Presentation is loading. Please wait.

Presentation is loading. Please wait.

Horizontal gene transfer (Lateral gene transfer)

Similar presentations


Presentation on theme: "Horizontal gene transfer (Lateral gene transfer)"— Presentation transcript:

1 Horizontal gene transfer (Lateral gene transfer)
Jer-Ming Hu 胡哲明 本著作除另有註明外,採取創用CC「姓名標示- 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)

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 橄欖 肉豆蔻 黃脈爵床 大戟 柿樹 橡膠樹 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 NAR OPEN ACCESS LICENCE AGREEMENT 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. 

53 RT: reverse transcriptase domains
Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick RT: reverse transcriptase domains X-domain: maturase domain NAR OPEN ACCESS LICENCE AGREEMENT 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
Work Licensing Author/Source Page Wikipedia A. G. Matthysse, K. V. Holmes, R. H. G. Gurlitz 2012/07/09 visited P7 Er-Min Lai 2000. Genetic and Environmental Factors Affecting T-Pilin Export and T-Pilus Biogenesis in Relation to Flagellation of Agrobacterium tumefaciens. Jorunal of Bacteriology 182: p 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 Act 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. 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 Act P11 Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p P12 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p P13 1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p P14

85 Work Licensing Author/Source Page
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 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 Act P15 Keith L. Adams, Yin-Long Qiu, Mark Stoutemyer, and Jeffrey D. Palmer 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 99: p P17 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 198. P18 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 197. P21

86 Work Licensing Author/Source Page Flickr Gerard's World
2012/07/09 visited P21 Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 199. 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 Act P22 Flickr .Bambo. P23

87 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. 199. 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 Act P23 Flickr BlueRidgeKitties 2012/07/09 visited p23 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: p. 200. P24 P26, P40 Flickr pennstatelive 2012/06/14 visited P26, P39, P41

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. 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 Act P27 Flickr adaduitokla 2012/07/09 visited P28 Hyosig Won and Susanne S. Renner 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p P29 P30

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 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 Act P31 Charles C. Davis and Kenneth J. Wurdack 2004. Host-to-Parasite Gene Transfer in Flowering Plants: Phylogenetic Evidence from Malpighiales. Science 345: p. 677. P33 Flickr cornstaruk 2012/07/09 visited 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. P34 Phyto Images D. L. Nickrent PhytoImages website Terms of Use

90 Work Licensing Author/Source Page Flickr thedangers
2012/07/09 visited P34 Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson 2004. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology 4: p. 40. P35 National Taiwan University Jer-Ming Hu P36 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. 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 Act 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 2003. Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: p P41

91 Work Licensing Author/Source Page
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 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 Act P43 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p P44 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p P45 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: p P46

92 Work Licensing Author/Source Page
Elena V. Sheveleva and Richard B. Hallick 2004. Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Research 32: p. 803. 2012/07/09 visited P50 P51 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 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 Act P52 P53

93 Work Licensing Author/Source Page
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. 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 Act P56 2004. A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 817. P57 Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer 2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p P58 2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. PNAS 107: p P59

94 Work Licensing Author/Source Page
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 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 Act P61 P62 2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. The Plant Cell 21: p P63 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. P64

95 Work Licensing Author/Source Page
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. 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 Act P65 Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 617. P66 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 616. P67

96 Work Licensing Author/Source Page Ovidiu Popa and Tal Dagan
2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 616. 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 Act P68 OpenWetWare Jennifer Auchtung 2012/07/10 visited P69 Ana Babić, Ariel B. Lindner, Marin Vulić, Eric J. Stewart, and Miroslav Radman 2008. Direct Visualization of Horizontal Gene Transfer. Science 319: p P70 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 2012/07/09 visited Tal Dagan 2011. Phylogenomic networks. Trends in Microbiology 19: p. 486. P71

97 Work Licensing Author/Source Page Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486. 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 Act P72 P73 2011. Phylogenomic networks. Trends in Microbiology 19: p. 484. P74 Ovidiu Popa and Tal Dagan 2011. Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 14: p. 618. P75 P76

98 Work Licensing Author/Source Page
National Taiwan University Jer-Ming Hu P79 P80 “Agrobacterium tumefaciens-angiosperms …(Furner et al. 1986)” Source: Ian J. Furner, Gary A. Huffman, Richard M. Amasino, David J. Garfinkel, Milton P. Gordon, and Eugene W. Nester. 1986. An Agrobacterium transformation in the evolution of the genus Nicotiana. Nature 319: p. 422. 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 Act P6 Marina Marcet-Houben and Toni Gabaldón 2010. Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics 26: p. 5. Wikipedia Strobilomyces 2012/08/22 visited


Download ppt "Horizontal gene transfer (Lateral gene transfer)"

Similar presentations


Ads by Google