Ph.D. Candidate Exam Slides

Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient

Horizontal Gene Transfer between Plants and Fungi

(Richards et al. 2009 Plant Cell)

8/27/2010

Bioinformatics & Genomics, Ph.D. Candidacy Exam

Bongsoo Park

OutlineOutlineIntroductionResults MethodsDiscussion

What is What is HHorizontal orizontal GGene ene TTransfer?ransfer?

vs Vertical Gene Transfer (reproduction)

HGT provides opportunities for rapid genome innovation.

Abundant in prokaryotes (e.g. transfer of antibiotic resistance genes among bacteria, metabolic capability of certain substrates as nutrient sources, etc.)

http://tolweb.org/tree/

Examples of HGTs in Examples of HGTs in EukaryotesEukaryotes

Plant Pathogen, Fusarium oxysporum (Li-Jun et al. Nature, 2010)

Pea Aphid, Acyrthosiphon pisum (Nancy A.M. Science, 2010)

‘Carotenoids’ biosynthesis genestransferred from fungi to an ancestor of aphids

Entire Lineage-specific Chromosomes transferred to another strain of F. oxysporum, making the recipient pathogenic to Tomato.

Fungi > Fungi Fungi > Insect

HGT Putative Functional Protein Annotation Direction of Transfer

1a L-Fucose permease, sugar transporter Fungi > Plant

1b Zinc binding alcohol dehydrogenase Plant > Fungi

1c Major facilitator superfamily, membrane transporter Fungi > Plant

2 Phospholipase/carboxylesterase family protein Fungi > Plant

3a iucA/iucC family protein, siderophore biosynthesis Fungi > Plant

3b Unknown/conserved hypothetical protein Fungi > Plant

4a DUF239 domain protein Plant > Fungi

4b Phosphate-responsive 1 family protein Plant > Fungi

4c Unknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) protein

Plant > Fungi

Table 2. Nine putative HGT candidate genes

Results

Arabidopsis thaliana (Arabidopsis)

Populus trichocarpa (Western poplar)

Oryza sativa (Rice)

Sorghum bicolor(Sorghum, edible grain)

Selaginella moellendorffii (spikemosses)

Physomitrella patens (Moss)

Total number of proteins

31,913 45,555 26,777 35,899 22,285 35,938

Top hit versus fungi 1,206 1,426 1,045 1,043 802 776

Top hit versus fungi excluding TEs

1,160 1,331 852 965 794 764

Table 1. Identification of Putative HGTs between Plants and Fungi for Phylogenetic Analyses

Fungi > PlantFungi > Plant

Plant > FungiPlant > Fungi

BLAST, OrthoMCL pipeline Phylogenomic analyses

Plants(Query)Plants

(Query)Fungi, Algae,

Protists, Animals, Prokaryotes

(Target)

Fungi, Algae, Protists, Animals,

Prokaryotes(Target)

BLASTp (e-value 10-20)(Plant-Fungi, the highest similarity)

BLASTp (e-value 10-20)(Plant-Fungi, the highest similarity)

6,298 protein

sequences

6,298 protein

sequences

5,586 protein sequences

5,586 protein sequences

Excluding TEs(Putative functional proteome)

Excluding TEs(Putative functional proteome)

1,689 groups Initial Screening

1,689 groups Initial Screening

RiceDB

RiceDB

3,177 Orthology

Groups

3,177 Orthology

Groups

4,866 sequence groups, Ready

4,866 sequence groups, Ready

4,866 sequence groups

4,866 sequence groups

Four evidencesFour evidences

Putative 9 HGT candidatesPutative 9 HGT candidates

3838GenBank NR

GenBank EST, TBestDB(Improve sampling)

GenBank NRGenBank EST, TBestDB

(Improve sampling)

3535

221

OrthoMCL(e-value 1e-20; inflation value 1.5)

OrthoMCL(e-value 1e-20; inflation value 1.5)

1414

Methods

PHYML, HGT like taxaPHYML, HGT like taxa

MrBayes, PHYML, RAxML, SH Test

MrBayes, PHYML, RAxML, SH Test

Target DBTarget DB

BLASTp (e-value 10-20)

BLASTp (e-value 10-20)

Fungi

Plants

Strong bootstrapvalues

Ascomycete fungi

Selaginella

Weak bootstrapvalues

11

22

Evidences

Alternative Topology Test(CONSEL)

Alternative Topology Test(CONSEL) SH (Shimodaria-Hasegawa)SH (Shimodaria-Hasegawa)

P-valueP-value

1

Bayesian PHYML RAxML SH test

L-Fucose permease, sugar transporterL-Fucose permease, sugar transporter

Fungi

Plants

Strong bootstrap values

A single fungal species

Plants specific Gene family

33

44

Evidences

Strong bootstrap values

Prokaryotes

HGT Based on a Prokaryote Tagged-Chain Transfer HypothesisHGT Based on a Prokaryote Tagged-Chain Transfer Hypothesis

