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1 Horizontal gene transfer (Lateral gene transfer) Jer-Ming Hu Jer-Ming Hu CC CC 3.0 3.0 Unless noted, the course materials are licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Taiwan (CC BY-NC-SA 3.0)-SA 3.0) Slide 2 2 Definition of horizontal gene transfer Horizontal gene transfer (HGT) can be defined as the transfer of genetic information from one genome to another. Three major types: Inter-species HGT: e.g. in lateral gene transfer (LGT) in bacteria Transformation Conjugation Transduction Intra-species HGT Within cell HGT Horizontal gene transfer (HGT) can be defined as the transfer of genetic information from one genome to another. Three major types: Inter-species HGT: e.g. in lateral gene transfer (LGT) in bacteria Transformation Conjugation Transduction Intra-species HGT Within cell HGT Slide 3 3 Mechanisms of HGT Hybridization Recombination of genomes Mitochondrial or chloroplast capture Lineage sorting Recurrence of HGT, e.g. mitochondria captured by transmissible cancer CTVT. Parasitism Grafting in plants Vectors like virus, fungi, aphids Hybridization Recombination of genomes Mitochondrial or chloroplast capture Lineage sorting Recurrence of HGT, e.g. mitochondria captured by transmissible cancer CTVT. Parasitism Grafting in plants Vectors like virus, fungi, aphids Slide 4 4 Interkingdom DNA transfer Bacteria fungi Bacteria animals Bacteria plants Eukaryotic DNA transfer Animals-animals Drosophila melanogaster and D. willistoni Bov-B LINEs in snake and lizard Plants-plants Plants-fungi Interkingdom DNA transfer Bacteria fungi Bacteria animals Bacteria plants Eukaryotic DNA transfer Animals-animals Drosophila melanogaster and D. willistoni Bov-B LINEs in snake and lizard Plants-plants Plants-fungi HGT that involves eukaryotes Slide 5 5 Catalases (Klotz et a., 1997, Mol. Biol. Evol. 14: 951-958.), proline racemase and PhzF, Mpk1, etc. (Fitzpatrick 2012. FEMS Microbiol. 329: 1) Incongruence in phylogeny Marcet-Houben & Gabaldon (2010, TIG 26:5) showed 713 genes from 60 fungal species are likely derived from bacteria. Catalases (Klotz et a., 1997, Mol. Biol. Evol. 14: 951-958.), proline racemase and PhzF, Mpk1, etc. (Fitzpatrick 2012. FEMS Microbiol. 329: 1) Incongruence in phylogeny Marcet-Houben & Gabaldon (2010, TIG 26:5) showed 713 genes from 60 fungal species are likely derived from bacteria. Interkingdom DNA transfers: bacteria- fungi Slide 6 6 HGT is highly concentrated in Pezizomycotina ( ) Helvella crispa (Pezizomycotina) Source: Marina Marcet-Houben and Toni Gabaldn 2010. Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics 26: p. 5. Wikipedia Strobilomyces Slide 7 7 PapD proteins in human cells (Leu-1/CD5) and E. coli (PapD) Holmgren & Branden (1989) Nature 342: 248- 251. Amino acids 4~252 of Leu-1/CD5 protein has 26% identity w/ PapD Note: CD5 (lymphocyte differentiation antigen) is variable in general Phosphoglucose isomerases (PGI) Katz (1996) J. Mol. Evol. 43: 453-459. Incongruence in phylogeny PapD proteins in human cells (Leu-1/CD5) and E. coli (PapD) Holmgren & Branden (1989) Nature 342: 248- 251. Amino acids 4~252 of Leu-1/CD5 protein has 26% identity w/ PapD Note: CD5 (lymphocyte differentiation antigen) is variable in general Phosphoglucose isomerases (PGI) Katz (1996) J. Mol. Evol. 43: 453-459. Incongruence in phylogeny Interkingdom DNA transfers: bacteria- animals Slide 8 8 Agrobacterium tumefaciens-angiosperms Agrobacterium rhizogenes and Nicotiana glauca Gene transfer from bacteria to plant rolC gene from Nicotiana is also present on the T-DNA of A. rhizogenes, showing 75% homology Southern blots shows only hybridized with Nicotiana spp. (Furner et al. 1986) Agrobacterium tumefaciens-angiosperms Agrobacterium rhizogenes and Nicotiana glauca Gene transfer from bacteria to plant rolC gene from Nicotiana is also present on the T-DNA of A. rhizogenes, showing 75% homology Southern blots shows only hybridized with Nicotiana spp. (Furner et al. 1986) Interkingdom DNA transfers: bacteria- plants Source: Ian J. Furner, Gary A. Huffman, Richard M. Amasino, David J. Garfinkel, Milton P. Gordon, and Eugene W. Nester. 1986. An Agrobacterium transformation in the evolution of the genus Nicotiana. Nature 319: p. 422. Slide 9 National Taiwan University Jer-Ming Hu 9 Agrobacterium-mediated transformation Crown gall on elm tree at UC Davis Source: Er-Min Lai 2000. Genetic and Environmental Factors Affecting T-Pilin Export and T-Pilus Biogenesis in Relation to Flagellation of Agrobacterium tumefaciens. Jorunal of Bacteriology 182: p. 3711. Slide 10 Source: Erh-Min Lai 1999. Genetic and Biochemical Characterization of the Agrobacterium T-pilus and Its Major T-pilin Subunit. PhD thesis, p. 33. University of California Davis, Davis, California, USA. 10 General Model of Agrobacterium-plant Interaction Slide 11 11 Detecting horizontal gene transfer HGT can be detected by outstanding discontinuity in the phylogenetic distribution of a certain gene. e.g. GluRS in eukaryotic organelles and some bacteria HGT can also be detected when a notable discrepancy is found between gene tree and species tree. Grouped