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Jeffrey Palmer

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Aaron O Richardson; Gregory J Young; Andrew J Alverson; Danny W Rice; Jeffrey D Palmer
The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate.
Daniel B Sloan; Martin Wu; Andrew J Alverson; John P Chuckalovcak; David E McCauley; Jeffrey D Palmer; Douglas R Taylor
Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates.
Daniel B Sloan; Andrew J Alverson; Jeffrey D Palmer; Martin Wu; Douglas R Taylor
Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene.

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All Publications

2013: Aaron O Richardson; Gregory J Young; Andrew J Alverson; Danny W Rice; Jeffrey D Palmer
The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate.
BMC biology 2013;11():29.
2012: Daniel B Sloan; Martin Wu; Andrew J Alverson; John P Chuckalovcak; David E McCauley; Jeffrey D Palmer; Douglas R Taylor
Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates.
PLoS biology 2012;10(1):e1001241.
2012: Daniel B Sloan; Andrew J Alverson; Jeffrey D Palmer; Martin Wu; Douglas R Taylor
Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene.
Genome biology and evolution 2012;4(3):294-306.
2011: Andrew J Alverson; Kerrie Barry; Stephanie Dickinson; Danny W Rice; Jeffrey D Palmer
Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber.
The Plant cell 2011;23(7):2499-513.
2011: Andrew J Alverson; Shi Zhuo; Danny W Rice; Daniel B Sloan; Jeffrey D Palmer
The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats.
PloS one 2011;6(1):e16404.
2010: Weilong Hao; Aaron O Richardson; Yihong Zheng; Jeffrey D Palmer
Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(50):21576-81.
2010: Daniel B Sloan; Alice H MacQueen; Andrew J Alverson; Jeffrey D Palmer; Douglas R Taylor
Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: selection vs. retroprocessing as the driving force.
Genetics 2010;185(4):1369-80.
2010: Daniel B Sloan; Andrew J Alverson; Helena Storchová; Jeffrey D Palmer; Douglas R Taylor
Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia.
BMC evolutionary biology 2010;10():274.
2009: Weilong Hao; Jeffrey D Palmer
Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(39):16728-33.
2008: Patrick J Keeling; Jeffrey D Palmer
Horizontal gene transfer in eukaryotic evolution.
Nature reviews. Genetics 2008;9(8):605-18.
2008: Douglas E Soltis; Victor A Albert; Jim Leebens-Mack; Jeffrey D Palmer; Rod A Wing; Claude W dePamphilis; Hong Ma; John E Carlson; Naomi Altman; Sangtae Kim; P Kerr Wall; Andrea Zuccolo; Pamela S Soltis
The Amborella genome: an evolutionary reference for plant biology.
Genome biology 2008;9(3):402.
2007: Peik Haugen; Debashish Bhattacharya; Jeffrey D Palmer; Seán Turner; Louise A Lewis; Kathleen M Pryer
Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns.
BMC evolutionary biology 2007;7():159.
2007: Jeffrey P Mower; Pascal Touzet; Julie S Gummow; Lynda F Delph; Jeffrey D Palmer
Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants.
BMC evolutionary biology 2007;7():135.
2007: Aaron O Richardson; Jeffrey D Palmer
Horizontal gene transfer in plants.
Journal of experimental botany 2007;58(1):1-9.
2006: Timothy W Chumley; Jeffrey D Palmer; Jeffrey P Mower; H Matthew Fourcade; Patrick J Calie; Jeffrey L Boore; Robert K Jansen
The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.
Molecular biology and evolution 2006;23(11):2175-90.
2006: Jeffrey P Mower; Jeffrey D Palmer
Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris.
Molecular genetics and genomics : MGG 2006;276(3):285-93.
2006: Danny W Rice; Jeffrey D Palmer
An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters.
BMC biology 2006;4():31.
2006: Han Chuan Ong; Jeffrey D Palmer
Pervasive survival of expressed mitochondrial rps14 pseudogenes in grasses and their relatives for 80 million years following three functional transfers to the nucleus.
BMC evolutionary biology 2006;6():55.
