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1 Horizontal gene transfer (Lateral gene transfer) Jer-Ming Hu 胡哲明 Jer-Ming Hu 胡哲明 本著作除另有註明外,採取創用 CC 「姓名標示-創用 CC 「姓名標示- 非商業性-相同方式分享」台灣 3.0 版非商業性-相同方式分享」台灣.

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Presentation on theme: "1 Horizontal gene transfer (Lateral gene transfer) Jer-Ming Hu 胡哲明 Jer-Ming Hu 胡哲明 本著作除另有註明外,採取創用 CC 「姓名標示-創用 CC 「姓名標示- 非商業性-相同方式分享」台灣 3.0 版非商業性-相同方式分享」台灣."— Presentation transcript:

1 1 Horizontal gene transfer (Lateral gene transfer) Jer-Ming Hu 胡哲明 Jer-Ming Hu 胡哲明 本著作除另有註明外,採取創用 CC 「姓名標示-創用 CC 「姓名標示- 非商業性-相同方式分享」台灣 3.0 版非商業性-相同方式分享」台灣 3.0 版授權釋出 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)

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

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

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

5 5 Catalases (Klotz et a., 1997, Mol. Biol. Evol. 14: ), proline racemase and PhzF, Mpk1, etc. (Fitzpatrick 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: ), proline racemase and PhzF, Mpk1, etc. (Fitzpatrick 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

6 6 HGT is highly concentrated in Pezizomycotina ( 盤菌 ) Helvella crispa (Pezizomycotina) Source: Marina Marcet-Houben and Toni Gabaldón Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics 26: p. 5. Wikipedia Strobilomyces

7 7 PapD proteins in human cells (Leu-1/CD5) and E. coli (PapD) Holmgren & Branden (1989) Nature 342: 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: Incongruence in phylogeny PapD proteins in human cells (Leu-1/CD5) and E. coli (PapD) Holmgren & Branden (1989) Nature 342: 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: Incongruence in phylogeny Interkingdom DNA transfers: bacteria- animals

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 An Agrobacterium transformation in the evolution of the genus Nicotiana. Nature 319: p. 422.

9 National Taiwan University Jer-Ming Hu 9 Agrobacterium-mediated transformation Crown gall on elm tree at UC Davis Source: Er-Min Lai Genetic and Environmental Factors Affecting T-Pilin Export and T-Pilus Biogenesis in Relation to Flagellation of Agrobacterium tumefaciens. Jorunal of Bacteriology 182: p

10 Source: Erh-Min Lai 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

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

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

13 13 Mitochondrial cox1 group I intron in angiosperms Adams et al. (1998) J. Mol. Evol. 46: Peperomia: first known case for the presence of mt cox1 intron Cho et al. (1998) PNAS 95: 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: Peperomia: first known case for the presence of mt cox1 intron Cho et al. (1998) PNAS 95: 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 The Peperomia Mitochondrial coxI Group I Intron: Timing of Horizontal Transfer and Subsequent Evolution of the Intron. Jorunal of Molecular Evolution 46: p. 694.

14 Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p 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

15 Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p 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

16 Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p 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 黃脈爵床 橄欖 蔓綠絨 楝 肉豆蔻 瓜 大戟 柿樹 橡膠樹 梓 日日春 天胡荽 竹竽 天芹菜 鼠李 灰木 冬青 椒草 毛地黃

17 Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p 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

18 18 HGT of mitochondrial rps2 and rps11 genes Adams et al. (2002) PNAS 99: Bergthorsson et al. (2003) Nature 424: Detecting mitochondrial genes by southern blot hybridization Sequenced for their identities and conducted phylogenetic analysis Adams et al. (2002) PNAS 99: Bergthorsson et al. (2003) Nature 424: Detecting mitochondrial genes by southern blot hybridization Sequenced for their identities and conducted phylogenetic analysis

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 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

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 Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 198.

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

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?

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 Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p Flickr Gerard's World

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 Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p Flickr.Bambo.

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 ( 血根草屬, Papaveraceae) Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p Flickr BlueRidgeKitties

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 Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 200.

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

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: Explanation: Two paralogues in Amborella Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p Flickr pennstatelive

29 29 The five HGT events in angiosperm mt DNA Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 200.

