Robert K Jansen

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. pmc The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms
    Michael G Bausher
    USDA ARS, Horticultural Research Laboratory, Fort Pierce, FL 34945 3030, USA
    BMC Plant Biol 6:21. 2006
  2. pmc The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms
    Seung Bum Lee
    Dept of Molecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Building 20, Orlando, FL 32816 2364, USA
    BMC Genomics 7:61. 2006
  3. pmc Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms
    Tracey Ruhlman
    Department of Molecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Building 20, Room 336, Orlando, FL 32816 2364, USA
    BMC Genomics 7:222. 2006
  4. pmc Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus
    Linda A Raubeson
    Biological Sciences, Central Washington University, Ellensburg, WA 98926 7537, USA
    BMC Genomics 8:174. 2007
  5. pmc Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes
    Mary E Cosner
    Department of Plant Biology, Ohio State University, Columbus OH 43210, USA
    BMC Evol Biol 4:27. 2004
  6. pmc Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 104:19369-74. 2007
  7. pmc Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
    BMC Evol Biol 6:32. 2006
  8. ncbi request reprint Methods for obtaining and analyzing whole chloroplast genome sequences
    Robert K Jansen
    Section of Integrative Biology, The University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, Texas 78712 0253, USA
    Methods Enzymol 395:348-84. 2005
  9. doi request reprint Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids
    P Roxanne Steele
    Section of Integrative Biology, The University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    Mol Phylogenet Evol 48:1013-26. 2008
  10. pmc Complete plastid genome sequences of three Rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, USA
    Mol Biol Evol 28:835-47. 2011