according to geographical proximity HGT can be detected by outstanding discontinuity in the phylogenetic distribution of a certain gene. e.g. GluRS in eukaryotic organelles and some bacteria HGT can also be detected when a notable discrepancy is found between gene tree and species tree. Grouped according to geographical proximity Slide 12 12 Mitochondrial coxI intron in angiosperms Mitochondrial rps2 and rps11 Mitochondrial nad1 intron2 Mitochondrial atp1 HGT between parasitic plants & their hosts Massive transfer of mtDNAs in Amborella Mitochondrial coxI intron in angiosperms Mitochondrial rps2 and rps11 Mitochondrial nad1 intron2 Mitochondrial atp1 HGT between parasitic plants & their hosts Massive transfer of mtDNAs in Amborella DNA transfers: plants-plants Slide 13 13 Mitochondrial cox1 group I intron in angiosperms Adams et al. (1998) J. Mol. Evol. 46: 689-696. Peperomia: first known case for the presence of mt cox1 intron Cho et al. (1998) PNAS 95: 14244-14249. Survey of 335 genera in angiosperms 48 genera found to be HGT Mitochondrial cox1 group I intron in angiosperms Adams et al. (1998) J. Mol. Evol. 46: 689-696. Peperomia: first known case for the presence of mt cox1 intron Cho et al. (1998) PNAS 95: 14244-14249. Survey of 335 genera in angiosperms 48 genera found to be HGT DNA transfers: plants-plants Source: Keith L. Adams, Martin J. Clements, and Jack C. Vaughn 1998. The Peperomia Mitochondrial coxI Group I Intron: Timing of Horizontal Transfer and Subsequent Evolution of the Intron. Jorunal of Molecular Evolution 46: p. 694. Slide 14 Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14245. 14 Intron distribution: Southern blots Probed w/ Beta vulgaris cox1 exon Probed w/ Zea mays cox2 group II intron Multiple acquisition of group I intron in various angiosperms? Probed w/ Veronica ugrestis cox1 intron Slide 15 Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14246. 15 Mt cox1 intron distribution Tree of chloroplast rbcL shows the sporadic distribution of the cox1 intron among 281 angiosperms 30 intron-containing clades are identified Slide 16 Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14247. 16 Phylogenies of mt cox1 genes ML tree of cox1 exon+intron ML tree of cox1 introns ML tree of rbcL/cox1 coding sequences I, D: synapomorphic intron gaps Slide 17 Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14248. 17 Models of mt cox1 intron transfer All non-plant to plant transfer model Single non-plant to plant; all others being plant to plant transfer model Donors Recipients Slide 18 18 HGT of mitochondrial rps2 and rps11 genes Adams et al. (2002) PNAS 99: 9905-9912. Bergthorsson et al. (2003) Nature 424: 197-201. Detecting mitochondrial genes by southern blot hybridization Sequenced for their identities and conducted phylogenetic analysis Adams et al. (2002) PNAS 99: 9905-9912. Bergthorsson et al. (2003) Nature 424: 197-201. Detecting mitochondrial genes by southern blot hybridization Sequenced for their identities and conducted phylogenetic analysis Slide 19 19 Detection of mt genes by southern blots Southern blots of 91 angiosperm DNAs (280 examined total). rps2 Source: Keith L. Adams, Yin-Long Qiu, Mark Stoutemyer, and Jeffrey D. Palmer 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 99: p. 9905. Slide 20 20 Evidences from mt rps2 and rps11 -Present -Absent rps2 rps11 Tree is based on other molecular systematic studies. Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 198. Slide 21 21 Intracellular gene transfer (IGT) Transfer from nucleus back to mitochondria Expect high divergence in this genes Extraordinarily frequent and pervasive loss in eudicots Horizontal gene transfer (HGT) Intracellular gene transfer (IGT) Transfer from nucleus back to mitochondria Expect high divergence in this genes Extraordinarily frequent and pervasive loss in eudicots Horizontal gene transfer (HGT) Models to explain the phenomenon of newly presented rps2 and rps11 Slide 22 22 Analysize levels of sequence divergence and the phylogenetic relationships of rps2 and rps11 genes 31 rps2 genes and 44 rps11 genes were used Analysize levels of sequence divergence and the phylogenetic relationships of rps2 and rps11 genes 31 rps2 genes and 44 rps11 genes were used How do we examine? Slide 23 23 Mitochondrial rps2 gene phylogeny Maximum likelihood tree of rps2 (474 nt alignment), showing Actinidia rps2 is closer to monocot homologues. Expected position Actual position Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. Flickr Gerard's World Slide 24 24 Evidence in mt rps11 rps11 (456bp) Upstream of rps11 (457bp) Expected position Actual position Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. Flickr.Bambo. Slide 25 25 Sanguinaria mt rps11 5 half of rps11 (219bp) 3 half of rps11 (237bp) Sanguinaria rps11 is chimeric: 5 half is as expected 3 half is closer to monocots Sanguinaria ( , Papaveraceae) Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. Flickr BlueRidgeKitties Slide 26 26 Chimaeric structure of Sanguinaria mt rps11 Bf: Bocconia frutescens (Papaveraceae) Sc: Sanguinaria canadensis (Papaveraceae) Dh: Disporum hookeri (Liliaceae) Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 200. Slide 27 27 Sanguinaria mt rps11 15 RT-PCR sequenced They are identical to the chimeric rps11, except 5 sites of C to U RNA editing. At least transcribed, may be functional. Amborella atp1 (HGT) is also transcribed. The others showed that half of them might be pseudogenes. 