Horizontal gene transfer
(Lateral gene transfer)
Jer-Ming Hu
胡哲明
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1
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
2
Mechanisms of HGT

Hybridization


Mitochondrial or chloroplast capture





Recombination of genomes
Lineage sorting
Recurrence of HGT, e.g. mitochondria captured by transmissible
cancer CTVT.
Parasitism
Grafting in plants
Vectors like virus, fungi, aphids
3
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
4
Interkingdom DNA transfers: bacteria-fungi

Catalases (Klotz et a., 1997, Mol. Biol. Evol. 14: 951-958.), proline racemase and PhzF,
Mpk1, etc. (Fitzpatrick 2012. FEMS Microbiol. 329: 1)


Incongruence in phylogeny
Marcet-Houben & Gabaldon (2010, TIG 26:5) showed 713 genes from 60
fungal species are likely derived from bacteria.
5
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.
6
Interkingdom DNA transfers: bacteria-animals

PapD proteins in human cells (Leu-1/CD5) and E. coli (PapD)
 Holmgren & Branden (1989) Nature 342: 248-251.

Amino acids 4~252 of Leu-1/CD5 protein has 26% identity w/ PapD
•

Note: CD5 (lymphocyte differentiation antigen) is variable in general
Phosphoglucose isomerases (PGI)
 Katz (1996) J. Mol. Evol. 43: 453-459.

Incongruence in phylogeny
7
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.
8
Agrobacterium-mediated transformation
Source: Er-Min Lai
2000. Genetic and Environmental Factors Affecting T-Pilin
Export and T-Pilus Biogenesis in Relation to Flagellation of
Agrobacterium tumefaciens. Jorunal of Bacteriology 182: p. 3711.
National Taiwan University Jer-Ming Hu
Crown gall on elm tree at UC Davis
9
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.
10
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
11
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
12
DNA transfers: plants-plants

Mitochondrial cox1 group I intron in angiosperms
 Adams et al. (1998) J. Mol. Evol. 46: 689-696.
•

Peperomia: first known case for the presence of mt cox1 intron
Cho et al. (1998) PNAS 95: 14244-14249.
•
•
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.
Survey of 335 genera in angiosperms
48 genera found to be HGT
13
Intron distribution: Southern blots
•Multiple acquisition of group I intron in various angiosperms?
Probed w/ Beta vulgaris cox1 exon
Probed w/ Veronica ugrestis cox1 intron
Probed w/ Zea mays cox2 group II intron
Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer
1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p. 14245.
14
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
Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer
1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95: p.
14246.
15
Phylogenies of mt cox1 genes
ML tree of cox1 exon+intron
楝
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
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. 14247.
16
Models of mt cox1 intron transfer
All non-plant to plant transfer model
Donors
Recipients
Single non-plant to plant; all others being plant to
plant transfer model
Source: Yangrae Cho, Yin-Long Qiu, Peter Kuhlman, and Jeffrey D. Palmer
1998. Explosive invasion of plant mitochondria by a group I intron. PNAS 95:
p. 14248.
17
HGT of mitochondrial rps2 and rps11 genes




Adams et al. (2002) PNAS 99: 9905-9912.
Bergthorsson et al. (2003) Nature 424: 197-201.
Detecting mitochondrial genes by southern blot hybridization
Sequenced for their identities and conducted phylogenetic analysis
18
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. 9905.
19
Evidences from mt rps2 and rps11
rps11
rps2
-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.
20
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)
21
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
22
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.
23
Evidence in mt rps11
rps11 (456bp)
Upstream of rps11 (457bp)
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.
24
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.
25
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)
26
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
27
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.
28
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.
29
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.
Gnetum (買麻藤)
Flickr adaduitokla
30
Source: Hyosig Won and Susanne S. Renner
2002. Punctuated evolution of mitochondrial gene content: High and variable rates of
mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p.
10824.
31
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. 10824.
Two types in Gnetum!
32
Two types of mt
nad1 found in
Tree based on LFY, nrITS,
rbcL, matK, and tRNALeu
intron
Gnetum
Source: Hyosig Won and Susanne S. Renner
2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial
gene loss and transfer to the nucleus during angiosperm evolution. PNAS 100: p. 10827.
33
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