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 ( 買麻藤 ) Flickr adaduitokla

31 31 Source: Hyosig Won and Susanne S. Renner 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

32 32 Alignment of mt nad1 exons b & c Two types in Gnetum! Source: Hyosig Won and Susanne S. Renner 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

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 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

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

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 Host-to-Parasite Gene Transfer in Flowering Plants: Phylogenetic Evidence from Malpighiales. Science 345: p Flickr cornstaruk

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

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 ( 奴草 ) National Taiwan University Jer-Ming Hu

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

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: From eudicots to Amborella Bergthorsson et al. (2003) Nature 424: 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: From eudicots to Amborella Bergthorsson et al. (2003) Nature 424: Massive transfer of mtDNAs in Amborella Interkingdom DNA transfers: plants- plants

40 40 Plantago ( 車前草 ) mt atp1 genes Source: Jeffrey P. Mower, Saša Stefanović, Gregory J. Young, and Jeffrey D. Palmer Plant genetics: Gene transfer from parasitic to host plants. Nature 432: p. 165.

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

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: Explanation: Two paralogues in Amborella Source: Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 197.

43 Source: Khidir W. Hilu, Thomas Borsch, Kai Müller, Douglas E. Soltis, Pamela S. Soltis, Vincent Savolainen, Mark W. Chase, Martyn P. Powell, Lawrence A. Alice, Rodger Evans, Hervé Sauquet, Christoph Neinhuis, Tracey A. B. Slotta, Jens G. Rohwer, Christopher S. Campbell, and Lars W. Chatrou Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: p Chloroplast matK phylogeny Amborella trichopoda Flickr pennstatelive

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)

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 Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p

46 Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p HGT from mosses to Amborella Purple: Core eudicots Red: Amborella Green: Mosses V: vertical transmisson H: Horizontal transmission

47 Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p HGT from eudicots to Amborella Blue: Core eudicots Red: Amborella V: vertical transmisson H: Horizontal transmission

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 I’Aoupinie at New Caledonia (801m altitude) Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p

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

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: 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: Suspected to be non-functional

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

52 Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick 52 Chloroplast psbA in Euglena Euglena gracilis Euglena myxocylindracea

53 Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick 53 RT: reverse transcriptase domains X-domain: maturase domain Zinc-finger: mobility

54 Source: Obed W. Odom, David L. Shenkenberg, joshuaa A. Garcia, David L. herrin 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 Chl psbA intron in Chlamydomonas Note: most of other algae/land plants do not have intron in their psbA

55 Source: Obed W. Odom, David L. Shenkenberg, joshuaa A. Garcia, David L. herrin 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 In vitro self-splicing of 32 P-labeled Chs.psbA1 pre-RNAs

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

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

58 Source: Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska A fragment of chloroplast DNA was transferred horizontally, probably from non- eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p pvs-trnA Philodendron ( 蔓綠絨屬 ) Magnolia ( 木蘭屬 ) Philodendron ( 蔓綠絨屬 ) Magnolia ( 木蘭屬 ) 58

59 Source: Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska A fragment of chloroplast DNA was transferred horizontally, probably from non- eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p Only pvs-trnA is caused by HGT; others are likely intracellular transfer

60 60 Chimeric mt genes by HGT and gene conversion Source: Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p

61 Source: Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p Differentially mosaic atp1 genes in Ternstroemia

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

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 Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p

64 Source: Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p Plant-fungi HGTs Fungi to plant HGT: major facilitator superfamily membrane transporter

65 Source: Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p Plant-fungi HGTs

66 66 Impact of HGT of TEs on genome evolution Source: Sarah Schaack, Clément Gilbert, and Cédric Feschotte Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 538.

67 67 Impact of horizontal transposon transfer Source: Sarah Schaack, Clément Gilbert, and Cédric Feschotte Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 543.

68 68 Interconnection in microbes Source: Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p Source: Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 617.