4/5 intact ORFs in Caprifoliaceae rps11 1/4 intact ORF in Betulaceae rps11 Sanguinaria mt rps11 15 RT-PCR sequenced They are identical to the chimeric rps11, except 5 sites of C to U RNA editing. At least transcribed, may be functional. Amborella atp1 (HGT) is also transcribed. The others showed that half of them might be pseudogenes. 4/5 intact ORFs in Caprifoliaceae rps11 1/4 intact ORF in Betulaceae rps11 Expression of possible HGT genes Slide 28 28 Evidence in mitochondrial atp1 Maximum likelihood tree of atp1 (1254 bp alignment) Previous studies on mt atp1 Qiu et al. (1999) Nature 402: 404 Explanation: Long-branch attraction Barkman et al. (2000) PNAS 97: 13166 Explanation: Two paralogues in Amborella Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. Flickr pennstatelive Slide 29 29 The five HGT events in angiosperm mt DNA Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 200. Slide 30 30 HGT from angiosperms to Gnetum Won & Renner (2003) PNAS 100:10824 Mitochondrial nad1 intron 2 and adjacent b and c are found to have HGT from an asterid to Gnetum. Gnetum has two copies of this intron and one of them showed a euasterid origin. Won & Renner (2003) PNAS 100:10824 Mitochondrial nad1 intron 2 and adjacent b and c are found to have HGT from an asterid to Gnetum. Gnetum has two copies of this intron and one of them showed a euasterid origin. Gnetum ( ) Flickr adaduitokla Slide 31 31 Source: Hyosig Won and Susanne S. Renner 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p. 10824. Slide 32 32 Alignment of mt nad1 exons b & c Two types in Gnetum! Source: Hyosig Won and Susanne S. Renner 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p. 10824. Slide 33 33 Tree based on LFY, nrITS, rbcL, matK, and tRNA Leu intron Two types of mt nad1 found in Gnetum Source: Hyosig Won and Susanne S. Renner 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p. 10827. Slide 34 34 HGT in parasitic plants & their hosts HGT of mt nad1 in Rafflesia Davis & Wurdack (2004) Science 305:676 HGT of mt atp1 and matR in Rafflesiales Nickrent et al. (2004) BMC Evol. Biol. 4:40 HGT of mt atp1 from Cuscuta & Bartsia to Plantago Mower et al. (2004) Nature 432: 165 HGT of mt nad1 in Rafflesia Davis & Wurdack (2004) Science 305:676 HGT of mt atp1 and matR in Rafflesiales Nickrent et al. (2004) BMC Evol. Biol. 4:40 HGT of mt atp1 from Cuscuta & Bartsia to Plantago Mower et al. (2004) Nature 432: 165 Slide 35 35 Rafflesia mt nad1 b-c exons Blue: Malpighiales Red: Rafflesia and Sapria Yellow: Vitaceae, including Tetrastigma Source: Charles C. Davis and Kenneth J. Wurdack 2004. Host-to-Parasite Gene Transfer in Flowering Plants: Phylogenetic Evidence from Malpighiales. Science 345: p. 677. Flickr cornstaruk Slide 36 Flickr thedangers 36 Apodanthes flowers Bold faces: Rafflesiaceae Pilostyles thurberi Parasitic plant connection mt matR phylogeny Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson Phyto Images D. L. Nickrent Slide 37 BMC Evolutionary Biology Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson 37 mt atp1 phylogeny Mitrastema yamamotoi ( ) National Taiwan University Jer-Ming Hu Slide 38 BMC Evolutionary Biology Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson 38 Possible HGT events in Rafflesiales Slide 39 39 Mitochondrial coxI intron in angiosperms Mitochondrial rps2 and rps11 Mitochondrial nad1 intron2 Mitochondrial atp1 From Cuscuta and Bartsia (both parasites) to Plantago Mower et al. (2004) Nature 432: 165-166 From eudicots to Amborella Bergthorsson et al. (2003) Nature 424: 197-201. Massive transfer of mtDNAs in Amborella Mitochondrial coxI intron in angiosperms Mitochondrial rps2 and rps11 Mitochondrial nad1 intron2 Mitochondrial atp1 From Cuscuta and Bartsia (both parasites) to Plantago Mower et al. (2004) Nature 432: 165-166 From eudicots to Amborella Bergthorsson et al. (2003) Nature 424: 197-201. Massive transfer of mtDNAs in Amborella Interkingdom DNA transfers: plants- plants Slide 40 40 Plantago ( ) mt atp1 genes Source: Jeffrey P. Mower, Saa Stefanovi, Gregory J. Young, and Jeffrey D. Palmer 2004. Plant genetics: Gene transfer from parasitic to host plants. Nature 432: p. 165. Slide 41 41 Mitochondrial coxI intron in angiosperms Mitochondrial rps2 and rps11 Mitochondrial nad1 intron2 Mitochondrial atp1 Massive transfer of mtDNAs in Amborella Mitochondrial coxI intron in angiosperms Mitochondrial rps2 and rps11 Mitochondrial nad1 intron2 Mitochondrial atp1 Massive transfer of mtDNAs in Amborella DNA transfers: plants-plants Flickr pennstatelive Slide 42 42 Evidence in mitochondrial atp1 Maximum likelihood tree of atp1 (1254 bp alignment) Previous studies on mt atp1 Qiu et al. (1999) Nature 402: 404 Explanation: Long-branch attraction Barkman et al. (2000) PNAS 97: 13166 Explanation: Two paralogues in Amborella Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 197. Slide 43 Source: Khidir W. Hilu, Thomas Borsch, Kai Mller, Douglas E. Soltis, Pamela S. Soltis, Vincent Savolainen, Mark W. Chase, Martyn P. Powell, Lawrence A. Alice, Rodger Evans, Herv Sauquet, Christoph Neinhuis, Tracey A. B. Slotta, Jens G. Rohwer, Christopher S. Campbell, and Lars W. Chatrou 2003. Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: p. 1762. 43 Chloroplast matK phylogeny Amborella trichopoda Flickr pennstatelive Slide 44 44 Screening HGT in Amborella mitochondria About 100 pairs of primers used for amplifying 40 mt genes in angiosperms For specific genes, 13 angiosperms, 3 gymnosperms, and some bryophytes were also PCR and sequenced. Other sequences obtained from GenBank MP and ML phylogenetic analyses Shimodaira-Hasegawa (SH) test for evaluating alternative topologies (HGT vs. paralog scenarios) About 100 pairs of primers used for amplifying 40 mt genes in angiosperms For specific genes, 13 angiosperms, 3 gymnosperms, and some bryophytes were also PCR and sequenced. Other sequences obtained from GenBank MP and ML phylogenetic analyses Shimodaira-Hasegawa (SH) test for evaluating alternative topologies (HGT vs. paralog scenarios) Slide 45 45 HGT of mt genes in Amborella Multiple bands found in most PCRs of Amborella Each band was cloned and sequenced Massive HGT! Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p. 17748. Slide 46 Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p. 17749. 46 HGT from mosses to Amborella Purple: Core eudicots Red: Amborella Green: Mosses V: vertical transmisson H: Horizontal transmission Slide 47 Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p. 17749. 47 HGT from eudicots to Amborella Blue: Core eudicots Red: Amborella V: vertical transmisson H: Horizontal transmission Slide 48 48 Further thoughts on the case of Amborella Massive HGT in Amborella The sequenced plant mt genomes show no sign of HGT Why Amborella? Massive HGT in Amborella The sequenced plant mt genomes show no sign of HGT Why Amborella? Amborella trichopoda leaf from Massif de IAoupinie at New Caledonia (801m altitude) Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p. 17751. Slide 49 49 Further thoughts on the case of Amborella Limits and logical basis of inferring HGT in plant mitochondrial genomes PCR approach Poor resolution in phylogenies Low substitution rate Stringency in SH test Paralogues are less likely to be highly divergent in mitochondria Repeats of 500bp in plant mtDNA are subjected to frequent concerted evolution Limits and logical basis of inferring HGT in plant mitochondrial genomes PCR approach Poor resolution in phylogenies Low substitution rate Stringency in SH test Paralogues are less likely to be highly divergent in mitochondria Repeats of 500bp in plant mtDNA are subjected to frequent concerted evolution Slide 50 50 Further thoughts on the case of Amborella Functionality of transferred genes in Amborella 8 of the 26 transferred genes are pseudogenes Both atp1 and atp8 are transcribed and RNA- edited Pseudogenes can do so as well in plant mitochondria Subramanian et al. (2001) Curr. Genet. 39: 264-272 Suspected to be non-functional Functionality of transferred genes in Amborella 8 of the 26 transferred genes are pseudogenes Both atp1 and atp8 are transcribed and RNA- edited Pseudogenes can do so as well in plant mitochondria Subramanian et al. (2001) Curr. Genet. 39: 264-272 Suspected to be non-functional Slide 51 51 How about chloroplast genes? Only a few examples are known of gene substitution in the evolution of chloroplast: Chloroplast RPL21 is substituted by a nuclear rpl21 gene of mitochondrial origin (Gallois et al. 2001). Chloroplast RPL23 is derived by substitution from a duplicated copy of cytosolic rpl23 (Bubunenko et al. 1994). Group II intron of psbA in algae Chl pvs-trnA intron into mt genome Only a few examples are known of gene substitution in the evolution of chloroplast: Chloroplast RPL21 is substituted by a nuclear rpl21 gene of mitochondrial origin (Gallois et al. 2001). Chloroplast RPL23 is derived by substitution from a duplicated copy of cytosolic rpl23 (Bubunenko et al. 1994). Group II intron of psbA in algae Chl pvs-trnA intron into mt genome Slide 52 Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick 52 Chloroplast psbA in Euglena Euglena gracilis Euglena myxocylindracea Slide 53 Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick 53 RT: reverse transcriptase domains X-domain: maturase domain Zinc-finger: mobility Slide 54 Source: Obed W. Odom, David L. Shenkenberg, joshuaa A. Garcia, David L. herrin 2004. A horizontally acquired group II intron in the chloroplast psbA gene of a psychrophilic Chlamydomonas: In vitro self-splicing and genetic evidence for maturase activity. RNA 10: p. 1100. 54 Chl psbA intron in Chlamydomonas Note: most of other algae/land plants do not have intron in their psbA Slide 55 Source: Obed W. Odom, David L. Shenkenberg, joshuaa A. Garcia, David L. herrin 2004. A horizontally acquired group II intron in the chloroplast psbA gene of a psychrophilic Chlamydomonas: In vitro self-splicing and genetic evidence for maturase activity. RNA 10: p. 1100. 