2005: Christopher L Parkinson; Jeffrey P Mower; Yin-Long Qiu; Andrew J Shirk; Keming Song; Nevin D Young; Claude W dePamphilis; Jeffrey D Palmer
Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae.
BMC evolutionary biology 2005;5():73.
2004: Patrick J Keeling; John M Archibald; Naomi M Fast; Jeffrey D Palmer
Comment on "The evolution of modern eukaryotic phytoplankton".
Science (New York, N.Y.) 2004;306(5705):2191; author reply 2191.
2004: Yangrae Cho; Jeffrey P Mower; Yin-Long Qiu; Jeffrey D Palmer
Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(51):17741-6.
2004: Ulfar Bergthorsson; Aaron O Richardson; Gregory J Young; Leslie R Goertzen; Jeffrey D Palmer
Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(51):17747-52.
2004: Jeffrey P Mower; Sasa Stefanović; Gregory J Young; Jeffrey D Palmer
Plant genetics: gene transfer from parasitic to host plants.
Nature 2004;432(7014):165-6.
2004: Jeffrey D Palmer; Douglas E Soltis; Mark W Chase
The plant tree of life: an overview and some points of view.
American journal of botany 2004;91(10):1437-45.
2004: Douglas E Soltis; Victor A Albert; Vincent Savolainen; Khidir Hilu; Yin-Long Qiu; Mark W Chase; James S Farris; Sasa Stefanović; Danny W Rice; Jeffrey D Palmer; Pamela S Soltis
Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics.
Trends in plant science 2004;9(10):477-83.
2004: Sasa Stefanović; Danny W Rice; Jeffrey D Palmer
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
BMC evolutionary biology 2004;4():35.
2004: Yin-Long Qiu; Jeffrey D Palmer
Many independent origins of trans splicing of a plant mitochondrial group II intron.
Journal of molecular evolution 2004;59(1):80-9.
2004: Delphine Gerbod; Emily Sanders; Shigeharu Moriya; Christophe Noel; Hirotoshi Takasu; Naomi M Fast; Pilar Delgado-Viscogliosi; Moriya Ohkuma; Toshiaki Kudo; Monique Capron; Jeffrey D Palmer; Patrick J Keeling; Eric Viscogliosi
Molecular phylogenies of Parabasalia inferred from four protein genes and comparison with rRNA trees.
Molecular phylogenetics and evolution 2004;31(2):572-80.
2003: Keith L Adams; Jeffrey D Palmer
Evolution of mitochondrial gene content: gene loss and transfer to the nucleus.
Molecular phylogenetics and evolution 2003;29(3):380-95.
2003: Ulfar Bergthorsson; Keith L Adams; Brendan Thomason; Jeffrey D Palmer
Widespread horizontal transfer of mitochondrial genes in flowering plants.
Nature 2003;424(6945):197-201.
2003: Michael P Cummings; Jacqueline M Nugent; Richard G Olmstead; Jeffrey D Palmer
Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms.
Current genetics 2003;43(2):131-8.
2002: Keith L Adams; Yin-Long Qiu; Mark Stoutemyer; Jeffrey D Palmer
Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(15):9905-12.
2002: Keith L Adams; Daniel O Daley; James Whelan; Jeffrey D Palmer
Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts.
The Plant cell 2002;14(4):931-43.
2002: Daniel O Daley; Keith L Adams; Rachel Clifton; Svenja Qualmann; A Harvey Millar; Jeffrey D Palmer; Elke Pratje; James Whelan
Gene transfer from mitochondrion to nucleus: novel mechanisms for gene activation from Cox2.
The Plant journal : for cell and molecular biology 2002;30(1):11-21.
2001: Keith L Adams; H C Ong; Jeffrey D Palmer
Mitochondrial gene transfer in pieces: fission of the ribosomal protein gene rpl2 and partial or complete gene transfer to the nucleus.
Molecular biology and evolution 2001;18(12):2289-97.
2001: Patrick J Keeling; Jeffrey D Palmer
Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(19):10745-50.
2001: Keith L Adams; M Rosenblueth; Yin-Long Qiu; Jeffrey D Palmer
Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution.