Weak bootstrap values

3

Bayesian PHYML RAxML SH test

DUF(Domain of Unknown Function)DUF(Domain of Unknown Function)iucA/iucC family protein, siderophore biosynthesisiucA/iucC family protein, siderophore biosynthesis

3A : iucA/iucC family protein, 3A : iucA/iucC family protein, siderophore biosynthesissiderophore biosynthesisSiderophores are small, high-affinity

iron chelating compounds

Non-pathogenic Bacteria, iron-poor environment Fungi, obtaining siderophore biosynthesis

survival in iron-poor environment

Lycophyte (Selaginella moellendorffii)

4

4

Bayesian PHYML RAxML SH test

DUF(Domain of Unknown Function)

Phosphate-responsive 1 family protein

HGT Putative Functional Protein Annotation Direction of Transfer

1a L-Fucose permease, sugar transporter Fungi > Plant

1b Zinc binding alcohol dehydrogenase Plant > Fungi

1c Major facilitator superfamily, membrane transporter Fungi > Plant

2 Phospholipase/carboxylesterase family protein Fungi > Plant

3a iucA/iucC family protein, siderophore biosynthesis Fungi > Plant

3b Unknown/conserved hypothetical protein Fungi > Plant

4a DUF239 domain protein (Domain of Unknown function) Plant > Fungi

4b Phosphate-responsive 1 family protein Plant > Fungi

4c Unknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) protein

Plant > Fungi

Putative functional assignments

Discussion

AngiospermAngiosperm

LycophyteLycophyteBryophyteBryophyte

Chytridiomycota

ZygomyceteBasidiomycet

e

Ascomycete

Fig 8.

Taphrinomycotina

My perspectivesMy perspectives

Genome SamplingTransposable ElementsApplying this methods to detect HGTs

in Fungal and Oomycete pathogens

This research, however, is a pioneer project to invest the eukaryote HGT by using currently available resources and methods.

Thank You

Bioinformatics and Genomics, Ph.D. Candidacy Exam

Bongsoo Park

Supplementary Slides

Bioinformatics and Genomics, Ph.D. Candidacy Exam

Bongsoo Park

History of HGTHistory of HGT

First described in Japan in 1959, 1960◦ Transfer of antibiotic resistance between different

species of bacteria; bacillary dysenteryTsutomu Watanabe, Bacteriology Review (1963)

Known mechanisms of Known mechanisms of HGTHGTTransformation, introduction, uptake

and expression of foreign genetic material

Transduction, transmission by virusBacterial conjugation, cell-to-cell

contact

http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens http://en.wikipedia.org/wiki/Transduction_(genetics) http://en.wikipedia.org/wiki/Bacterial_conjugation

1

Bayesian

PHYML RAxML SH test

1

1

2 2

3

3

4

4

4

Gene appears unique to genome

Could not confirm vertical inheritance

Phylogeny suggests vertical inheritance

Taxon distribution of gene family suggests vertical inheritance

Transposable element

1A

L-fucose permease, sugar transporterPhpa(173818)

1B

Zinc binding alcohol dehydrogenaseBDEG_06896

Fig 7. Strong vertical inheritance

HGT Putative Functional Protein Annotation Direction of Transfer

GenBank Accession No.

Phylogeny construction

1a L-Fucose permease, sugar transporter Fungi > Plant EDQ83581 98 sequences and 341 length62 sequences and 349 length

1b Zinc binding alcohol dehydrogenase Plant > Fungi EDQ61140*

95 sequences and 207 length

1c Major facilitator superfamily, membrane transporter

Fungi > Plant EAU93280*

40 sequences and 354 length

2 Phospholipase/carboxylesterase family protein

Fungi > Plant XP_389330*

122 sequences and 158 length62 sequences and 349 length

3a iucA/iucC family protein, siderophore biosynthesis

Fungi > Plant EDR08700*

44 sequences and 218 length15 sequences and 262 length

3b Unknown/conserved hypothetical protein Fungi > Plant EDQ68642 55 sequences and 174 length34 sequences and 247 length

4a DUF239 domain protein Plant > Fungi EDR02747 87 sequences and 210 length

4b Phosphate-responsive 1 family protein Plant > Fungi ABK92591*

93 sequences and 198 length

4c Unknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) protein

Plant > Fungi EDN23584 13 sequences and 222 length

GenBank accession numbers of transferred genes are given, and the asterisks indicate accession numbers of the closest BLAST hit in GenBank to the HGT, rather than that of the recipient gene

Table 1. Nine putative HGT candidate genes

Challenging QuestionsChallenging Questions

How long ago HGT processes occurred?DNA move back and forth between

donors and recipients?How environmental factors (light,

water, temperature, pH) affect the gene transfers?

Any new mechanisms of transfer?How transferred genes can be fixed in a

population successfully?