55 In vitro self-splicing of 32 P-labeled Chs.psbA1 pre-RNAs Slide 56 56 Chl. pvs-trnA intron The mitochondrial genomes of some Phaseolus species contain a fragment of chloroplast trnA gene intron (pvs-trnA) within the Phaseolus vulgaris sterility sequence (pvs) Mt pvs is generally thought to be chimeric that arose by multiple recombination The pvs-trnA is about 190 bp The mitochondrial genomes of some Phaseolus species contain a fragment of chloroplast trnA gene intron (pvs-trnA) within the Phaseolus vulgaris sterility sequence (pvs) Mt pvs is generally thought to be chimeric that arose by multiple recombination The pvs-trnA is about 190 bp Slide 57 57 Chl. pvs-trnA intron Three other species have it in mt genomes Citrus sp. (2.3 kb franking trnA) Helianthus annuus (0.8 kb, including trnA exon 1 and 541 bp of intron) Zea mays (12 kb, partial trnA and 576 bo intron) In order to identify the origin of pvs-trnA, 41 plants were examined for the presence of chl. trnA fragment in their mitochondrial genome Three other species have it in mt genomes Citrus sp. (2.3 kb franking trnA) Helianthus annuus (0.8 kb, including trnA exon 1 and 541 bp of intron) Zea mays (12 kb, partial trnA and 576 bo intron) In order to identify the origin of pvs-trnA, 41 plants were examined for the presence of chl. trnA fragment in their mitochondrial genome Slide 58 Source: Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska 2004. A fragment of chloroplast DNA was transferred horizontally, probably from non- eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 816. 58 pvs-trnA Philodendron ( ) Magnolia ( ) Philodendron ( ) Magnolia ( ) 58 Slide 59 Source: Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska 2004. A fragment of chloroplast DNA was transferred horizontally, probably from non- eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 817. 59 Only pvs-trnA is caused by HGT; others are likely intracellular transfer Slide 60 60 Chimeric mt genes by HGT and gene conversion Source: Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer 2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p. 21577. Slide 61 Source: Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer 2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p. 21578. 61 Differentially mosaic atp1 genes in Ternstroemia Slide 62 62 HGT does occur during plant evolution, and it may only represent one of the many. What are the vectoring agents? Viruses, bacteria, fungi, insects, pollen or even meteorites? Partial mt genome or entire mitochondrion Naked plant DNA in soil? Occasionally grafting between two plants? How does foreign DNA integrated into plant genomes? HGT does occur during plant evolution, and it may only represent one of the many. What are the vectoring agents? Viruses, bacteria, fungi, insects, pollen or even meteorites? Partial mt genome or entire mitochondrion Naked plant DNA in soil? Occasionally grafting between two plants? How does foreign DNA integrated into plant genomes? Further thoughts Slide 63 63 Plant-fungi HGTs Plant to fungi HGT: L-fucose permease sugar transporter Source: Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot 2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1900. Slide 64 Source: Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot 2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1900. 64 Plant-fungi HGTs Fungi to plant HGT: major facilitator superfamily membrane transporter Slide 65 Source: Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot 2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1907. 65 Plant-fungi HGTs Slide 66 66 Impact of HGT of TEs on genome evolution Source: Sarah Schaack, Clment Gilbert, and Cdric Feschotte 2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 538. Slide 67 67 Impact of horizontal transposon transfer Source: Sarah Schaack, Clment Gilbert, and Cdric Feschotte 2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 543. Slide 68 68 Interconnection in microbes Source: Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 617. Source: Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 617. Slide 69 Source: Sarah Schaack, Clment Gilbert, and Cdric Feschotte 2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 616. 69 Slide 70 Source: Sarah Schaack, Clment Gilbert, and Cdric Feschotte 2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 616. 70 Slide 71 OpenWetWare Jennifer Auchtung 71 How to visualize and quantify gene transfer? Case study of ICE Slide 72 72 Successful mating in the donors that contain ICEBs1 with a lacO array, and recipients that express LacI-GFP. 81% of recipient cell turned into a donor and transconjugated the ICE to the next within 30 min Source: Ana Babi, Ariel B. Lindner, Marin Vuli, Eric J. Stewart, and Miroslav Radman 2008. Direct Visualization of Horizontal Gene Transfer. Science 319: p. 1533. mBio Ana Babic, Melanie B. Berkmen, Catherine A. Lee, and Alan D. Grossman Slide 73 73 Phylogenomic network Source: Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 486. Slide 74 74 Data matrix in phylogenomic network 30% a.a. identity cutoff70% a.a. identity cutoff No. of shared genes Source: Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 486. Slide 75 75 3D network of the gammaproteobacterial minimal lateral network (MLN) 5083 internal-external edges 2191 internal-internal edges 3432 external-external edges (laterally shared genes) Source: Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 486. Slide 76 Source: Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 484. 