Collaborators

Detail Information

Publications44

  1. pmc The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms
    Michael G Bausher
    USDA ARS, Horticultural Research Laboratory, Fort Pierce, FL 34945 3030, USA
    BMC Plant Biol 6:21. 2006
    ..We have sequenced the Citrus chloroplast genome to facilitate genetic improvement of this crop and to assess phylogenetic relationships among major lineages of angiosperms...
  2. pmc The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms
    Seung Bum Lee
    Dept of Molecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Building 20, Orlando, FL 32816 2364, USA
    BMC Genomics 7:61. 2006
    ..In addition, the sequence data were used to assess phylogenetic relationships among the major clades of rosids using cotton and 25 other completely sequenced angiosperm chloroplast genomes...
  3. pmc Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms
    Tracey Ruhlman
    Department of Molecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Building 20, Room 336, Orlando, FL 32816 2364, USA
    BMC Genomics 7:222. 2006
    ..Additionally, the sequence data add to the rapidly growing database of plastid genomes for assessing phylogenetic relationships among angiosperms...
  4. pmc Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus
    Linda A Raubeson
    Biological Sciences, Central Washington University, Ellensburg, WA 98926 7537, USA
    BMC Genomics 8:174. 2007
    ....
  5. pmc Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes
    Mary E Cosner
    Department of Plant Biology, Ohio State University, Columbus OH 43210, USA
    BMC Evol Biol 4:27. 2004
    ..However, chloroplast genomes of Campanulaceae represent an exception and phylogenetic analyses solely based on chloroplast rearrangement characters support a reasonably well-resolved tree...
  6. pmc Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 104:19369-74. 2007
    ..Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements...
  7. pmc Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
    BMC Evol Biol 6:32. 2006
    ..We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids...
  8. ncbi request reprint Methods for obtaining and analyzing whole chloroplast genome sequences
    Robert K Jansen
    Section of Integrative Biology, The University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, Texas 78712 0253, USA
    Methods Enzymol 395:348-84. 2005
    ....
  9. doi request reprint Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids
    P Roxanne Steele
    Section of Integrative Biology, The University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    Mol Phylogenet Evol 48:1013-26. 2008
    ..This reduced set of primer pairs for amplifying low-copy nuclear markers along with a recommended experimental strategy provide a framework for identifying phylogenetically informative regions in angiosperms...
  10. pmc Complete plastid genome sequences of three Rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, USA
    Mol Biol Evol 28:835-47. 2011
    ..Using previously published angiosperm divergence time estimates, we suggest that these transfers occurred approximately 56-58, 34-37, and 26-27 Ma for the Fabaceae, Fagaceae, and Passifloraceae, respectively...
  11. ncbi request reprint Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae)
    Debra R Hansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA
    Mol Phylogenet Evol 45:547-63. 2007
    ....
  12. pmc Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA
    Mol Phylogenet Evol 48:1204-17. 2008
    ..The availability of the complete chickpea plastid genome sequence also provides valuable information on intergenic spacer regions among legumes and endogenous regulatory sequences for plastid genetic engineering...
  13. doi request reprint Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes
    Rosemarie C Haberle
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    J Mol Evol 66:350-61. 2008
    ..Genes for tRNAs occur at many but not all inversion endpoints, so some combination of repeats and tRNA genes may have mediated these rearrangements...
  14. pmc Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae
    Mary M Guisinger
    Section of Integrative Biology, University of Texas, Austin, TX 78712, USA
    J Mol Evol 70:149-66. 2010
    ..The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes...
  15. pmc Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids
    Zhengqiu Cai
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
    BMC Evol Biol 6:77. 2006
    ....
  16. doi request reprint Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage
    Mary M Guisinger
    Section of Integrative Biology, University of Texas, Austin, USA
    Mol Biol Evol 28:583-600. 2011
    ..We propose that increases in genomic rearrangements, repetitive DNA, nucleotide substitutions, and GC content may be caused by relaxed selection resulting from improper DNA repair...
  17. doi request reprint Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)
    J Chris Blazier
    Section of Integrative Biology, University of Texas, Austin, TX 78712, USA
    Plant Mol Biol 76:263-72. 2011
    ..Comparative biochemistry between Erodium species with and without plastid-encoded ndh genes may elucidate changes in photosynthetic function and the role of the Ndh complex...
  18. pmc Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions
    Mary M Guisinger
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin TX 78712, USA
    Proc Natl Acad Sci U S A 105:18424-9. 2008
    ..To explain these remarkable substitution patterns in the highly rearranged Geraniaceae plastid genomes, we propose a model of aberrant DNA repair coupled with altered gene expression...
  19. doi request reprint Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions
    Zhengqiu Cai
    The University of Texas at Austin, Austin, TX 78712, USA
    J Mol Evol 67:696-704. 2008
    ..At least some of this unique DNA may represent horizontal transfer from bacterial genomes. These unusual features provide direction for the development of more complex models of plastid genome evolution...
  20. ncbi request reprint The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants
    Timothy W Chumley
    The University of Texas at Austin, TX, USA
    Mol Biol Evol 23:2175-90. 2006
    ..We propose simple models that account for the major rearrangements with a minimum of 8 IR boundary changes and 12 inversions in addition to several insertions of duplicated sequence...
  21. doi request reprint Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology
    Michael Gruenstaeudl
    Department of Systematic and Evolutionary Botany, Faculty Center of Botany, University of Vienna, Vienna, Austria
    Mol Phylogenet Evol 51:572-87. 2009
    ..An early vicariance in the subfamily's distribution is revealed. X=9 is supported as the ancestral base chromosome number for both Barnadesioideae and the family as a whole...
  22. doi request reprint Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae)
    Mao Lun Weng
    Section of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
    Mol Phylogenet Evol 64:654-70. 2012
    ....
  23. ncbi request reprint Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms
    Andrew J Alverson