34
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.
35
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
36
mt atp1 phylogeny
National Taiwan University Jer-Ming Hu
Mitrastema yamamotoi (奴草)
BMC Evolutionary Biology Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina
Vidal-Russell, and Frank E Anderson
37
Possible HGT events in Rafflesiales
BMC Evolutionary Biology Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E Anderson
38
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

•

From eudicots to Amborella
•

Mower et al. (2004) Nature 432: 165-166
Bergthorsson et al. (2003) Nature 424: 197-201.
Massive transfer of mtDNAs in Amborella
39
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.
40
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
41
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.
42
Chloroplast matK phylogeny
Flickr pennstatelive
Amborella trichopoda
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. 1762.
43
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)
44
HGT of mt genes in Amborella

Multiple bands found in most PCRs of
Amborella


Each band was cloned and sequenced
Massive HGT!
Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R. Goertzen, and Jeffrey D. Palmer
2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal
angiosperm Amborella. PNAS 101: p. 17748.
45
HGT from mosses to Amborella
Purple: Core eudicots
Red: Amborella
Green: Mosses
V: vertical transmisson
H: Horizontal transmission
Source: Ulfar Bergthorsson, Aaron O. Richardson, Gregory J. Young, Leslie R.
Goertzen, and Jeffrey D. Palmer
2004. Massive horizontal transfer of mitochondrial genes from diverse land plant
donors to the basal angiosperm Amborella. PNAS 101: p. 17749.
46
HGT from eudicots to
Amborella
Blue: Core eudicots
Red: Amborella
V: vertical transmisson
H: Horizontal transmission
Source: Ulfar Bergthorsson, Aaron
O. Richardson, Gregory J. Young,
Leslie R. Goertzen, and Jeffrey D.
Palmer
2004. Massive horizontal transfer
of mitochondrial genes from
diverse land plant donors to the
basal angiosperm Amborella.
PNAS 101: p. 17749.
47
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. 17751.
48
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
49
Further thoughts on the case of Amborella

Functionality of transferred genes in Amborella


8 of the 26 transferred genes are pseudogenes
Both atp1 and atp8 are transcribed and RNA-edited
•

Pseudogenes can do so as well in plant mitochondria
• Subramanian et al. (2001) Curr. Genet. 39: 264-272
Suspected to be non-functional
50
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
51
Chloroplast psbA in Euglena
Euglena gracilis
Euglena myxocylindracea
Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick
52
RT: reverse transcriptase domains
X-domain: maturase domain
Zinc-finger: mobility
Nucleic Acids Research Elena V. Sheveleva and Richard B. Hallick
53
Chl psbA intron in Chlamydomonas
Note: most of other algae/land plants do
not have intron in their psbA
Source: Obed W. Odom, David L. Shenkenberg, joshuaa A. Garcia, David L. herrin
2004. A horizontally acquired group II intron in the chloroplast psbA gene of a
psychrophilic Chlamydomonas: In vitro self-splicing and genetic evidence for
maturase activity. RNA 10: p. 1100.
54
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. 1100.
55
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
56
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


57
pvs-trnA
Philodendron (蔓綠絨屬)
Magnolia (木蘭屬)
pvs-trnA
Philodendron (蔓綠絨屬)
Magnolia (木蘭屬)
Source: Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska
2004. A fragment of chloroplast DNA was transferred horizontally, probably from noneudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 816.
58
Only pvs-trnA is caused by HGT; others are likely
intracellular transfer
Source: Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska
2004. A fragment of chloroplast DNA was transferred horizontally, probably from noneudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 817.
59
Chimeric mt genes by HGT and gene conversion
Source: Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer
2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene
conversion. PNAS 107: p. 21577.
60
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. 21578.
61
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?
62
Plant-fungi HGTs
Plant to fungi HGT: L-fucose permease sugar transporter
Source: Thomas A. Richards, Darren M. Soanes, Peter G. Foster, Guy Leonard,
Christopher R. Thornton, and Nicholas J. Talbot
2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal
Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1900.
63
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. 1900.
64
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. 1907.
65
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.
66
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.
67
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.
68
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.
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
How to visualize and quantify gene transfer?
Case study of ICE
OpenWetWare Jennifer Auchtung
71
•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
2008. Direct Visualization of
Horizontal Gene Transfer. Science
319: p. 1533.
mBio Ana Babic, Melanie B. Berkmen, Catherine A. Lee, and Alan D. Grossman
72
Phylogenomic network
Source: Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.
73
Data matrix in phylogenomic network
30% a.a. identity cutoff
No. of shared genes
70% a.a. identity cutoff
Source: Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.
74
3D network of the gammaproteobacterial minimal lateral
network (MLN)
5083 internal-external edges
3432 external-external edges
(laterally shared genes)
2191 internal-internal edges
Source: Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.
75
Weighting of network
A network of vertices
(circles) and edges
(lines)
Directed network
Source: Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 484.
76
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.
77
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.
78
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)
79
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: 75-97.
Etherington, G. J. et al. (2005) Bioinformatics 21: 278-281
80
Components of BBTV
Component
Function
DNA 1
Master replicase (Rep)
DNA 2
Unknown
DNA 3
Coat protein (Coat)
DNA 4
Virus movement
DNA 5
Host-cell cycle manipulation
DNA 6
Virus movement
Stem loop (SL)
3’ Common region (CR-M)
5’ CR
National Taiwan University Jer-Ming Hu
National Taiwan University Jer-Ming Hu
Note: some additional replicases have been found
81
Detecting recombination using RAT
Query by Australia DNA 3 sequence
Fiji
Egypt_Kalubia
National Taiwan University Jer-Ming Hu
82
Copyright Declaration
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Wikipedia A. G. Matthysse, K. V. Holmes, R. H. G. Gurlitz
http://zh.wikipedia.org/wiki/File:Agrobacterium-tumefaciens.gif
2012/07/09 visited
Er-Min Lai
2000. Genetic and Environmental Factors Affecting T-Pilin Export and T-Pilus
Biogenesis in Relation to Flagellation of Agrobacterium tumefaciens. Jorunal of
Bacteriology 182: p. 3711.
http://jb.asm.org/content/182/13/3705.figures-only
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P7
National Taiwan University Jer-Ming Hu
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Major T-pilin Subunit. PhD thesis, p. 33. University of California Davis, Davis,
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Work
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Source: Keith L. Adams, Martin J. Clements, and Jack C. Vaughn
1998. The Peperomia Mitochondrial coxI Group I Intron: Timing of Horizontal Transfer
and Subsequent Evolution of the Intron. Jorunal of Molecular Evolution 46: p. 694.
http://www.springerlink.com/content/6jrqaghfxt4ppgnw/
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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. 14245.
http://www.pnas.org/content/95/24/14244.full.pdf+html
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2002. Punctuated evolution of mitochondrial gene content: High and variable rates of
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99: p. 9905.
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Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer
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424: p. 198.
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http://www.flickr.com/photos/bambolia/4112019870/sizes/l/in/photostream/
2012/07/09 visited
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2012/07/09 visited
Ulfar Bergthorsson, Keith L. Adams, Brendan Thomason, and Jeffrey D. Palmer
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2012/07/09 visited
Hyosig Won and Susanne S. Renner
2002. Punctuated evolution of mitochondrial gene content: High and variable rates of
mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS
100: p. 10824.
http://www.pnas.org/content/100/19/10824.full?sid=e7b0f45c-0a50-442d-955cbf1caa711ed9
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mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS
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Malpighiales. Science 345: p. 677.
http://www.sciencemag.org/content/305/5684/676.full.pdf
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P33
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http://www.flickr.com/photos/scornish/275469883/sizes/l/in/photostream/
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.
http://www.biomedcentral.com/about/license
2012/07/09 visited
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Phyto Images D. L. Nickrent
http://phytoimages.siu.edu/imgs/paraman1/r/Apodanthaceae_Apodanthes_casearieae_42
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National Taiwan University Jer-Ming Hu
Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, and Frank E
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2004. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and
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http://www.biomedcentral.com/about/license
2012/07/09 visited
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.
http://www.nature.com/nature/journal/v432/n7014/pdf/432165b.pdf
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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. 1762.
http://www.amjbot.org/content/90/12/1758.full.pdf+html
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Work
Licensin
g
Author/Source
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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. 17748.
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91
Work
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Author/Source
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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.
http://nar.oxfordjournals.org/content/32/2/803.full?sid=47ffe95d-af73-42ac-a436e7845675d3dc
2012/07/09 visited
P50
Elena V. Sheveleva and Richard B. Hallick
2004. Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Research
32: p. 803.
http://nar.oxfordjournals.org/content/32/2/803.full?sid=47ffe95d-af73-42ac-a436e7845675d3dc
2012/07/09 visited
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. 1100.
http://rnajournal.cshlp.org/content/10/7/1097.full.pdf+html
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psychrophilic Chlamydomonas: In vitro self-splicing and genetic evidence for maturase
activity. RNA 10: p. 1100.
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P52
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Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska
2004. A fragment of chloroplast DNA was transferred horizontally, probably from noneudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 816.
http://www.springerlink.com/content/t7688556u420038p/fulltext.pdf
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Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, and Hanna Janska
2004. A fragment of chloroplast DNA was transferred horizontally, probably from noneudicots, to mitochondrial genome of Phaseolus. Plant Molecular Biology 56: p. 817.
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P57
Weilong Hao, Aaron O. Richardson, Yihong Zheng, and Jeffrey D. Palmer
2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene
conversion. PNAS 107: p. 21577.
http://www.pnas.org/content/107/50/21576.full.pdf+html
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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. 21578.
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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. 1900.
http://www.plantcell.org/content/21/7/1897.full.pdf+html
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Thornton, and Nicholas J. Talbot
2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal
Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1900.
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Thornton, and Nicholas J. Talbot
2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal
Gene Transfer between Plants and Fungi. The Plant Cell 21: p. 1907.
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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. 538.
http://www.sciencedirect.com/science/article/pii/S0169534710001230
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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. 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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Ovidiu Popa and Tal Dagan
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Microbiology 14: p. 617.
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Microbiology 14: p. 616.
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P69
OpenWetWare Jennifer Auchtung
http://openwetware.org/wiki/User:Jen17
2012/07/10 visited
Ana Babić, Ariel B. Lindner, Marin Vulić, Eric J. Stewart, and Miroslav Radman
2008. Direct Visualization of Horizontal Gene Transfer. Science 319: p. 1533.
http://www.sciencemag.org/content/319/5869/1533.full.pdf
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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: e00027-11. p.3
http://mbio.asm.org/content/2/2/e00027-11.full.html
2012/07/09 visited
P70
Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.
http://www.sciencedirect.com/science/article/pii/S0966842X11001387
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Tal Dagan
2011. Phylogenomic networks. Trends in Microbiology 19: p. 486.
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Tal Dagan
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Ovidiu Popa and Tal Dagan
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Microbiology 14: p. 618.
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P79
National Taiwan University Jer-Ming Hu
P79
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P80
National Taiwan University Jer-Ming Hu
“Agrobacterium tumefaciensangiosperms
…(Furner et al. 1986)”
Source: Ian J. Furner, Gary A. Huffman, Richard M. Amasino, David J. Garfinkel,
Milton P. Gordon, and Eugene W. Nester.
1986. An Agrobacterium transformation in the evolution of the genus Nicotiana. Nature
319: p. 422.
http://www.nature.com/nature/journal/v319/n6052/abs/319422a0.html
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P6
Marina Marcet-Houben and Toni Gabaldón
2010. Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics 26: p. 5.
http://www.cell.com/trends/genetics/abstract/S0168-9525%2809%2900235-2
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P6
Wikipedia Strobilomyces
http://zh.wikipedia.org/wiki/File:Helvella_crispa_031111w.jpg
2012/08/22 visited
98