69 Source: Sarah Schaack, Clément Gilbert, and Cédric Feschotte Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p

70 Source: Sarah Schaack, Clément Gilbert, and Cédric Feschotte Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p

71 OpenWetWare Jennifer Auchtung 71 How to visualize and quantify gene transfer? Case study of ICE

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 Babić, Ariel B. Lindner, Marin Vulić, Eric J. Stewart, and Miroslav Radman Direct Visualization of Horizontal Gene Transfer. Science 319: p mBio Ana Babic, Melanie B. Berkmen, Catherine A. Lee, and Alan D. Grossman

73 73 Phylogenomic network Source: Tal Dagan Phylogenomic networks. Trends in Microbiology 19: p. 486.

74 74 Data matrix in phylogenomic network 30% a.a. identity cutoff70% a.a. identity cutoff No. of shared genes Source: Tal Dagan Phylogenomic networks. Trends in Microbiology 19: p. 486.

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 Phylogenomic networks. Trends in Microbiology 19: p. 486.

76 Source: Tal Dagan Phylogenomic networks. Trends in Microbiology 19: p Weighting of network A network of vertices (circles) and edges (lines) Directed network

77 77 A directed network of LGT, showing that LGT happened more frequently in closely related bacteria. Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 618.

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 Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 618.

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)

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: Etherington, G. J. et al. (2005) Bioinformatics 21:

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

82 82 Detecting recombination using RAT Egypt_Kalubia Query by Australia DNA 3 sequence Fiji

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84 WorkLicensingAuthor/SourcePage Source: Keith L. Adams, Martin J. Clements, and Jack C. Vaughn The Peperomia Mitochondrial coxI Group I Intron: Timing of Horizontal Transfer and Subsequent Evolution of the Intron. Jorunal of Molecular Evolution 46: p 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/ 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/ OCW-Oct29.pdf P11 Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p 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/ 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/ OCW-Oct29.pdf P12 Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p 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/ 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/ OCW-Oct29.pdf P13 Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p 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/ 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/ OCW-Oct29.pdf P14

85 85 WorkLicensingAuthor/SourcePage Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p 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/ 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/ OCW-Oct29.pdf P15 Keith L. Adams, Yin-Long Qiu, Mark Stoutemyer, and 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. PNAS 99: p 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/ 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/ OCW-Oct29.pdf P17 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P18 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P21

86 86 WorkLicensingAuthor/SourcePage Flickr Gerard's World 2012/07/09 visited P21 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P22 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P22 Flickr.Bambo /07/09 visited P22 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P23

87 87 WorkLicensingAuthor/SourcePage Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P23 Flickr BlueRidgeKitties 2012/07/09 visited p23 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P24 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P26, P40 Flickr pennstatelive 2012/06/14 visited P26, P39, P41

88 88 WorkLicensingAuthor/SourcePage Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p 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/ 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/ OCW-Oct29.pdf P27 Flickr adaduitokla 2012/07/09 visited P28 Hyosig Won and Susanne S. Renner 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 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/ 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/ OCW-Oct29.pdf P29 Hyosig Won and Susanne S. Renner 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 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/ 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/ OCW-Oct29.pdf P30

89 89 WorkLicensingAuthor/SourcePage Hyosig Won and Susanne S. Renner 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 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/ 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/ OCW-Oct29.pdf P31 Charles C. Davis and Kenneth J. Wurdack Host-to-Parasite Gene Transfer in Flowering Plants: Phylogenetic Evidence from Malpighiales. Science 345: p 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/ 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/ OCW-Oct29.pdf P33 Flickr cornstaruk 2012/07/09 visited P33 Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology 4: p /07/09 visited P34 Phyto Images D. L. Nickrent 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/ 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/ OCW-Oct29.pdf P34

90 90 WorkLicensingAuthor/SourcePage Flickr thedangers 2012/07/09 visited P34 Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology 4: p /07/09 visited P35 National Taiwan University Jer-Ming Hu P35 Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology 4: p /07/09 visited P36 Jeffrey P. Mower, Saša Stefanović, Gregory J. Young, and Jeffrey D. Palmer Plant genetics: Gene transfer from parasitic to host plants. Nature 432: p 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/ 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/ OCW-Oct29.pdf P38 Khidir W. Hilu, Thomas Borsch, Kai Müller, Douglas E. Soltis, Pamela S. Soltis, Vincent Savolainen, Mark W. Chase, Martyn P. Powell, Lawrence A. Alice, Rodger Evans, Hervé Sauquet, Christoph Neinhuis, Tracey A. B. Slotta, Jens G. Rohwer, Christopher S. Campbell, and Lars W. Chatrou Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: p 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/ 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/ OCW-Oct29.pdf P41

