Papers/Publications

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Recent Papers:

2007

Jansen, R.K., Z. Cai, L.A. Raubeson, H. Daniell, C.W. dePamphilis, J. Leebens-Mack, K.F. Muller, M. Guisinger-Bellian, R.C. Haberle, A.K. Hansen, T.W. Chumley, S.B. Lee, R. Peery, J.R. McNeal, J.V. Kuehl, J.L. Boore. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc. Nat. Acad. Sci. USA 2007, 104(49):19369-19374.
Kong, H., L. Landherr, M. Frohlich, J. Leebens-Mack, H. Ma and C.W. dePamphilis. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. The Plant Journal 2007, 50:873-885.
Barakat, A., K. Wall, J. Leebens-Mack, Y.J. Wang, J.E. Carlson and C.W. dePamphilis. Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. The Plant Journal 2007, 51(6):991-1003.
Soltis, D.E., H. Ma, M.W. Frohlich, P.S. Soltis, V.A. Albert, D.G. Oppenheimer, N.S. Altman, C.W dePamphilis and J. Leebens-Mack. The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends in Plant Science 2007, 12(8):358-67.

2006

Duarte, J.M., Wall, P.K., Leebens-Mack, J.H. and C.W. dePamphilis. Utility of Amborella trichopoda and Nuphar advena ESTs for phylogeny and comparative sequence analysis. Taxon (submitted) June 2006. ABSTRACT - Expressed sequence tags (ESTs) for Amborella trichopoda and the water lily Nuphar advena have proven valuable in identification of gene pairs to study the timing of duplication events relative to the most recent common ancestor (MRCA) of all extant angiosperms. Here we discuss how ESTs for these taxa are also useful for deducing gene families that were present in the MRCA of all flowering plants. For example, 4572 gene clusters identified in an analysis of the rice and Arabidopsis proteomes contained putative orthologs of Amborella or Nuphar. Homologs of many developmentally important genes were identified from Amborella or Nuphar in these gene clusters. This number of ancestral genes is expected to increase as the number of Amborella and water lily ESTs increases. Genes found unduplicated in the rice and Arabidopsis genomes may be especially useful for phylogenetic analyses including diverse angiosperm lineages. We identify 595 of these single copy genes with putative orthologs in Amborella or Nuphar. Phylogenetic analysis of one family of nuclear single-copy genes encoding the enzyme carboxymethylenebutenolidase yields a topology that places Amborella and Nuphar as the earliest branching extant lineages of angiosperms and is generally consistent with current angiosperm phylogenies based mainly on chloroplast, mitochondrial, and nuclear ribosomal sequences.

Altman, N., Leebens-Mack, J., Zahn, L., Chanderbali, A., Tian, D., Werner, L., Ma, H. and dePamphilis, C. Behind the scenes: Planning a mulitspecies microarray experiment. Chance 2006, 19(3):28-39.

Cai, Z., C. Penaflor, J.V. Kuehl, J.H. Leebens-Mack, J.E. Carlson, C.W. dePamphilis , J.L. Boore and R.K. Jansen. Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids. BMC Evolutionary Biology 2006, 6(1):77.

Carlson, J.E., J.H. Leebens-Mack, P.K. Wall, L.M. Zahn, L.A. Mueller, L.L. Landherr, Y. Hu, D.C. Ilut, J.M. Arrington S. Choirean, A. Becker, D. Field, S.D. Tanksley, H. Ma, C.W. dePamphilis. EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot. Plant Molecular Biology 2006, 62:351-369.

Cui, L., P.K. Wall, J.H. Leebens-Mack, B.G. Lindsay, D.E. Soltis, J.J. Doyle, P.S. Soltis, J.E. Carlson, K. Arumuganathan, A. Barakat, V.A. Albert, H. Ma and C.W. dePamphilis. Widespread genome duplications throughout the history of flowering plants. Genome Research 2006, 16:738-739.

Cui, L., J.H. Leebens-Mack, L-S.Wang, J. Tang, L. Rymarquis, D.B. Stern, and C.W. dePamphilis. Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evolutionary Biology 2006, 6:13.

Cui, L, N. Veeraraghavan, A. Richter, K. Wall, R.K. Jansen, J. Leebens-Mack, I. Makalowska, and C. W. dePamphilis. ChloroplastDB: the chloroplast genome database. Nucleic Acids Research, 2006, vol. 34, Database issue, D692-D696.

Link to: ChloroplastDB

Duarte, J.M., L. Cui, K. Wall, Q. Zhang, X. Zhang, J.H. Leebens-Mack, H. Ma, N. Altman, and C.W. dePamphilis. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Molecular Biology and Evolution 2006, 23(2):469-478.

Leebens-Mack, J.H., Wall, K., Duarte, J., Zheng, Z., Oppenheimer, D. and dePamphilis, C.W. A Genomics Approach to the Study of Ancient Polyploidy and Floral Developmental Genetics. In Developmental Genetics of the Flower, D.E. Solits, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series, Elsevier Limited, London, 2006, vol. 44, pp. 527-549.

Leebens-Mack, J.H., T. Vision, E. Brenner, J.E. Bowers, S. Cannon, M.J. Clement, C.W. Cunningham, C.W. dePamphilis, R. deSalle, J.J. Doyle, J.A. Eisen, X. Gu, J. Harshman, R.K. Jansen, E.A. Kellogg, E.V. Koonin, B.D. Mishler, H. Philippe, J.C. Pires, Y.L. Qiu, S.Y. Rhee, K. Sjolander, D.E. Soltis, P.S. Soltis, D.W. Stevenson, K. Wall, T. Warnow, C. Zmasek. Taking the first steps towards a standard for reporting on phylogenies: minimal information about a phylogenetic analysis (MIAPA). Omics 2006, 10(2):231-237.

McNeal, J.R., J.H. Leebens-Mack, K. Arumuganathan, J. Kuehl, J.L. Boore and C.W. dePamphilis. Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques 2006, 41:69-73.

Modliszewski, J.L., D.T. Thomas, C. Fan, C.J. Crawford, C.W. dePamphilis, and Q-Y. (Jenny) Xiang. Ancestral chloroplast polymorphism and historical secondary contact in a broad hybrid zone of Aesculus (Sapindaceae). American Journal of Botany 2006, 93(3):377-388.

Tuskan, G.A. and 103 others. The genome of black cottonwood, Populus trichcarpa (Torr. and Gray ex Brayshaw). Science 2006, 313:1596-1604.

Zahn, L.M., J. Leebens-Mack, J.M. Arrington, Y. Hu, L. Landherr, C.W. dePamphilis, A. Becker, G. Theissen, and H. Ma. Conservation and divergence in the AGAMOUS Subfamily of MADS-Box Genes: evidence of independent sub- and neofunctionalization events. Evolution and Development 2006, 8(1):30-45.

2005

Albert, V.A., D.E. Soltis, J. Carlson, W.G. Farmerie, K. Wall, D.C. Ilut, T. M. Solow, L.A. Mueller, L.L. Landherr, Y. Hu, M. Buzgo, S. Kim, M-J. Yoo, M.W. Frohlich, R. Perl-Treves, S. Schlarbaum, B. Bliss, X. Zhang, S. Tanksley, D.G. Oppenheimer, P.S. Soltis, H. Ma, C.W. dePamphilis, and J.H. Leebens-Mack. Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biology 2005, 5:5.
Jansen, R.K., L.A. Raubeson, J.L. Boore, C.W. dePamphilis, T.W. Chumley, R.C. Haberle, S.K. Wyman, A.J. Alverson, R. Peery, S.J. Herman, H.M. Fourcade, J.V. Kuehl, J.R. McNeal, J.H. Leebens-Mack, and L. Cui. Methods for obtaining and analyzing chloroplast genome sequences. In Methods in Enzymology Vol. 395, pp. 348-384. E. A. Zimmer, ed., Elsevier 2005.

Leebens-Mack, J.H., L.A. Raubeson, L. Cui, J.V. Kuehl, M.H. Fourcade, T.W. Chumley, J.L. Boore, R.K. Jansen, and C.W. dePamphilis. Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way Out of the Felsenstein Zone. Molecular Biology and Evolution 2005, 22(10):1948-1963.

Parkinson, C.L., J.P. Mower, Y-L. Qiu, A.J. Shirk, K. Song, N.D. Young, C.W. dePamphilis and J.D. Palmer. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evolutionary Biology 2005, 5:73.

Sampedro, J., Y. Lee, R.E. Carey, C. dePamphilis and D.J. Cosgrove. Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family. The Plant Journal 2005, 44(3):409-419.

Soltis, D.E., V.A. Albert, S. Kim, M.-J. Yoo, P.S. Soltis, M.W. Frohlich, J.H. Leebens-Mack, H.-Z. Kong, K. Wall, H. Ma, and C.W. dePamphilis. Evolution of the Flower. In Plant Diversity and Evolution: Genotype and Phenotypic Variation in Higher Plants, Ed. R.J. Henry. CABI Publishers. 2005.

Wang, J.Z., B.G. Lindsay, L. Cui, P.K. Wall, J. Marion, J. Zhang, and C.W. dePamphilis Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. BMC Bioinformatics 2005, 6:300. Advanced access

; Provisional publication

Wang, W., M. Tanurdzic, M. Luo, N. Sisneros, H.R. Kim, J-K. Weng, D. Kudrna, C. Mueller, K. Arumuganathan, J. Carlson, C. Chapple, C.W. dePamphilis, D. Mandoli, J. Tomkins, R.A. Wing, and J.A. Banks. Construction of a bacterial artificial chromosome library from spikemoss Selaginella moellendorffii: A new resource for plant comparative genomics. BMC Plant Biology. 2005, 5:10.

Young, N.D. and C.W. dePamphilis. Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function. BMC Evolutionary Biology 2005, 5:16.

Zahn, L.M., J.H. Leebens-Mack, C.W. dePamphilis, H. Ma, and G. Theissen. To B or not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of angiosperms. Journal of Heredity2005, 96(3): 225-240.

Zahn, L.M., H.-Z. Kong, J.H. Leebens-Mack, S. Kim, P.S. Soltis, L.L. Landherr, D.E. Soltis, C.W. dePamphilis, and H. Ma The evolution of the SEPALLATA subfamily of MADS-box genes: A pre-angiosperm origin with multiple duplications throughout angiosperm history. Genetics 2005, 169: 2209-2223.

2004

Kong, H.-Z., J. Leebens-Mack, W. Ni, C.W. depamphilis and H. Ma. Highly heterogeneous rates of evolution in the SKP1 gene family in animals and plants: functional and evolutionary implications. Molecular Biology and Evolution 2004, 21:117-128.

Tang, J., B.M.E. Moret, L. Cui, and C.W. dePamphilis Phylogenetic reconstruction from arbitrary gene-order data. Proc. 4th IEEE Conf. on Bioinformatics and Bioengineering BIBE'04 592-599, IEEE Press [online, peer-review publication].

Wang, G.*, H. Kong*, Y. Sun*, X. Zhang, W. Zhang, N. Altman, C.W. dePamphilis, and H. Ma Genome-wide analysis of cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. Plant Physiol 2004, 135: 1084-1099. (* equal contribution)

Wang J-P. Z., B.G. Lindsay, J. Leebens-Mack, L. Cui, K. Wall, W.C. Miller, and C.W. dePamphilis EST Clustering Error Evaluation and Correction. Bioinformatics 2004, 20:2973-84.

Selected Older "Favorites":

(search PubMed for dePamphilis papers)

Barkman, T.J., G. Chenery, J.R. McNeal, J. Lyons-Weiler, W.J. Elisens, G. Moore, A.D. Wolfe, and C.W. dePamphilis. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. Proceedings of the National Academy of Sciences 2000, 97: 13166-13171.
Bowe, L.M., G. Coat, and Claude W. dePamphilis. Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales'closest relatives are conifers. Proceedings of the National Academy of Sciences 2000, 97: 4092-4097.

Bowe, L.M. and C.W. dePamphilis. Effects of RNA editing and gene processing on phylogenetic reconstruction. Molecular Biology and Evolution 1996, 13: 1159-1166.

Burke, J.M., R. Wyatt, C.W. dePamphilis and M.L. Arnold. Nectar characteristics of interspecific hybrids and their parents in Aesculus (Hippocastanaceae) and Iris (Iridaceae). Journal of the Torrey Botanical Club 2002, 127: 200-206.

dePamphilis, C.W. Genes and genomes (of parasitic plants). pp. 177-205. In Parasitic Plants. Edited by Malcolm C. Press and Jonathan D. Graves. Chapman and Hall, London. 1995. ISBN 0 412 37120 0.

dePamphilis, C.W. and H.S. Neufeld Phenology and ecophysiology of Aesculus sylvatica, a vernal understory tree. Canadian Journal of Botany 1988, 67:2161-2167.

dePamphilis, C.W. and Palmer, J.D. Loss of photosynthetic and chlororespiratory genes from the plastid genome of a nonphotosynthetic plant. Nature 1990, 348:337-339.

dePamphilis, C.W. and R. Wyatt. Electrophoretic confirmation of interspecific hybridization in Aesculus and the genetic structure of a broad hybrid zone. Evolution 1990, 44: 1295-1317.

dePamphilis, C.W. and R. Wyatt. Hybridization and introgression in buckeyes (Aesculus: Hippocastanaceae): A review of the evidence and a hypothesis to explain long-distance gene flow. Systematic Botany 1989, 14: 593-611.

dePamphilis, C.W., N.D. Young and A.D. Wolfe. Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: Many losses of photosynthesis and complex patterns of rate variation. Proceedings of the National Academy of Sciences 1997, 94:7367-7372.

Ems, S.C., C.W. Morden, C.K. Dixon, K.H. Wolfe, C.W. dePamphilis and J.D. Palmer. Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Molecular Biology 1995, 29:721-733.

Leebens-Mack, J.H. and C.W. dePamphilis. Power analysis of tests for loss of selective constraint in cave crayfish and nonphotosynthetic plant lineages. Molecular Biology and Evolution 2002, 19:1292-1302.

Ma, H. and Claude dePamphilis. The ABCs of flower evolution. Cell 2000, 101: 5-8.

Maul, J.E., J.W. Lilly, L. Cui., C.W. dePamphilis, W. Miller, E.H. Harris, and D.B. Stern The Chlamydomonas reinhardtii plastid chromosome: Islands of genes in a sea of repeats. The Plant Cell 2002, 14: 2659-2679.

Nam, J., C.W. dePamphilis, H. Ma, and M. Nei Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Molecular Biology Evolution 2003, 20:1435-47.

Nickrent , D.L., R.J. Duff, A.E. Colwell, A.D. Wolfe, N.D. Young, K.E. Steiner, and C.W. dePamphilis. Molecular phylogenetic and evolutionary studies of parasitic plants. D. Soltis, P. Soltis, and J. Doyle, eds. Chapter 14 for Molecular Systematics of Plants, II. pp. 211-241. 1998.

Nickrent, D., Y. Ouyang, J. Duff, and C.W. dePamphilis. Do nonasterid holoparasitic flowering plants have plastid genomes? Plant Molecular Biology 1997, 34: 717-729.

Olmstead, R.G., C.W. dePamphilis, A.D. Wolfe, N.D. Young, W. Elisens, P. Reeves. Disintegration of the Scrophulariaceae. American Journal of Botany 2001, 88(2): 348-361.

Smith, D., T. J., Barkman, and C.W. dePamphilis. Hemiparasitism. S.A. Levin, ed. In Encyclopedia of Biodiversity. V. 3, pp. 317-328. Academic Press. 2001.

Soltis, D.E., P.S. Soltis, V.A. Albert, D.G. Oppenheimer, C.W. dePamphilis, H. Ma, M.W. Frohlich, and G. Theissen Missing Links: The genetic architecture of the flower and floral diversification. Trends In Plant Science 2002, 7: 22-31.

Wolfe, A.D. and C.W. dePamphilis. The effect of relaxed functional constraints on rbcL in photosynthetic and nonphotosynthetic plants. Molecular Biology and Evolution 1998, 15: 1243-1258

Wolfe, A.D. and C.W. dePamphilis. Alternate paths of evolution for the photosynthetic gene rbcL in four nonphotosynthetic species of Orobanche. Plant Molecular Biology 1997, 33: 965-977.

Xiang, Q-Y., D.J. Crawford, A.D. Wolfe, Y-C Tang, and C.W. dePamphilis. Origin and biogeography of Aesculus L. (Hippocastanaceae) in a molecular phylogenetic perspective. Evolution 1998, 52:988-997.

Young, N.D., K.E. Steiner, and C.W. dePamphilis. Evolution of parasitism in the Scrophulariaceae/Orobanchaceae: Plastid gene sequences refute an evolutionary transition series. Annals of the Missouri Botanical Garden. 1999, 86:876-893.

Young, N.D. and Claude W. dePamphilis. Purifying selection detected in the plastid matK and flanking ribozyme regions within a group II intron of non-photosynthetic plants. Molecular Biology and Evolution 2000, 17: 1933-1941.

(search PubMed for dePamphilis papers)

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