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Richard A. Jorgensen

Comparative Genomics

Richard A. Jorgensen

Comparative Genomics

Previous positions

1997 – 2010 Professor, School of Plant Sciences, University of Arizona, Tucson

1991 - 1997 Research Geneticist, University of California, Davis

1983 - 1990 Director, Floriculture Genetic Engineering Research; DNA Plant Technology Corp. & Advanced Genetic Sciences, Inc., Oakland, CA

1981 - 1983 Research Geneticist, Department of Genetics, University of California, Davis

Education and training

1978 - 1981 Postdoctoral Fellow, Department of Plant Biology, Carnegie Institution of Washington, Stanford, California

1973 - 1978 Ph.D., Biochemistry, University of Wisconsin; Madison, Wisconsin

1969 1973 M.S., Chemistry; B.S., Biomedical Engineering; Northwestern University, Evanston, Illinois


Martin Gibbs Medal, American Society of Plant Biologists, July, 2007, for pioneering work leading to the discovery of RNAi.

Inaugural ASPB Fellow, July, 2007 (American Society of Plant Biologists)

AAAS Fellow, February, 2006 (American Association for the Advancement of Sciences)

Editor-in-Chief, The Plant Cell, 2003 – 2007

Bud Antle Endowed Chair for Excellence in Agriculture and Life Sciences, College of Agriculture and Life Sciences, University of Arizona, 2008-2010.

Selected as one of the ‘Top 5 Research Articles in The Plant Cell’s First 20 Years’, 2008 (Napoli et al., 1990).

Outstanding University Achievement, University of Arizona, for leadership of the iPlant Collaborative the largest NSF grant ($50 million/5 years) ever awarded to the State of Arizona, February, 2008.

RNAi Innovator Award, May, 2006, 4th International Boston RNAi Conference

Publications list

Petsch, K.A., C. Ma, M.J. Scanlon1 and R.A. Jorgensen.. 2010. Functionally targeted mutagenesis by transitive RNAi. Plant Journal 61, 873–882

DePaoli, E., A.E. Dorantes-Acosta, J. Zhai, M. Accerbi, D.H. Jeong, B.C. Meyers, R.A. Jorgensen, P.J. Green. 2009. Distinct extremely abundant siRNAs associated with cosuppression in Petunia. RNA 15: 1949-1964.

Hayden, C.A., and R.A. Jorgensen. 2007. Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes. BMC Biology 5:32.

Lin, M-K., H. Belanger, Y-J. Lee, E. Varkonyi-Gasic, K-I Taoka, E. Miura, B. Xoconostle-Cázares, K. Gendler, R.A. Jorgensen, B. Phinney, T.J. Lough and W.J. Lucas. FT protein but not FT mRNA is present in the phloem sap of flowering cucurbits. 2007. Plant Cell 19:1488-1506.

Müller, AE, Atkinson, RG, Sandoval, RG, and RA Jorgensen. 2007. Microhomologies between T-DNA ends and target sites often occur in inverted orientation and may be responsible for the high frequency of T-DNA-associated inversions. Plant Cell Rep. 26:617-630.

Merchant, S., et al. 2007. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848):245-50.

Palenik, B., et al. 2007. The genome sequence of Ostreococcus lucimarinus: Tiny Eukaryotes Provide Genomic Insights Into The Paradox Of The Plankton. Proc. Natl. Acad. Sci. 104(18): 7705 - 7710.

Jorgensen R.A., N. Doetsch, A.E. Müller, Q. Que, K. Gendler and C.A. Napoli. 2006. A Paragenetic Perspective on Integration of RNA Silencing into the Epigenome and Its Role in the Biology of Higher Plants. Cold Spring Harbor Symp. Quant. Biol. 71:481-485.

Tuskan, G., et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313: 1596-1604.

Hayden, C.A., Wheeler, T.J., and R.A. Jorgensen. 2005. Evaluating and improving cDNA sequence quality with cQC. Bioinformatics 21: 4414 - 4415.

*Jorgensen, R.A. 2005. Restructuring the genome in response to adaptive challenge: McClintock’s bold conjecture revisited. Cold Spring Harbor Symp. Quant. Biol. 69:349-354.

Kerschen, A., C.A. Napoli, R.A. Jorgensen, and A.E. Muller. 2004. Effectiveness of RNA interference in transgenic plants. FEBS Letters 566:223-228.

*Jorgensen, R.A. 2003. Sense cosuppression in plants: past, present and future. In: RNAi: a Guide to Gene Silencing (ed. G. J. Hannon), Cold Spring Harbor Laboratory Press, pp. 5-21.

Jorgensen, R.A., Q. Que, and C.A. Napoli. 2002. Maternally controlled ovule abortion results from cosuppression of dihydroflavonol-4-reductase or flavonoid-3′, 5′-hydroxylase genes in Petunia hybrida. Functional Plant Biology 29:1501-1506.