    Plant Biology Graduate Program, The University of Texas at Austin, 1 University Station A6700, Austin, TX 78712, USA
    Mol Phylogenet Evol 45:193-210. 2007
    ....
  24. doi request reprint Reconstruction of the ancestral plastid genome in geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates
    Mao Lun Weng
    Department of Integrative Biology, University of Texas, Austin
    Mol Biol Evol 31:645-59. 2014
    ..Possible mechanisms that might contribute to this correlation, including DNA repair system and selection, are discussed. ..
  25. ncbi request reprint A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats
    Ruth E Timme
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station C0930, Austin, Texas 78712 USA
    Am J Bot 94:302-12. 2007
    ..These detailed analyses in Asteraceae contribute to a broader understanding of plastid evolution across flowering plants...
  26. ncbi request reprint Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae)
    Michael J Moore
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A6700, Austin, TX 78712, USA
    Mol Phylogenet Evol 39:668-87. 2006
    ..This sequence of divergence events in Tiquilia agrees well with earlier researchers' ideas concerning North American desert flora assembly...
  27. doi request reprint The plastid genomes of flowering plants
    Tracey A Ruhlman
    Integrative Biology, University of Texas at Austin, Austin, TX, USA
    Methods Mol Biol 1132:3-38. 2014
    ....
  28. pmc Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids
    Seongjun Park
    Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
    BMC Genomics 15:405. 2014
    ....
  29. pmc Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing
    Jin Zhang
    Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W, 24th St, Stop C0930, Austin, TX 78712, USA
    BMC Plant Biol 13:228. 2013
    ..To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum...
  30. ncbi request reprint ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae
    Leslie R Goertzen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Mol Phylogenet Evol 29:216-34. 2003
    ..Combined analyses of ndhF and ITS sequences provide additional resolution and support for relationships in the family...
  31. ncbi request reprint Automatic annotation of organellar genomes with DOGMA
    Stacia K Wyman
    Department of Computer Sciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Bioinformatics 20:3252-5. 2004
    ..Annotations are stored on our password-protected server to enable repeated sessions of working on the same genome. Finished annotations can be extracted for direct submission to GenBank...
  32. ncbi request reprint Distance-based genome rearrangement phylogeny
    Li San Wang
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Mol Evol 63:473-83. 2006
    ..Our study shows that tree reconstruction under these two methods is much more accurate when based on EDE distances than when based on other distances previously suggested for whole genomes...
  33. ncbi request reprint Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions
    Hae Lim Lee
    School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
    Mol Biol Evol 24:1161-80. 2007
    ..However, their genome organization is surprisingly similar despite the distant relationship of these 2 angiosperm families...
  34. ncbi request reprint The influence of the Miocene Mediterranean desiccation on the geographical expansion and genetic variation of Androcymbium gramineum (Cav.) McBride (Colchicaceae)
    Juli Caujapé-Castells
    Laboratorio de Biodiversidad Molecular, Jardín Botánico Canario Viera y Clavijo, Ap de correos 14 de Tafira Alta, 35017 Las Palmas de Gran Canaria, Spain
    Mol Ecol 12:1515-25. 2003
    ..24, average DNei = 0.089), but did not hinder the maintenance of considerable levels of genetic variation in either geographical area (A = 2.14, HE = 0.230 and A = 1.90, HE = 0.213, respectively)...
  35. pmc Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes
    Christopher Saski
    Clemson University Genomics Institute, Clemson University, Biosystems Research Complex, 51 New Cherry Street, Clemson, SC 29634, USA
    Theor Appl Genet 115:571-90. 2007
    ..Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae...
  36. pmc The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms
    Nalapalli Samson
    University of Central Florida, Department of Molecular Biology and Microbiology, Biomolecular Science, Building 20, Orlando, FL 32816 2364, USA
    Plant Biotechnol J 5:339-53. 2007
    ..The availability of the complete chloroplast genome of coffee provides regulatory and intergenic spacer sequences for utilization in chloroplast genetic engineering to improve this important crop...
  37. ncbi request reprint Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae)
    Ki Joong Kim
    School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
    Mol Biol Evol 22:1783-92. 2005
    ..The divergence time estimates also suggest that the Asteraceae originated in the mid Eocene (42-47 MYA)...
  38. pmc The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron
    Henry Daniell
    Department Molecular Biology and Microbiology, College of Medicine, University of Central Florida, 4000 Central Florida Blvd, Biomolecular Science Bldg 20, Room 336, Orlando, FL 32816 2364, USA
    Theor Appl Genet 116:723-37. 2008
    ....
  39. ncbi request reprint Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes
    Christopher Saski
    Clemson University Genomics Institute, Clemson University, Biosystems Research Complex, 51 New Cherry Street, Clemson, SC 29634, USA
    Plant Mol Biol 59:309-22. 2005
    ..The presence of small repeats of psbA and rbcL in legumes that have lost one copy of the IR indicate that this loss has only occurred once during the evolutionary history of legumes...
  40. pmc ChloroplastDB: the Chloroplast Genome Database
    Liying Cui
    Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802, USA
    Nucleic Acids Res 34:D692-6. 2006
    ....
  41. ncbi request reprint Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasets
    Janet C Barber
    Department of Biology, University of Missouri, 8001 Natural Bridge Road, St Louis 63121, USA
    Mol Phylogenet Evol 23:293-306. 2002
    ..The phylogenies also demonstrate a distinct increase in woodiness among the Macaronesian species relative to their continental congeners, providing further support for the secondary nature of woodiness in island plants...
  42. ncbi request reprint Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes
    Henry Daniell
    Department of Molecular Biology and Microbiology, Biomolecular Science, University of Central Florida, 4000 Central Florida Blvd, Bldg 20, Room 336, Orlando, FL 32816 2364, USA
    Theor Appl Genet 112:1503-18. 2006
    ..It is possible that there has been a loss of conserved editing sites in potato and tomato...
  43. ncbi request reprint Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of Life Sciences, The Pennsylvania State University, PA, USA
    Mol Biol Evol 22:1948-63. 2005
    ....
  44. pmc Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    OMICS 10:231-7. 2006
    ..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors...