Jeremiah D. Hackett

Assistant Professor
University of Arizona

Ecology and Evolutionary Biology Department
Biosciences West 336
Tucson, AZ 85721
Ph: (520) 621-7514
Fax: (520) 621-9190
Email: hackettj@email.arizona.edu

Research Interests:

My interests are in the origin and evolution of plastids and protists. In particular, I am interested how endosymbiosis has shaped the evolution of the nuclear genome in photosynthetic protists. In organisms with simple plastids (red algae, green algae and land plants), plastid genes are encoded either on the plastid genome or in the nucleus of the organism. The red algae are particularly important because they have provided plastids to a diverse group of protists through secondary endosymbiosis, giving rise to the plastids of the cryptophytes, haptophytes, and stramenopiles. In the cryptophytes, the remnants of the nucleus of the engulfed algae persist as the nucleomorph. During this “secondary” endosymbiosis, genes of plastid function were transferred to the nucleus of the new host cell. There is also evidence that genes of cytoplasmic function were also transferred from the red algal endosymbiont the new host nucleus. The dinoflagellates appear to be the champoins of endosymbiosis, with 5 different plastid types in this lineage. The peridinin containing dinoflagellates also have a drastically reduced plastid genome, encoding the fewest genes in the plastid of any photosynthetic eukaryote. I hope to characterize the endosymbiont’s contribution to the nuclear genome and the migration of the plastid genome to the nucleus in these organisms.

We are doing this by creating cDNA libraries from a peridinin-containing dinoflagellate (Alexandrium tamarense), and from the haptophyte (Emiliania huxleyi). We will sequence ~30,000 expressed sequence tags (ESTs) from these libraries and generate about 10,000 unique cDNA sequences for each organism, using normalized and serially subtracted cDNA libraries to achieve a high gene discovery rate. This work is done in collaboration with M. Bento Soares and Tom Casavant at the University of Iowa. Through this study, I hope to shed light on the genome composition of these photosynthetic organisms and the role endosymbiosis has played in the evolution of photosynthetic protists by finding genes that have been transferred from the haptophyte endosymbiont to the nucleus of the dinoflagellate host.

Education:

University of Wisconsin-Milwaukee- B.S. (Biology and History)

University of Iowa- Ph.D.

 

Academic Honors:

2005 Woods Hole Oceanographic Institution Postdoctoral Fellowship.
2002 Honorable Mention, National Science Foundation Graduate Research Fellowship.
2001 Fellow, National Institutes of Health Institutional Training Grant (T32 GM98629).
1999 Member, Golden Key National Honor Society.

 

Research Positions:

University of University of Iowa: Lab of Dr. Debashish Bhattacharya
  Graduate Research Assistant/Teaching Assistant: 05/2001-2005.
  
  Evolutionary genomics of algae and protists
  

University of Wisconsin-Madison: Lab of Dr. Fredrick Blattner  
  Research Assistant: 06/99 - 07/00  
  Comparative genomics of Escherichia coli.  
 

Project: Assembly of the genome sequence of E. coli strains O157:H7 and CFT073 from shotgun sequencing data.

  

University of Wisconsin-Milwaukee: Lab of Dr. Ruth Phillips
  Undergraduate Researcher: 08/97 - 05/99  
  Evolutionary genetics of salmonid fishes  


Teaching Experience:

Teaching Assistant, Introduction to Bioinformatics 002:170. Fall 2003.
Teaching Assistant, Principles in Molecular and Cell Biology 156:201. Fall 2001.
Undergraduate Tutor, University of Wisconsin-Milwaukee, 1997-1999.


Publications:

Algal Evolution and Genomics:

  Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, Bhattacharya D. Phylogenomic analysis supports the
monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates.
Mol Biol Evol. 2007 Aug;24(8):1702-13. 		 
 
Hwan Su Yoon, Jeremiah D. Hackett and Debashish Bhattacharya. 2006. A genomic and phylogenetic perspective on endosymbiosis and algal origin. Journal of Applied Phycology (2006) 18: 475–481. 		 
 
Li, S., T. Nosenko, J.D. Hackett, and D. Bhattacharya. 2006. Phylogenomic analysis provides evidence for the endosymbiotic transfer of red algal genes in chromalveolates. Mol. Biol. Evol. 23:663-674.		  
 
Hackett, J.D., T.E. Scheetz, H.S. Yoon, M.B. Soares, M.F. Bonaldo, T.L. Casavant, and D. Bhattacharya. 2005. Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6:80.		  
 