Pandey, R., A. Muller, CA Napoli, DA Selinger, CS Pikaard, EJ Richards, J Bender, DW Mount, and RA Jorgensen. 2002. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eucaryotes. Nucleic Acids Research 30:5036-5055.

The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.

Que, Q., and R.A. Jorgensen. 1998. Homology-based control of gene expression patterns in transgenic petunia flowers. Developmental Genetics 22:100-109.

Que, Q., H.-Y. Wang, and R.A. Jorgensen. 1998. Distinct patterns of pigment suppression are produced by allelic sense and antisense chalcone synthase transgenes in petunia flowers. Plant Journal 13: 401-409.

*Jorgensen, R.A., R.G. Atkinson, R.L.S. Forster, and W.J. Lucas. 1998. An RNA-based information superhighway in plants. Science 279: 1486-1487.

Que, Q., H.-Y. Wang, J.J. English, and R.A. Jorgensen. 1997. The frequency and degree of cosuppression by chalcone synthase transgenes are dependent on transgene promoter strength and are reduced by premature nonsense codons in the transgene coding sequence. Plant Cell 9:1357-1368.

Jorgensen, R.A., P.D. Cluster, J. English, Q. Que, and C.A. Napoli. 1996. Chalcone synthase cosuppression phenotypes in petunia flowers: comparison of sense vs. antisense constructs and single copy vs. complex T-DNA sequences. Plant Molecular Biology 31:957-973.

°Jorgensen, R.A., Q. Que, J. English, and H. Wang. 1996. Sense cosuppression of flower color genes: Metastable morphology-based phenotypes and the prepattern-threshold hypothesis. In: V. Russo, R. Martienssen, and A. Riggs, eds., Epigenetics, CSHL Press: Cold Spring Harbor. pp. 393-402.

°Jorgensen, R.A., and C.A. Napoli. 1996. A responsive regulatory system is revealed by sense suppression of pigment genes in Petunia flowers. In: JP Gustafson and RB Flavell, eds., Genomes of Plants and Animals: 21st Stadler Genetics Symposium, Plenum Press: New York. pp. 159-176. (original research)

Jorgensen, R.A. 1995. Cosuppression, flower color patterns, and metastable gene expression states. Science 268: 686-691.

Robbins, T.P., A.G.M. Gerats, H. Fiske, and R. A. Jorgensen. 1995. Suppression of recombination in wide hybrids of Petunia hybrida as revealed by genetic mapping of marker transgenes. Theoretical and Applied Genetics 90:957-968.

Jorgensen, R. 1994. Developmental significance of epigenetic impositions on the plant genome: a paragenetic function for chromosomes. Developmental Genetics 15(6): 523-532.

°Jorgensen, R. 1994. The genetic origins of biosynthesis and light-responsive control of the chemical UV screen of land plants. In: BE Ellis et al, ed., Genetic Engineering of Plant Secondary Metabolism, Plenum Press: New York, pp.179-192.

*Jorgensen, R. 1993. The germinal inheritance of epigenetic information in plants. Philosophical Transactions of the Royal Society London Series B 339:173-181.

°Jorgensen, R. 1993. Elicitation of organized pigmentation patterns by a chalcone synthase transgene. In: R. Amasino, ed., Cellular Communication in Plants. Plenum Press: New York, pp. 87-92.

Jorgensen, R. 1993. The origin of land plants: a union of alga and fungus advanced by flavonoids? Biosystems 31:193-207. (original research)

°Jorgensen, R. 1993. The modification of horticultural plant phenotypes by direct gene transfer. Scientia Horticulturae 55:1-4.

Taylor, L.P., and R. Jorgensen. 1992. Conditional male fertility in chalcone synthase-deficient petunia. Journal of Heredity 83:11-17.

*Jorgensen, R. 1992. Silencing of plant genes by homologous transgenes. AgBiotech News and Information 4(9): 265N-273N.

°Jorgensen, R., and J. Mol. 1991. Modulation of flower color and its intensity via directed gene manipulation. In: J. Harding, F. Singh, and J. Mol (eds.) Genetics and Breeding of Ornamental Species. Kluwer Academic Publishers: Dortrecht, pp. 309-316.

DNA Plant Technology Corp. (engineering plant gene expression)

*Dooner, H.K., T.P. Robbins, and R.A. Jorgensen. 1991. Genetic and developmental control of anthocyanin biosynthesis. Annual Review of Genetics. 25:173-199.

Napoli, C., C. Lemieux, and R. Jorgensen. 1990. Introduction of a chimeric chalcone synthase gene into petunia results in reversible cosuppression of expression of homologous genes in trans. Plant Cell 2:279289.