Genetics 2001;158(3):1289-300.
2001: R S Millen; R G Olmstead; Keith L Adams; Jeffrey D Palmer; Nga T Lao; Laura Heggie; T A Kavanagh; Julian M Hibberd; John C Gray; C W Morden; P J Calie; L S Jermiin; Kenneth H Wolfe
Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus.
The Plant cell 2001;13(3):645-58.
2000: Daniel L Nickrent; Christopher L Parkinson; Jeffrey D Palmer; RJ Duff
Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants.
Molecular biology and evolution 2000;17(12):1885-95.
2000: Keith L Adams; Daniel O Daley; Yin-Long Qiu; James Whelan; Jeffrey D Palmer
Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants.
Nature 2000;408(6810):354-7.
2000: Jeffrey D Palmer; Keith L Adams; Yangrae Cho; Christopher L Parkinson; Yin-Long Qiu; Keming Song
Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(13):6960-6.
2000: Patrick J Keeling; Jeffrey D Palmer
Parabasalian flagellates are ancient eukaryotes.
Nature 2000;405(6787):635-7.
2000: S M Chaw; Christopher L Parkinson; Y Cheng; T M Vincent; Jeffrey D Palmer
Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(8):4086-91.
2000: A Besendahl; Y L Qiu; J Lee; Jeffrey D Palmer; Debashish Bhattacharya
The cyanobacterial origin and vertical transmission of the plastid tRNA(Leu) group-I intron.
Current genetics 2000;37(1):12-23.
1999: Christopher L Parkinson; Keith L Adams; Jeffrey D Palmer
Multigene analyses identify the three earliest lineages of extant flowering plants.
Current biology : CB 1999;9(24):1485-8.
1999: Keith L Adams; Keming Song; P G Roessler; J M Nugent; Jane L Doyle; Jeff J Doyle; Jeffrey D Palmer
Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(24):13863-8.
1999: S Turner; K M Pryer; V P Miao; Jeffrey D Palmer
Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis.
The Journal of eukaryotic microbiology 1999;46(4):327-38.
1998: Yangrae Cho; Yin-Long Qiu; P Kuhlman; Jeffrey D Palmer
Explosive invasion of plant mitochondria by a group I intron.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(24):14244-9.
1998: Yin-Long Qiu; Yangrae Cho; J C Cox; Jeffrey D Palmer
The gain of three mitochondrial introns identifies liverworts as the earliest land plants.
Nature 1998;394(6694):671-4.
1997: A Stoltzfus; JM Logsdon; Jeffrey D Palmer; W Ford Doolittle
Intron "sliding" and the diversity of intron positions.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(20):10739-44.
1997: Mary E Cosner; Robert K Jansen; Jeffrey D Palmer; S R Downie
The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families.
Current genetics 1997;31(5):419-29.
1997: Jeffrey D Palmer
Organelle genomes: going, going, gone!
Science (New York, N.Y.) 1997;275(5301):790-1.
1997: N Y Stassen; JM Logsdon; G J Vora; H H Offenberg; Jeffrey D Palmer; Miriam E Zolan
Isolation and characterization of rad51 orthologs from Coprinus cinereus and Lycopersicon esculentum, and phylogenetic analysis of eukaryotic recA homologs.
Current genetics 1997;31(2):144-57.
1996: S M Barns; C F Delwiche; Jeffrey D Palmer; Norman R Pace
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(17):9188-93.
1996: Jeffrey D Palmer; C F Delwiche
Second-hand chloroplasts and the case of the disappearing nucleus.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(15):7432-5.
1996: C F Delwiche; Jeffrey D Palmer
Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids.
Molecular biology and evolution 1996;13(6):873-82.
1996: Jeff J Doyle; Jane L Doyle; J A Ballenger; Jeffrey D Palmer
The distribution and phylogenetic significance of a 50-kb chloroplast DNA inversion in the flowering plant family Leguminosae.
Molecular phylogenetics and evolution 1996;5(2):429-38.
1996: S M Barns; C F Delwiche; Jeffrey D Palmer; S C Dawson; K L Hershberger; Norman R Pace
Phylogenetic perspective on microbial life in hydrothermal ecosystems, past and present.