76 Weighting of network A network of vertices (circles) and edges (lines) Directed network Slide 77 77 A directed network of LGT, showing that LGT happened more frequently in closely related bacteria. Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 618. Slide 78 78 GC% are very similar for donors and recipients. Most of the transfer also occurred within habitats. Biological and ecological barriers of LGT Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 618. Slide 79 79 Functional barriers Fixation of acquired DNA depends on the functionality to the recipient Acquired genes need to insert within existing regulatory circuits Acquired genes with suboptimal codon will not fit the tRNA pool, thus put a barrier of LGT LGT is more frequent among enzymes involved in peripheral reactions (metabolic), compared to those involved in central reaction (biomass production) Fixation of acquired DNA depends on the functionality to the recipient Acquired genes need to insert within existing regulatory circuits Acquired genes with suboptimal codon will not fit the tRNA pool, thus put a barrier of LGT LGT is more frequent among enzymes involved in peripheral reactions (metabolic), compared to those involved in central reaction (biomass production) Slide 80 80 Detecting recombination Five methods (Posada et al. 2002) Similarity methods Distance methods Recombination Analysis Tool (RAT) Java-based application Phylogenetic methods Compatibility methods Substitution distribution Five methods (Posada et al. 2002) Similarity methods Distance methods Recombination Analysis Tool (RAT) Java-based application Phylogenetic methods Compatibility methods Substitution distribution Posada, D. et al. (2002) Annu. Rev. Genet. 36: 75-97. Etherington, G. J. et al. (2005) Bioinformatics 21: 278-281 80 Slide 81 81 Components of BBTV Compon ent Function DNA 1Master replicase (Rep) DNA 2Unknown DNA 3Coat protein (Coat) DNA 4Virus movement DNA 5Host-cell cycle manipulation DNA 6Virus movement Note: some additional replicases have been found 5 CR Stem loop (SL) 3 Common region (CR-M) National Taiwan University Jer-Ming Hu Slide 82 82 Detecting recombination using RAT Egypt_Kalubia Query by Australia DNA 3 sequence Fiji Slide 83 83 WorkLicensingAuthor/SourcePage Wikipedia A. G. Matthysse, K. V. Holmes, R. H. G. Gurlitz http://zh.wikipedia.org/wiki/File:Agrobacterium-tumefaciens.gif 2012/07/09 visited P7 Er-Min Lai 2000. Genetic and Environmental Factors Affecting T-Pilin Export and T-Pilus Biogenesis in Relation to Flagellation of Agrobacterium tumefaciens. Jorunal of Bacteriology 182: p. 3711. http://jb.asm.org/content/182/13/3705.figures-only It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P7 National Taiwan University Jer-Ming Hu P7 Erh-Min Lai 1999. Genetic and Biochemical Characterization of the Agrobacterium T-pilus and Its Major T-pilin Subunit. PhD thesis, p. 33. University of California Davis, Davis, California, USA. It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P8 Copyright Declaration Slide 84 WorkLicensingAuthor/SourcePage Source: Keith L. Adams, Martin J. Clements, and Jack C. Vaughn 1998. The Peperomia Mitochondrial coxI Group I Intron: Timing of Horizontal Transfer and Subsequent Evolution of the Intron. Jorunal of Molecular Evolution 46: p. 694. http://www.springerlink.com/content/6jrqaghfxt4ppgnw/ It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P11 Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14245. http://www.pnas.org/content/95/24/14244.full.pdf+html http://www.pnas.org/content/95/24/14244.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P12 Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14246. http://www.pnas.org/content/95/24/14244.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P13 Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14247. http://www.pnas.org/content/95/24/14244.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P14 Slide 85 85 WorkLicensingAuthor/SourcePage Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14248. http://www.pnas.org/content/95/24/14244.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P15 Keith L. Adams, Yin-Long Qiu, Mark Stoutemyer, and Jeffrey D. Palmer 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 99: p. 9905. http://www.pnas.org/content/99/15/9905.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P17 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 198. http://www.nature.com/nature/journal/v424/n6945/pdf/nature01743.pdf It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P18 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 197. http://www.nature.com/nature/journal/v424/n6945/pdf/nature01743.pdf It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P21 Slide 86 86 WorkLicensingAuthor/SourcePage Flickr Gerard's World http://www.flickr.com/photos/a3aanse/4906645238/sizes/l/in/photostream/ 2012/07/09 visited P21 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. http://www.nature.com/nature/journal/v424/n6945/full/nature01743.