Hackett, J.D., D.M. Anderson, D. Erdner, and D. Bhattacharya. 2004. Dinoflagellates: a remarkable evolutionary experiment. Am. J. Bot. 91(10).		  
 
Hackett, J.D., H.S. Yoon, M.B. Soares, M.F. Bonaldo, T.L. Casavant, T.E. Scheetz, T. Nosenko, and D. Bhattacharya. 2004. Migration of the plastid genome to the nucleus in a peridinin dinoflagellate. Curr Biol. 2004 Feb 3;14(3):213-8.		  
 
Yoon, H.S., Hackett, J.D., Cingula, C., Pinto, G., Bhattacharya, D. 2004. A timeline for the origin of photosynthetic eukaryotes. Molecular Biology and Evolution MBE Advance Access published February 12, 2004, 10.1093/molbev/msh075.		  
 
Hackett J.D., Yoon H.S., Soares M.B., Bonaldo M.F, Casavant T.L., Scheetz T.E., Nosenko, T. and Bhattacharya D. Migration of a plastid genome to the nucleus in a peridinin dinoflagellate. Current Biology 14: 213-218.		  
 
Bhattacharya, D., Yoon, H.S., Hackett J.D. 2004. Photosynthetic eukaryotes unite: endosymbiosis connects the dots. Bioessays 26: 50-60.		  
 
Hackett, J.D., Maranda L., Yoon H.S., and Bhattacharya D. 2003. Phylogenetic evidence for the cryptophyte origin of the plastid of Dinophysis (Dinophysiales, Dinophyceae). Journal of Phycology 39: 440-448.		  
 
Yoon H.S., Hackett J.D., Pinto G., Bhattacharya D. 2002. The single, ancient origin of chromist plastids. Proceedings of the National Academy of Sciences USA. 99: 15507-12.		  
 
Yoon H.S., Hackett J.D., Bhattacharya D. 2002. A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis. Proceedings of the National Academy of Sciences USA. 99:11724-9.		  

E. coli Genomics:

  Welch R.A., Burland V., Plunkett G. 3rd, Redford P., Roesch P., Rasko D., Buckles E.L., Liou S.R., Boutin A., Hackett J., Stroud D., Mayhew G.F., Rose D.J., Zhou S., Schwartz D.C., Perna N.T., Mobley H.L., Donnenberg M.S., Blattner F.R. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proceedings of the National Academy of Sciences USA. 99:17020-4  
 
Lim, A., Dimalamta, E.T., Potamousis, K.D.,Yen, G., Apodaca, J., Tao, C., Lin, J., Qi, R., Skiadas, J., Ramanathan, A., Perna, N.T., Plunkett, G., Burland, V., Mau, B., Hackett, J., Blattner, F.R., Anantharaman, T.S., Mishra, B., Schwartz, D.C., 2001. Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome. Genome Research 11(9): 1584-93.		  
 
Perna, N.T., Plunkett, G., Burland, V., Mau, B, Glasner, J.D., Rose, D.J., Mayhew, G. F., Evans, P.S., Gregor, J., Kirkpatrick, H.A., Posfai, G., Hackett, J., Klink, S., Boutin, A., Shao, Y., Miller, L., Grotbeck, E.J., Davis, N.W., Lim, A., Dimalamta, E.T., Potamousis, K.D., Apodaca, J., Anantharaman, T.S., Lin, J., Ten, G., Schwartz, D.C., Welch, R.A., Blattner, F.R., 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409: 529-533.		  

Salmonid rDNA cistron Evolution:

  Reed, K.M., Hackett, J.D., Phillips R.B., 2000. Comparative analysis of intra-individual and inter-species DNA sequence variation in salmonid ribosomal DNA cistrons. Gene 249: 115-125.  


Public Presentations:

  Hackett J.D., Yoon, H.S., Bhattacharya D. Endosymbiosis and the evolution of the dinoflagellate genome. Evolution 2003, Chico, CA.  
 
Hackett, J.D., Maranda, L., Yoon, H.S., Bhattacharya, D. 2002. Phylogenetic evidence for the cryptophyte origin of the plastid of Dinophysis (Dinophysiales, Dinophyceae).ISEP XIV (June 2002, Vancouver, BC) and Botany 2002 (August 2002, Madison, WI).		  
 
Hackett, J.D., Reed K.M., Phillips, R.B., 1999. Comparative analysis of intra-individual and inter-species sequence variation in Salmonid rDNA cistrons. Evolution 99, Madison, WI. Poster.