91 91 Work Licensin g Author/SourcePage Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p 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/ 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/ OCW-Oct29.pdf P43 Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p 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/ 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/ OCW-Oct29.pdf P44 Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p 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/ 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/ OCW-Oct29.pdf P45 Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p 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/ 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/ OCW-Oct29.pdf P46

92 92 WorkLicensingAuthor/SourcePage Elena V. Sheveleva and Richard B. Hallick Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Research 32: p e d3dc 2012/07/09 visited P50 Elena V. Sheveleva and Richard B. Hallick Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Research 32: p e d3dc 2012/07/09 visited P51 Obed W. Odom, David L. Shenkenberg, joshuaa A. Garcia, David L. herrin 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 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/ 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/ OCW-Oct29.pdf P52 Obed W. Odom, David L. Shenkenberg, joshuaa A. Garcia, David L. herrin 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 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/ 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/ OCW-Oct29.pdf P53

93 93 WorkLicensingAuthor/SourcePage Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska A fragment of chloroplast DNA was transferred horizontally, probably from non- eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p 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/ 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/ OCW-Oct29.pdf P56 Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska A fragment of chloroplast DNA was transferred horizontally, probably from non- eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p 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/ 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/ OCW-Oct29.pdf P57 Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p 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/ 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/ OCW-Oct29.pdf P58 Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p 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/ 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/ OCW-Oct29.pdf P59

94 94 WorkLicensingAuthor/SourcePage Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p 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/ 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/ OCW-Oct29.pdf P61 Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p 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/ 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/ OCW-Oct29.pdf P62 Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard, Christopher R. Thornton, and Nicholas J. Talbot Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p 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/ 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/ OCW-Oct29.pdf P63 Sarah Schaack, Clément Gilbert, and Cédric Feschotte Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p 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/ 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/ OCW-Oct29.pdf P64

95 95 WorkLicensingAuthor/SourcePage Sarah Schaack, Clément Gilbert, and Cédric Feschotte Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p 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/ 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/ OCW-Oct29.pdf P65 Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p 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/ 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/ OCW-Oct29.pdf P66 Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p 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/ 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/ OCW-Oct29.pdf P66 Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p 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/ 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/ OCW-Oct29.pdf P67

96 96 WorkLicensingAuthor/SourcePage Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p 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/ 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/ OCW-Oct29.pdf P68 OpenWetWare Jennifer Auchtung 2012/07/10 visited P69 Ana Babić, Ariel B. Lindner, Marin Vulić, Eric J. Stewart, and Miroslav Radman Direct Visualization of Horizontal Gene Transfer. Science 319: p 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/ 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/ OCW-Oct29.pdf P70 Ana Babic, Melanie B. Berkmen, Catherine A. Lee, and Alan D. Grossman Efficient Gene Transfer in Bacterial Cell Chains. mBio 2: e p /07/09 visited P70 Tal Dagan Phylogenomic networks. Trends in Microbiology 19: p 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/ 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/ OCW-Oct29.pdf P71

97 97 WorkLicensingAuthor/SourcePage Tal Dagan Phylogenomic networks. Trends in Microbiology 19: p 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/ 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/ OCW-Oct29.pdf P72 Tal Dagan Phylogenomic networks. Trends in Microbiology 19: p 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/ 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/ OCW-Oct29.pdf P73 Tal Dagan Phylogenomic networks. Trends in Microbiology 19: p 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/ 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/ OCW-Oct29.pdf P74 Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p 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/ 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/ OCW-Oct29.pdf P75 Ovidiu Popa and Tal Dagan Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p 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/ 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/ OCW-Oct29.pdf P76

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 An Agrobacterium transformation in the evolution of the genus Nicotiana. Nature 319: p 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/ 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/ OCW-Oct29.pdf P6 Marina Marcet-Houben and Toni Gabaldón Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics 26: p. 5. 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/ 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/ OCW-Oct29.pdf P6 Wikipedia Strobilomyces 2012/08/22 visited P6


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