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P22 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. http://www.nature.com/nature/journal/v424/n6945/full/nature01743.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P22 Flickr.Bambo. http://www.flickr.com/photos/bambolia/4112019870/sizes/l/in/photostream/ 2012/07/09 visited P22 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. http://www.nature.com/nature/journal/v424/n6945/full/nature01743.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P23 Slide 87 87 WorkLicensingAuthor/SourcePage Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. http://www.nature.com/nature/journal/v424/n6945/full/nature01743.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P23 Flickr BlueRidgeKitties http://www.flickr.com/photos/blueridgekitties/4503712719/sizes/l/in/photostream/ 2012/07/09 visited p23 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 200. http://www.nature.com/nature/journal/v424/n6945/full/nature01743.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P24 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. http://www.nature.com/nature/journal/v424/n6945/full/nature01743.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P26, P40 Flickr pennstatelive http://www.flickr.com/photos/pennstatelive/5609235215/sizes/l/in/photostream/ 2012/06/14 visited P26, P39, P41 Slide 88 88 WorkLicensingAuthor/SourcePage Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 200. http://www.nature.com/nature/journal/v424/n6945/full/nature01743.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P27 Flickr adaduitokla http://www.flickr.com/photos/adaduitokla/6241526866/sizes/l/in/photostream/ 2012/07/09 visited P28 Hyosig Won and Susanne S. Renner 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p. 10824. http://www.pnas.org/content/100/19/10824.full?sid=e7b0f45c-0a50-442d-955c- bf1caa711ed9 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P29 Hyosig Won and Susanne S. Renner 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p. 10824. http://www.pnas.org/content/100/19/10824.full?sid=e7b0f45c-0a50-442d-955c- bf1caa711ed9 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P30 Slide 89 89 WorkLicensingAuthor/SourcePage Hyosig Won and Susanne S. Renner 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p. 10827. http://www.pnas.org/content/100/19/10824.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P31 Charles C. Davis and Kenneth J. Wurdack 2004. Host-to-Parasite Gene Transfer in Flowering Plants: Phylogenetic Evidence from Malpighiales. 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Nickrent http://phytoimages.siu.edu/imgs/paraman1/r/Apodanthaceae_Apodanthes_casearieae_42 209.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 PhytoImages website Terms of UseTerms of Use The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P34 Slide 90 90 WorkLicensingAuthor/SourcePage Flickr thedangers http://www.flickr.com/photos/dangerfamily/5484907422/sizes/l/in/photostream/ 2012/07/09 visited P34 Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson 2004. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. 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PNAS 101: p. 17749. http://www.pnas.org/content/101/51/17747.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P44 Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p. 17750. http://www.pnas.org/content/101/51/17747.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P45 Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p. 17751. http://www.pnas.org/content/101/51/17747.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P46 Slide 92 92 WorkLicensingAuthor/SourcePage Elena V. Sheveleva and Richard B. Hallick 2004. Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Research 32: p. 803. http://nar.oxfordjournals.org/content/32/2/803.full?sid=47ffe95d-af73-42ac-a436- e7845675d3dc 2012/07/09 visited P50 Elena V. Sheveleva and Richard B. Hallick 2004. Recent horizontal intron transfer to a chloroplast genome. 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A horizontally acquired group II intron in the chloroplast psbA gene of a psychrophilic Chlamydomonas: In vitro self-splicing and genetic evidence for maturase activity. RNA 10: p. 1100. http://rnajournal.cshlp.org/content/10/7/1097.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P53 Slide 93 93 WorkLicensingAuthor/SourcePage Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska 2004. A fragment of chloroplast DNA was transferred horizontally, probably from non- eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 816. http://www.springerlink.com/content/t7688556u420038p/fulltext.pdf It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P56 Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska 2004. A fragment of chloroplast DNA was transferred horizontally, probably from non- eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 817. http://www.springerlink.com/content/t7688556u420038p/fulltext.pdf It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P57 Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer 2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p. 21577. http://www.pnas.org/content/107/50/21576.