1. Horizontal gene transfer (Lateral gene transfer)
Jer-Ming Hu
胡哲明
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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

3. Mechanisms of HGT Hybridization Mitochondrial or chloroplast capture
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. HGT that involves eukaryotes
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

5. Interkingdom DNA transfers: bacteria-fungi
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.

6. HGT is highly concentrated in Pezizomycotina (盤菌)
Wikipedia Strobilomyces
Helvella crispa (Pezizomycotina)
Source: Marina Marcet-Houben and Toni Gabaldón
2010. Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics 26: p. 5.

7. Interkingdom DNA transfers: bacteria-animals
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

8. Interkingdom DNA transfers: bacteria-plants
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)
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.

9. Agrobacterium-mediated transformation
National Taiwan University Jer-Ming Hu
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
Crown gall on elm tree at UC Davis

10. General Model of Agrobacterium-plant Interaction
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.

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

12. DNA transfers: plants-plants
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

13. DNA transfers: plants-plants
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
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.

14. Intron distribution: Southern blots
Multiple acquisition of group I intron in various angiosperms?
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
Probed w/ Beta vulgaris cox1 exon
Probed w/ Veronica ugrestis cox1 intron
Probed w/ Zea mays cox2 group II intron

15. Mt cox1 intron distribution
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
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. Phylogenies of mt cox1 genes
ML tree of cox1 exon+intron
ML tree of cox1 introns
ML tree of rbcL/cox1 coding sequences 椒草
蔓綠絨 楝 橄欖
肉豆蔻
黃脈爵床 瓜 大戟 柿樹
橡膠樹 梓
日日春
天胡荽 竹竽
天芹菜 鼠李 灰木
毛地黃 冬青
I, D: synapomorphic intron gaps
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

17. Models of mt cox1 intron transfer
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
All non-plant to plant transfer model
Donors
Recipients
Single non-plant to plant; all others being plant to plant transfer model

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

19. Detection of mt genes by southern blots
rps2
Southern blots of 91 angiosperm DNAs (280 examined total).
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

20. Evidences from mt rps2 and rps11
-Present
-Absent
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.

21. Models to explain the phenomenon of newly presented rps2 and rps11
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)

22. How do we examine?
Analysize levels of sequence divergence and the phylogenetic relationships of rps2 and rps11 genes
31 rps2 genes and 44 rps11 genes were used

23. Mitochondrial rps2 gene phylogeny
Maximum likelihood tree of rps2 (474 nt alignment), showing Actinidia rps2 is closer to monocot homologues.
Flickr Gerard's World
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.

24. Evidence in mt rps11 Upstream of rps11 (457bp) rps11 (456bp)
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.
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.

25. Sanguinaria mt rps11 5’ half of rps11 (219bp) 3’ half of rps11 (237bp)
Flickr BlueRidgeKitties
Sanguinaria (血根草屬, Papaveraceae)
Sanguinaria rps11 is chimeric:
5’ half is as expected
3’ half is closer to monocots
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.

26. Chimaeric structure of Sanguinaria mt rps11
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.
Bf: Bocconia frutescens (Papaveraceae)
Sc: Sanguinaria canadensis (Papaveraceae)
Dh: Disporum hookeri (Liliaceae)

27. Expression of possible HGT genes
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

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
Flickr pennstatelive
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.

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.

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.
Flickr adaduitokla
Gnetum (買麻藤)

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

32. Alignment of mt nad1 exons b & c
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
Two types in Gnetum!

33. Two types of mt nad1 found in Gnetum
Tree based on LFY, nrITS, rbcL, matK, and tRNALeu 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

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

35. Rafflesia mt nad1 b-c exons
Blue: Malpighiales
Red: Rafflesia and Sapria
Flickr cornstaruk
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.

36. Phyto Images D. L. Nickrent
mt matR phylogeny
Phyto Images D. L. Nickrent
Apodanthes flowers
Pilostyles thurberi
Flickr thedangers
Bold faces: Rafflesiaceae
Parasitic plant connection
Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson

37. mt atp1 phylogeny Mitrastema yamamotoi (奴草)
BMC Evolutionary Biology Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson
mt atp1 phylogeny
National Taiwan University Jer-Ming Hu
Mitrastema yamamotoi (奴草)

38. Possible HGT events in Rafflesiales
BMC Evolutionary Biology Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson

39. Interkingdom DNA transfers: plants-plants
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

40. Plantago (車前草) mt atp1 genes
Source: Jeffrey P. Mower, Saša Stefanović, Gregory J. Young, and Jeffrey D. Palmer
2004. Plant genetics: Gene transfer from parasitic to host plants. Nature 432: p. 165.

41. DNA transfers: plants-plants
Mitochondrial coxI intron in angiosperms
Mitochondrial rps2 and rps11
Mitochondrial nad1 intron2
Mitochondrial atp1
Massive transfer of mtDNAs in Amborella
Flickr pennstatelive

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.

43. Chloroplast matK phylogeny
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
2003. Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: p
Flickr pennstatelive
Amborella trichopoda

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)

45. HGT of mt genes in Amborella
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
Multiple bands found in most PCRs of Amborella
Each band was cloned and sequenced
Massive HGT!