*Jorgensen, R. 1990. Altered gene expression in plants due to trans interactions between homologous genes. Trends in Biotechnology 8:340-344.

*Mol, J., A. Stuitje, A. Gerats, A. van der Krol, and R. Jorgensen. 1989. Saying it with genes: molecular flower breeding. Trends in Biotechnology, 7:148-153.

Jorgensen, R., C. Snyder, and J. Jones. 1987. TDNA is organized predominantly in inverted repeat structures in plants transformed with Agrobacterium tumefaciens C58 derivatives. Molec Gen Genet 207:471-477.

Jones, J., D. Gilbert, K. Grady, and R. Jorgensen. 1987. TDNA structure and gene expression in petunia plants transformed by Agrobacterium tumefaciens C58 derivatives. Molec Gen Genet 207:478485.

Jorgensen, R. 1987. A hybrid seed production method based on synthesis of novel linkages between marker and malesterile genes. Crop Science 27:806-810.

°Jorgensen, R. 1987. Synthetic linkages and genetic stability in transgenic plants: implications for breeding. In: DJ Nevins and RA Jones, eds., Tomato Biotechnology. Alan R Liss, Inc.: New York, pp. 179188.

Chyi, Y.S., R. Jorgensen, D. Goldstein, S. Tanksley, and F. LoaizaFigueroa. 1986. Locations of Agrobacteriummediated TDNA insertions in the Lycopersicon genome. Molec. Gen. Genet., 204:6469.

Postdoctoral research (molecular genetics, population genetics, molecular evolution)

Allard, R., M. SaghaiMaroof, Q. Zhang, and R. Jorgensen. 1990. Genetic and molecular organization of ribosomal DNA (rDNA) variants in wild and cultivated barley. Genetics 126:743751.

Neale, D., M. SaghaiMaroof, R. Allard, and R. Jorgensen. 1988. Chloroplast DNA diversity in populations of wild and cultivated barley. Genetics 120:1105-1110.

Jorgensen, R., and P. Cluster. 1988. Modes and tempos in the evolution of nuclear ribosomal DNA: new characters for evolutionary studies useful at several taxonomic levels. Annals of Missouri Botanical Garden 75:1238-1247.

Jorgensen, R., R. Cuellar, W. Thompson, and T Kavanaugh. 1987. Structure and variation in ribosomal RNA genes of pea. Plant Mol Biol 8:3-12.

Palmer, J., R. Jorgensen, and W. Thompson. 1985. Chloroplast DNA variation and evolution in Pisum: patterns of change and phylogenetic analysis. Genetics 109:195213.

SaghaiMaroof, M., K. Soliman, R. Jorgensen, and R. Allard. 1984. Ribosomal DNA spacerlength polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. PNAS 81:80148018.

Thompson, W., M. Everett, N. Polans, R. Jorgensen, and J. Palmer. 1983. Phytochrome control of RNA levels in developing pea and mung bean leaves. Planta 158:487500.

Palmer, J., H. Edwards, R. Jorgensen, and W. Thompson. 1982. Novel evolutionary variation in transcription and location of two chloroplast genes. Nucleic Acids Research 10:68196832.

Graduate research (bacterial genetics – transposable elements)

Schmidt, F., R. Jorgensen, M. DeWilde and J. Davies. 1981. A specific tetracycline induced low molecular weight RNA encoded by the inverted repeats of Tn10 (IS10). Plasmid 6:148150.

Wray, L., R. Jorgensen, and W. Reznikoff. 1981. Identification of the tetracycline resistance promoter and repressor in transposon Tn10. J Bacteriol 147(2):297304.

Rothstein, S., R. Jorgensen, J.C.P. Yin, Y. Zang, R. Johnson, and W. Reznikoff. 1981. Genetic organization of Tn5. Cold Spring Harbor Symp Quant Biol 45:99105.

Berg, D., C. Egner, B. Hirschel, J. Howard, L. Johnsrud, R. Jorgensen, and T. Tlsty. 1981. Insertion, excision and inversion of Tn5. Cold Spring Harbor Symp Quant Biol 45:115123.

Rothstein, S., R. Jorgensen, K. Postle, and W. Reznikoff. 1980. The inverted repeats of Tn5 are functionally different. Cell 19:795805.

Jorgensen, R., S. Rothstein, and W. Reznikoff. 1979. A restriction enzyme cleavage map of Tn5 and physical location of a region encoding neomycin resistance. Molec Gen Genetics 177:6572.

Jorgensen, R., and W. Reznikoff. 1979. Organization of structural and regulatory genes that mediate tetracycline resistance in the Tn10 transposon. J Bacteriol 138:705714.

Jorgensen, R., D. Berg, B. Allet, and W. Reznikoff. 1979. A restriction enzyme cleavage map of Tn10, a transposon that encodes tetracycline resistance. J Bacteriol 137: 681685.

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