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P58 Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer 2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p. 21578. http://www.pnas.org/content/107/50/21576.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P59 Slide 94 94 WorkLicensingAuthor/SourcePage Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot 2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1900. http://www.plantcell.org/content/21/7/1897.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P61 Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot 2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1900. http://www.plantcell.org/content/21/7/1897.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P62 Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot 2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1907. http://www.plantcell.org/content/21/7/1897.full.pdf+html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P63 Sarah Schaack, Clment Gilbert, and Cdric Feschotte 2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 538. http://www.sciencedirect.com/science/article/pii/S0169534710001230 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P64 Slide 95 95 WorkLicensingAuthor/SourcePage Sarah Schaack, Clment Gilbert, and Cdric Feschotte 2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 543. http://www.sciencedirect.com/science/article/pii/S0169534710001230 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P65 Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 617. http://www.sciencedirect.com/science/article/pii/S1369527411001111 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P66 Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 617. http://www.sciencedirect.com/science/article/pii/S1369527411001111 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P66 Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 616. http://www.sciencedirect.com/science/article/pii/S1369527411001111 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P67 Slide 96 96 WorkLicensingAuthor/SourcePage Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 616. http://www.sciencedirect.com/science/article/pii/S1369527411001111 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P68 OpenWetWare Jennifer Auchtung http://openwetware.org/wiki/User:Jen17 2012/07/10 visited P69 Ana Babi, Ariel B. Lindner, Marin Vuli, Eric J. Stewart, and Miroslav Radman 2008. Direct Visualization of Horizontal Gene Transfer. Science 319: p. 1533. http://www.sciencemag.org/content/319/5869/1533.full.pdf It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P70 Ana Babic, Melanie B. Berkmen, Catherine A. Lee, and Alan D. Grossman 2011. Efficient Gene Transfer in Bacterial Cell Chains. mBio 2: e00027-11. p.3 http://mbio.asm.org/content/2/2/e00027-11.full.html 2012/07/09 visited P70 Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 486. http://www.sciencedirect.com/science/article/pii/S0966842X11001387 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P71 Slide 97 97 WorkLicensingAuthor/SourcePage Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 486. http://www.sciencedirect.com/science/article/pii/S0966842X11001387 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P72 Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 486. http://www.sciencedirect.com/science/article/pii/S0966842X11001387 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P73 Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 484. http://www.sciencedirect.com/science/article/pii/S0966842X11001387 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P74 Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 618. http://www.sciencedirect.com/science/article/pii/S1369527411001111 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P75 Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 618. http://www.sciencedirect.com/science/article/pii/S1369527411001111 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P76 Slide 98 98 WorkLicensingAuthor/SourcePage National Taiwan University Jer-Ming Hu P79 National Taiwan University Jer-Ming Hu P79 National Taiwan University Jer-Ming Hu P80 Agrobacterium tumefaciens- angiosperms (Furner et al. 1986) Source: Ian J. Furner, Gary A. Huffman, Richard M. Amasino, David J. Garfinkel, Milton P. Gordon, and Eugene W. Nester. 1986. An Agrobacterium transformation in the evolution of the genus Nicotiana. Nature 319: p. 422. http://www.nature.com/nature/journal/v319/n6052/abs/319422a0.html It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P6 Marina Marcet-Houben and Toni Gabaldn 2010. Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics 26: p. 5. http://www.cell.com/trends/genetics/abstract/S0168-9525%2809%2900235-2 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf P6 Wikipedia Strobilomyces http://zh.wikipedia.org/wiki/File:Helvella_crispa_031111w.jpg 2012/08/22 visited P6