46. HGT from mosses to Amborella
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
Purple: Core eudicots
Red: Amborella
Green: Mosses
V: vertical transmisson
H: Horizontal transmission

47. HGT from eudicots to Amborella
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
HGT from eudicots to Amborella
Blue: Core eudicots
Red: Amborella
V: vertical transmisson
H: Horizontal transmission

48. Further thoughts on the case of 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
2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p

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

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

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 ).
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. Chloroplast psbA in Euglena
Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick
Euglena gracilis
Euglena myxocylindracea
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53. RT: reverse transcriptase domains
Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick
RT: reverse transcriptase domains
X-domain: maturase domain
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NAR authors are asked to sign an Open Access license agreement which reflects the Open Access model outlined below. Articles published under this NAR Open Access model are made freely available online immediately upon publication, as part of a long-term archive, without subscription barriers to access. We have chosen to implement the Creative Commons Attribution-Non Commercial licence for articles published under theNAR Open Access model. 
Zinc-finger: mobility

54. Chl psbA intron in Chlamydomonas
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
Note: most of other algae/land plants do not have intron in their psbA

55. In vitro self-splicing of 32P-labeled Chs.psbA1 pre-RNAs
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
In vitro self-splicing of 32P-labeled Chs.psbA1 pre-RNAs

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

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

58. pvs-trnA Philodendron (蔓綠絨屬) Magnolia (木蘭屬) pvs-trnA
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.
Philodendron (蔓綠絨屬)
Magnolia (木蘭屬)
pvs-trnA
Philodendron (蔓綠絨屬)
Magnolia (木蘭屬) 58

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.
Only pvs-trnA is caused by HGT; others are likely intracellular transfer

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

61. Differentially mosaic atp1 genes in Ternstroemia
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

62. Further thoughts
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?

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

64. Plant-fungi HGTs
Fungi to plant HGT: major facilitator superfamily membrane 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

65. Plant-fungi HGTs
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

66. Impact of HGT of TEs on genome evolution
Source: Sarah Schaack, Clément Gilbert, and Cédric Feschotte
2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 538.

67. Impact of horizontal transposon transfer
Source: Sarah Schaack, Clément Gilbert, and Cédric Feschotte
2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 543.

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.

69. Source: Sarah Schaack, Clément Gilbert, and Cédric Feschotte
2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 616.

70. Source: Sarah Schaack, Clément Gilbert, and Cédric Feschotte
2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 616.

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

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
mBio Ana Babic, Melanie B. Berkmen, Catherine A. Lee, and Alan D. Grossman
Source: Ana Babić, Ariel B. Lindner, Marin Vulić, Eric J. Stewart, and Miroslav Radman
2008. Direct Visualization of Horizontal Gene Transfer. Science 319: p
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

73. Phylogenomic network Source: Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.

74. Data matrix in phylogenomic network
30% a.a. identity cutoff
70% a.a. identity cutoff
Source: Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.
No. of shared genes

75. 3D network of the gammaproteobacterial minimal lateral network (MLN)
Source: Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.
5083 internal-external edges
3432 external-external edges (laterally shared genes)
2191 internal-internal edges

76. Weighting of network A network of vertices (circles) and edges (lines)
Source: Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 484.
A network of vertices (circles) and edges (lines)
Directed network

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.

78. Biological and ecological barriers of LGT
GC% are very similar for donors and recipients. Most of the transfer also occurred within habitats.
Ovidiu Popa and Tal Dagan
2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 618.

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)

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
Posada, D. et al. (2002) Annu. Rev. Genet. 36:
Etherington, G. J. et al. (2005) Bioinformatics 21: 80

81. Components of BBTV Component Function DNA 1 Master replicase (Rep)
Unknown
DNA 3
Coat protein (Coat)
DNA 4
Virus movement
DNA 5
Host-cell cycle manipulation
DNA 6
Stem loop (SL)
National Taiwan University Jer-Ming Hu
5’ CR
3’ Common region (CR-M)
National Taiwan University Jer-Ming Hu
Note: some additional replicases have been found

82. Detecting recombination using RAT
Query by Australia DNA 3 sequence
Fiji
National Taiwan University Jer-Ming Hu
Egypt_Kalubia

83. Copyright Declaration
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Wikipedia A. G. Matthysse, K. V. Holmes, R. H. G. Gurlitz
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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
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National Taiwan University Jer-Ming Hu
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. P8

84. Work Licensing Author/Source Page
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.
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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
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1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p
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1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p
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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
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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
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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.
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2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 197.
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86. Work Licensing Author/Source Page Flickr Gerard's World
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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.
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2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199.
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2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 200.
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88. Work Licensing Author/Source Page
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.
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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
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89. Work Licensing Author/Source Page 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
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Charles C. Davis and Kenneth J. Wurdack
2004. Host-to-Parasite Gene Transfer in Flowering Plants: Phylogenetic Evidence from Malpighiales. Science 345: p. 677.
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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. BMC Evolutionary Biology 4: p. 40.
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2004. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology 4: p. 40.
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Jeffrey P. Mower, Saša Stefanović, Gregory J. Young, and Jeffrey D. Palmer
2004. Plant genetics: Gene transfer from parasitic to host plants. Nature 432: p. 166.
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2003. Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: p
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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
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2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p
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Elena V. Sheveleva and Richard B. Hallick
2004. Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Research 32: p. 803.
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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
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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.
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2004. A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 817.
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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
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2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p
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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
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2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 538.
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Sarah Schaack, Clément Gilbert, and Cédric Feschotte
2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: p. 543.
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Ovidiu Popa and Tal Dagan
2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 617.
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2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 616.
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2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 616.
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Ana Babić, Ariel B. Lindner, Marin Vulić, Eric J. Stewart, and Miroslav Radman
2008. Direct Visualization of Horizontal Gene Transfer. Science 319: p
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Ana Babic, Melanie B. Berkmen, Catherine A. Lee, and Alan D. Grossman
2011. Efficient Gene Transfer in Bacterial Cell Chains. mBio 2: e p.3
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Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.
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2011. Phylogenomic networks. Trends in Microbiology 19: p. 484.
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“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.
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Marina Marcet-Houben and Toni Gabaldón
2010. Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics 26: p. 5.
Wikipedia Strobilomyces
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