Debashish Bhattacharya Professor Rutgers University Dept. of Ecology, Evolution & Natural Resources Foran Hall, Room 102 School of Env & Biol Sciences New Brunswick. NJ 08903 (732) 932-8165. Ext. 184 FAX- 8746 bhattacharya@aesop.rutgers.edu

Algal evolution, genomics, endosymbiosis, red tides, plastids, tree of life

The breathtaking diversity of life that surrounds us is the underlying inspiration for my lab’s research. We have long-standing interests in algal/protist evolution and genomics and specific projects include elucidating the endosymbiotic origin of photosynthetic organelles (plastids), functional genomics of “red tide”-causing dinoflagellates, erecting the eukaryotic tree of life, and studying microRNA evolution.

Key questions that drive ongoing research in our lab are:

1. How do photosynthetic endosymbionts become organelles and how does intracellular gene transfer from the endosymbiont shape nuclear genome evolution?
The long-term goal is to explain the origin of one of the fundamental characters that define eukaryotes, intracellular organelles of foreign origin.

2. What is the origin of the processes and molecular machines that are essential for the integration of plastid function with overall cellular function?
Using the expanding genome data, bioinformatics, and experimental methods, provide a detailed model of the integration of the plastid endosymbiont into “host” cell biochemistry.

3. Which environmental and genetic factors control formation of harmful algal blooms (e.g., red tides) and which genes comprise the saxitoxin biosynthetic pathway in the toxic dinoflagellate Alexandrium tamarense?
The long-term goal is to predict and potentially ameliorate red tides that devastate coastal fisheries worldwide.

4. How do the “simple” genomes of unicellular algae respond to the highly complex, changing aquatic environments in which they live?
Using comparative genomics and analysis of small RNAs in model algae we seek to understand how variation in the genome and gene expression confers adaptation to different environmental niches.

5. What is the framework of the eukaryotic tree of life?
Using phylogenetic and phylogenomic approaches infer an accurate and broadly sampled tree of life for microbial eukaryotes.

Selected Publications

Borchert GM, Gilmore BL, Spengler RM, Xing Y, Lanier W, Bhattacharya D, Davidson BL. (2009) Adenosine deamination in human transcripts generates novel microRNA binding sites. Hum Mol Genet. Sep 23. [Epub ahead of print]

Moustafa, A., Beszteri, B., Maier, U.G., Bowler, C., Valentin, K. and Bhattacharya, D. (2009) Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 324: 1724-1726.

Worden, A.Z., Lee, J.-H., Mock, T., Rouzé, P., Simmons, M.P., Aerts, A.L., Allen, A.E., Cuvelier, M.L., Derelle, E., Everett, M.V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S.M., Schnitzler Parker, M., Rombauts, S., Salamov, A., Von Dassow, P., Badger, J.H., Coutinho, P.M., Demir, E., Dubchak, I., Gentemann, W. Eikrem, J.E. Gready, U. John, W. Lanier, E.A. Lindquist, S. Lucas, K.F.X. Mayer, C., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E.V., Bhattacharya, D., Goodenough, U.W., Van de Peer, Y. and Grigoriev, I.V. (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324: 268-272.

Moustafa, A., Loram, J.E., Hackett, J.D., Anderson, D.M., Plumley, F.G. and Bhattacharya, D. (2009) Origin of saxitoxin biosynthetic genes in cyanobacteria. PLoS One 4: e5758.

Reeb, V.C., Peglar, M.T., Yoon, H.S., Bai, J.R., Wu, M., Shiu, P., Grafenberg, J.L., Reyes-Prieto, A., Rümmele, S.E., Gross, J. and Bhattacharya, D. (2009) Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists. Mol Phylogenet Evol 53: 202-11.

Soares, M.B., de Fatima Bonaldo,M., Hackett,J.D. and Bhattacharya, D. (2009) Expressed sequence tags: normalization and subtraction of cDNA libraries expressed sequence tags\ normalization and subtraction of cDNA libraries. Methods Mol Biol 533: 109-122.

Wu, M., Comeron, J.M., Yoon, H.S. and Bhattacharya, D. (2009) Unexpected dynamic gene family evolution in algal actins. Mol Biol Evol 26: 249-253.

Gross, J., and Bhattacharya, D. (2009) Mitochondrial and plastid evolution in eukaryotes: an outsider’s perspective. Nature Rev Genet 10: 495-505.

Rumpho, M.E., Worful,J.M., Lee, J., Kannan, K., Tyler, M.S., Bhattacharya, D., Moustafa, A. and Manhart, J.R. (2008) Horizontal gene transfer of the algal nuclear gene psbO to the nucleus of the photosynthetic sea slug Elysia chlorotica. Proc Natl Acad Sci USA 105: 17867-17871.