Ciba Foundation symposium 1996;202():24-32; discussion 32-9.
1995: Jeffrey D Palmer
Rubisco rules fall; gene transfer triumphs.
BioEssays : news and reviews in molecular, cellular and developmental biology 1995;17(12):1005-8.
1995: P Kuhlman; Jeffrey D Palmer
Isolation, expression, and evolution of the gene encoding mitochondrial elongation factor Tu in Arabidopsis thaliana.
Plant molecular biology 1995;29(5):1057-70.
1995: S C Ems; C W Morden; C K Dixon; K H Wolfe; C W dePamphilis; Jeffrey D Palmer
Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana.
Plant molecular biology 1995;29(4):721-33.
1995: J M Logsdon; Michael G Tyshenko; C Dixon; J D-Jafari; Virginia K Walker; Jeffrey D Palmer
Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(18):8507-11.
1995: C F Delwiche; M Kuhsel; Jeffrey D Palmer
Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids.
Molecular phylogenetics and evolution 1995;4(2):110-28.
1994: S R Downie; D S Katz-Downie; K H Wolfe; P J Calie; Jeffrey D Palmer
Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution.
Current genetics 1994;25(4):367-78.
1993: J M Nugent; Jeffrey D Palmer
Characterization of the Brassica campestris mitochondrial gene for subunit six of NADH dehydrogenase: nad6 is present in the mitochondrion of a wide range of flowering plants.
Current genetics 1993;23(2):148-53.
1992: K H Wolfe; C W Morden; Jeffrey D Palmer
Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(22):10648-52.
1992: K H Wolfe; C W Morden; S C Ems; Jeffrey D Palmer
Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes.
Journal of molecular evolution 1992;35(4):304-17.
1992: K H Wolfe; D S Katz-Downie; C W Morden; Jeffrey D Palmer
Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes.
Plant molecular biology 1992;18(6):1037-48.
1992: Jeffrey D Palmer; D Soltis; P Soltis
Large size and complex structure of mitochondrial DNA in two nonflowering land plants.
Current genetics 1992;21(2):125-9.
1992: K H Wolfe; C W Morden; Jeffrey D Palmer
Small single-copy region of plastid DNA in the non-photosynthetic angiosperm Epifagus virginiana contains only two genes. Differences among dicots, monocots and bryophytes in gene organization at a non-bioenergetic locus.
Journal of molecular biology 1992;223(1):95-104.
1992: C W Morden; C F Delwiche; M Kuhsel; Jeffrey D Palmer
Gene phylogenies and the endosymbiotic origin of plastids.
Bio Systems 1992;28(1-3):75-90.
1991: K H Wolfe; C W Morden; Jeffrey D Palmer
Ins and outs of plastid genome evolution.
Current opinion in genetics & development 1991;1(4):523-9.
1991: Jeffrey D Palmer; J M Logsdon
The recent origins of introns.
Current opinion in genetics & development 1991;1(4):470-7.
1991: G W Taylor; K H Wolfe; C W Morden; C W dePamphilis; Jeffrey D Palmer
Lack of a functional plastid tRNA(Cys) gene is associated with loss of photosynthesis in a lineage of parasitic plants.
Current genetics 1991;20(6):515-8.
1991: C W Morden; K H Wolfe; C W dePamphilis; Jeffrey D Palmer
Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes.
The EMBO journal 1991;10(11):3281-8.
1990: M G Kuhsel; R Strickland; Jeffrey D Palmer
An ancient group I intron shared by eubacteria and chloroplasts.
Science (New York, N.Y.) 1990;250(4987):1570-3.
1990: C W dePamphilis; Jeffrey D Palmer
Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant.
Nature 1990;348(6299):337-9.
1990: S L Baldauf; J R Manhart; Jeffrey D Palmer
Different fates of the chloroplast tufA gene following its transfer to the nucleus in green algae.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(14):5317-21.
1990: Jeffrey D Palmer
Contrasting modes and tempos of genome evolution in land plant organelles.
Trends in genetics : TIG 1990;6(4):115-20.