sequences (particularly transposon-like elements). Thus, a modest sequencing effort using the 454 (or equivalent long-read platform) is a cost-effective and highly informative first step in the development of molecular-genetic resources for a non-model organism.

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Acknowledgments

This work was supported by NSF grant (DEB 0416169). Instrumentation and computational resources were provided by NSF Major Research Instrumentation grant (DBI 0923502), Texas A&M Agrilife, and the Office of the Vice President for Research, Texas A&M University.

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Correspondence to Alan E. Pepper.

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Burrell, A.M., No, EG. & Pepper, A.E. Discovery of nuclear and plastid microsatellites, and other key genomic information, in the rare endemic plant (Caulanthus amplexicaulis var. barbarae) using minimal 454 pyrosequencing. Conservation Genet Resour 3, 753–755 (2011). https://doi.org/10.1007/s12686-011-9450-3

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Keywords

  • Next-generation sequencing
  • Chloroplast
  • Marker
  • Ultramafic
  • Edaphic
  • Brassicaceae