David Hufnagel

Graduate Research and Teaching Assistant
Hufford Lab
Dave Hufnagel


Michigan State University, Plant Biology Department, Undergraduate Research Assistant / Programmer, Mentor: Dr. Shin-Han Shiu, June 2011 to Present

  • Worked on a project studying the evolution of duplicate genes and pseudogenization following whole genome duplication in the family Brassicaceae.
  • Assembled transcriptome from next-generation sequencing data in Raphanus raphanistrum (wild radish).
  • With colleagues, currently combining our new R. raphanistrum data with that of Arabidopsis thaliana, Arabidopsis lyrata and Brassica rapa, in order to answer three major questions:
    • How has the evolution of genome structure in the Brassicaceae family been affected by whole genome duplication?
    • Are duplicate genes more likely to pseudogenize early in the life of a duplicate gene than later on?
    • What patterns of functional gene category enrichment are observed amongst species that have undergone recent whole genome duplication?
  • Currently playing an active role in helping to write the manuscript for this project.
  • Developed proficiency in Unix and Python programming and in use of various bioinformatics programs.

Michigan State University, Horticulture Department, Undergraduate Research Assistant; Mentor: Dr. Cornelius Barry; January 2009 to August 2011

  • Became proficient in general lab procedures including preparation of solutions, PCR, gel electrophoresis, DNA purification, DNA and RNA extraction and purification, RT-PCR, DNA cloning and DNA sequencing.
  • Became experienced in the use of genetic markers and molecular mapping.
  • Conducted independent research project to map the easy peel (ep) locus to the molecular map of tomato. The ep locus alters the general adhesion of the skin to the fruit. Molecular mapping of the ep locus revealed linkage to tomato chromosome 8.
  • Assisted in writing a grant proposal for the project.
  • Worked with Dr. Barry performing research in two areas:
    • 1) The cloning and the sequencing of genes involved in terpene biosynthesis in the glandular trichomes of Solanum species.
    • 2) The cloning and sequencing of a candidate gene involved in fruit quality of tomato together with the sequencing of this gene from several heirloom varieties.

Special Experiences: Darwin Conference at Chicago, October 2009

  • Attended 18 Lectures over the course of 3 days on a wide range of topics including evolution, ecology, paleontology, genetics, ethics and history of science.
  • Study Abroad March 2009
  • Traveled to Nicaragua for 9 days to learn about tropical ecology and Nicaraguan culture.
  • Observed rainforests, dry forests and cloud forests with volcanoes as well as the diverse species inhabiting them.
  • Met with many locals all around the country and gained insight into Nicaraguan life and culture.
  • Science Olympiad February 2009, April 2011
  • Volunteered teaching children biology through games and competition.


  • Gonzales-Vigil E, Hufnagel DE, Kim J, Last RL, Barry CS (2012) Evolution of TPS20-related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative Solanum habrochaites.The Plant Journal. DOI: 10.1111/j.1365-313X.2012.05040.x. Accepted and available online. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3466413/ .
  • Moghe G, Hufnagel DE, Tang H, Massa AN, Town CD, Dworkin I, Conner JK, Shiu SH.
  • Sequencing of the wild radish genome reveals extensive turnover of duplicate genes post-polyploidization. In preparation.
Area of Expertise: 
Evolutionary Biology