Research Topics
| Robert K JansenSummaryAffiliation: University of Texas Country: USA Publications
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Detail Information
Publications
The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiospermsMichael 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...- The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiospermsSeung 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... - Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiospermsTracey 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... - Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthusLinda A Raubeson
Biological Sciences, Central Washington University, Ellensburg, WA 98926 7537, USA
BMC Genomics 8:174. 2007.... - Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomesMary E Cosner
Department of Plant Biology, Ohio State University, Columbus OH 43210, USA
BMC Evol Biol 4:27. 2004..The rearrangement characters, though relatively few in number, support robust and meaningful phylogenetic hypotheses and provide new insights into evolutionary relationships within the Campanulaceae... - Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patternsRobert 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... - Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosidsRobert 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... 
Methods for obtaining and analyzing whole chloroplast genome sequencesRobert 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....
Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosidsP 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...- 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... - 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.... - Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genesRosemarie 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... - Complete plastid genome sequences of three Rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleusRobert 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... - Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliidsZhengqiu 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.... - Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceaeMary 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... - Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usageMary 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... - 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... - Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutionsMary 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... - Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertionsZhengqiu 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... - Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphologyMichael 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... - The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plantsTimothy 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... - 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.... - Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatomsAndrew 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.... - A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeatsRuth 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... - 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... - Automatic annotation of organellar genomes with DOGMAStacia 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... - ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the AsteraceaeLeslie 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... - 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 intronHenry 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.... - Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomesChristopher 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... - 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)... - 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)... - Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zoneJim 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.... - Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomesChristopher 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... - ChloroplastDB: the Chloroplast Genome DatabaseLiying 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.... - Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomesHenry 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... - Distance-based genome rearrangement phylogenyLi 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... - The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiospermsNalapalli 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... - Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversionsHae 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... - Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasetsJanet 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... - 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...