Plastid publications

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Sequencing and informatics with both academic and corporate partners

Some of our scientists' publications on plastid genomes:

Guisinger, M. M., J. V. Kuehl, J. L. Boore and R. K. Jansen, 2011 Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: Rearrangements, repeats, and codon usage. Molecular Biology and Evolution 28: 583-600.

Karol, K. G., K. Arumuganathan, J. L. Boore, A. M. Duffy, K. D. E. Everett, J. D. Hall, S. K. Hansen, J. V. Kuehl, D. F. Mandoli, B. D. Mishler, R. G. Olmstead, K. S. Renzaglia and P. G. Wolf, 2010 Complete plastome sequences of Equisetum arvense and Isoetes flaccida: Implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evolutionary Biology 10: 321.

Oliver, M. J., A. G. Murdock, B. D. Mishler, J. V. Kuehl, J. L. Boore, D. F. Mandoli, K. Everett, P. G. Wolf and K. G. Karol, 2010 Chloroplast genome sequence of the moss Tortula ruralis: Gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. BMC Genomics 11: 143.

Guisinger, M. M., T. W. Chumley, J. V. Kuehl, J. L. Boore and R. K. Jansen, 2010 Implications of the plastid genome sequence of Typha (Typhaceae, Poales) for understanding genome evolution in Poaceae. Journal of Molecular Evolution 70: 149-166.

McNeal, J. R., J. Kuehl, J. L. Boore, J. Leebens-Mack and C. W. dePamphilis, 2009 Parallel loss of plastid introns and their maturase in the genus Cuscuta. PLoS One 4: e5982.

Zhengqiu, C., H.-G. Kim, E. Ruck, M. Guisinger, V. McMurtry, J. V. Kuehl, J. L. Boore and R. K. Jansen, 2008 Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. Journal of Molecular Evolution 67: 696-704.

Guisinger, M. M., J. V. Kuehl, J. L. Boore and R. K. Jansen, 2008 Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions. Proceedings of the National Academy of Sciences USA 105: 18424-18429.

McCoy, S. K. R., J. V. Kuehl, J. L. Boore and L. A. Raubeson, 2008 Complete plastid genome sequence of Welwitschia mirabilis: An usually compact plastome with accelerated divergence rates. BMC Evolutionary Biology 8: 130.

Haberle, R. C., H. M. Fourcade, J. L. Boore and R. K. Jansen, 2008 Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. Journal of Molecular Evolution 66: 350-361.

Wickett, N. J., Y. Zhang, S. K. Hansen, J. M. Roper, J. V. Kuehl, S. A. Plock, P. G. Wolf, C. W. dePamphilis, J. L. Boore and B. Goffinet, 2008 Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis (Metzgeriales, Aneuraceae). Molecular Biology and Evolution 25: 393-401.

McNeal, J. R., K. Arumugunathan, J. V. Kuehl, J. L. Boore and C. W. dePamphilis, 2007 Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). BMC Biology 5: 55.

Jansen, R. K., Z. Cai, L. A. Raubeson, H. Daniell, C. W. dePamphilis, J. Leebens-Mack, K. Müller, M. Guisinger-Bellian, R. C. Haberle, A. K. Hansen, T. W. Chumley, S.-B. Lee, R. Peery, J. McNeal, J. V. Kuehl and J. L. Boore, 2007 Analysis of 81 genes from 64 chloroplast genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences USA 104: 19369-19374.

McNeal, J. R., J. Kuehl, J. L. Boore and C. W. dePamphilis, 2007 Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biology 7: 57.

Hansen, D. R, S. G. Dastidar, Z. Cai, C. Penaflor, J. V. Kuehl, J. L. Boore and R. K. Jansen, 2007 Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Molecular Phylogenetics and Evolution 45: 547-563.

Roper, J., S. K. Hansen, P. G. Wolf, K. G. Karol, D. F. Mandoli, K. Everett, J. Kuehl and J. L. Boore, 2007 The complete plastid genome sequence of Angiopteris evecta (G. Forst.) Hoffm. (Marattiaceae). American Fern Journal 97: 95-106.

Timme, R. E., J. V. Kuehl, J. L. Boore and R. K. Jansen, 2007 A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: Identification of divergent regions and categorization of shared repeats. American Journal of Botany 94: 302-312.

Raubeson, L. A., R. Peery, T. W. Chumley, C. Dziubek, H. M. Fourcade, J. L. Boore and R. K. Jansen, 2007 Comparative chloroplast genomics: Analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8: 174.

Cai, Z., C. Penaflor, J. V. Kuehl, J. Leebens-Mack, J. Carlson, C. W. dePamphilis, J. L. Boore and R. K. Jansen, 2006 Complete plastid genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogenetic relationships of magnoliids. BMC Evolutionary Biology 6: 77.

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

Chumley, T. W., J. D. Palmer, J. P. Mower, H. Matthew Fourcade, P. J. Calie, J. L. Boore and R. K. Jansen, 2006 The complete chloroplast genome sequence of Pelargonium * hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Molecular Biology and Evolution 23: 2175-2190.

Leebens-Mack, J., L. A. Raubeson, L. Cui, J. V. Kuehl, H. M. Fourcade, T. W. Chumley, J. L. Boore, R. K. Jansen and C. W. dePamphilis, 2005 Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution 22: 1948-1963.

Jansen, R. K., L. A. Raubeson, J. L. Boore, C. W. dePamphilis, T. W. Chumley, R. C. Haberle, S. K. Wyman, A. Alverson, R. Peery, S. J. Herman, H. M. Fourcade, J. V. Kuehl, J. R. McNeal, J. Leebens-Mack and L. Cui, 2005 Methods for obtaining and analyzing whole chloroplast genome sequences. In Molecular Evolution: Producing the Biochemical Data, Part B (E. A. Zimmer and E. Roalson, eds.). Volume 395 of the Methods in Enzymology series, Elsevier, Burlington, Massachusetts, pp. 348-384.

Wolf, P. G., K. G. Karol, D. F. Mandoli, J. Kuehl, K. Arumuganathan, M. W. Ellis, B. D. Mishler, D. Kelch, R. Olmstead, J. L. Boore, 2005 The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae): Implications for land plant phylogeny. Gene 350(2): 117-128.

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