Ph.D. Candidate Exam Slides

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Bongsoo's Ph.D. Candidate Exam 8/27/2010

Text of 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)

  • OutlineIntroductionResults MethodsDiscussion

  • What is Horizontal Gene Transfer?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 EukaryotesPlant 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.

  • Table 2. Nine putative HGT candidate genesResultsTable 1. Identification of Putative HGTs between Plants and Fungi for Phylogenetic AnalysesFungi > PlantPlant > Fungi

    HGTPutative Functional Protein AnnotationDirection of Transfer1aL-Fucose permease, sugar transporterFungi > Plant1bZinc binding alcohol dehydrogenasePlant > Fungi1cMajor facilitator superfamily, membrane transporterFungi > Plant2Phospholipase/carboxylesterase family proteinFungi > Plant3aiucA/iucC family protein, siderophore biosynthesisFungi > Plant3bUnknown/conserved hypothetical proteinFungi > Plant4aDUF239 domain proteinPlant > Fungi4bPhosphate-responsive 1 family proteinPlant > Fungi4cUnknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) proteinPlant > Fungi

    Arabidopsis thaliana (Arabidopsis)Populus trichocarpa (Western poplar)Oryza sativa (Rice)Sorghum bicolor(Sorghum, edible grain)Selaginella moellendorffii (spikemosses)Physomitrella patens (Moss)Total number of proteins31,91345,55526,77735,89922,28535,938Top hit versus fungi1,2061,4261,0451,043802776Top hit versus fungi excluding TEs1,1601,331852965794764

  • BLAST, OrthoMCL pipelinePhylogenomic analysesPlants(Query)Fungi, Algae, Protists, Animals, Prokaryotes(Target)5,586 protein sequencesExcluding TEs(Putative functional proteome)1,689 groups Initial ScreeningRiceDB3,177 Orthology Groups4,866 sequence groups, Ready4,866 sequence groupsFour evidencesPutative 9 HGT candidates38GenBank NRGenBank EST, TBestDB(Improve sampling)3521OrthoMCL(e-value 1e-20; inflation value 1.5)14MethodsMrBayes, PHYML, RAxML, SH TestTarget DBBLASTp (e-value 10-20)

  • FungiPlantsStrong bootstrapvaluesAscomycete fungiSelaginellaWeak bootstrapvalues12EvidencesAlternative Topology Test(CONSEL)SH (Shimodaria-Hasegawa)P-value

  • 1BayesianPHYMLRAxMLSH testL-Fucose permease, sugar transporter

  • FungiPlantsStrong bootstrap valuesA single fungal speciesPlants specific Gene family34EvidencesStrong bootstrap valuesProkaryotesHGT Based on a Prokaryote Tagged-Chain Transfer HypothesisWeak bootstrap values

  • 3BayesianPHYMLRAxMLSH testDUF(Domain of Unknown Function)iucA/iucC family protein, siderophore biosynthesis

  • 3A : iucA/iucC family protein, siderophore biosynthesisSiderophores are small, high-affinity iron chelating compoundsNon-pathogenic Bacteria, iron-poor environmentFungi, obtaining siderophore biosynthesissurvival in iron-poor environmentLycophyte (Selaginella moellendorffii)

  • 44BayesianPHYMLRAxMLSH test

  • Putative functional assignmentsDiscussion

    HGTPutative Functional Protein AnnotationDirection of Transfer1aL-Fucose permease, sugar transporterFungi > Plant1bZinc binding alcohol dehydrogenasePlant > Fungi1cMajor facilitator superfamily, membrane transporterFungi > Plant2Phospholipase/carboxylesterase family proteinFungi > Plant3aiucA/iucC family protein, siderophore biosynthesisFungi > Plant3bUnknown/conserved hypothetical proteinFungi > Plant4aDUF239 domain protein (Domain of Unknown function)Plant > Fungi4bPhosphate-responsive 1 family proteinPlant > Fungi4cUnknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) proteinPlant > Fungi

  • AngiospermLycophyteBryophyteChytridiomycotaZygomyceteBasidiomyceteAscomyceteFig 8.Taphrinomycotina

  • My perspectivesGenome 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

  • Supplementary Slides

  • History of HGTFirst described in Japan in 1959, 1960Transfer of antibiotic resistance between different species of bacteria; bacillary dysenteryTsutomu Watanabe, Bacteriology Review (1963)

  • Known mechanisms of HGTTransformation, introduction, uptake and expression of foreign genetic materialTransduction, transmission by virusBacterial conjugation, cell-to-cell contact

  • 1BayesianPHYMLRAxMLSH test

  • 1

  • 1

  • 22

  • 3

  • 3

  • 44

  • 4

  • Gene appears unique to genomeCould not confirm vertical inheritancePhylogeny suggests vertical inheritanceTaxon distribution of gene family suggests vertical inheritanceTransposable element1AL-fucose permease, sugar transporterPhpa(173818)1BZinc binding alcohol dehydrogenaseBDEG_06896Fig 7. Strong vertical inheritance

  • Table 1. Nine putative HGT candidate genes

    HGTPutative Functional Protein AnnotationDirection of TransferGenBank Accession No.Phylogeny construction 1aL-Fucose permease, sugar transporterFungi > PlantEDQ8358198 sequences and 341 length62 sequences and 349 length1bZinc binding alcohol dehydrogenasePlant > FungiEDQ61140*95 sequences and 207 length1cMajor facilitator superfamily, membrane transporterFungi > PlantEAU93280*40 sequences and 354 length2Phospholipase/carboxylesterase family proteinFungi > PlantXP_389330*122 sequences and 158 length 62 sequences and 349 length3aiucA/iucC family protein, siderophore biosynthesisFungi > PlantEDR08700*44 sequences and 218 length 15 sequences and 262 length3bUnknown/conserved hypothetical proteinFungi > PlantEDQ6864255 sequences and 174 length 34 sequences and 247 length4aDUF239 domain proteinPlant > FungiEDR0274787 sequences and 210 length4bPhosphate-responsive 1 family proteinPlant > FungiABK92591*93 sequences and 198 length4cUnknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) proteinPlant > FungiEDN2358413 sequences and 222 lengthGenBank 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

  • Challenging QuestionsHow 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?

  • Good afternoon everyone. First, I would like to thank you for agreeing to serve on my candidacy exam committee.The topic I chose to present concerns Horizontal Gene Transfers between kingdoms of fungi and plants.

    Here is the outline of my presentation. I will begin my presentation by briefly outlining what Horizontal Gene Transfer is, how it occurs, and why it matters. And then, I will summarize and discuss key findings in the paper I chosen, which is a Plant Cell paper published by Richards et al. in 2009. The main goal of this paper is to test whether Horizontal Gene Transfers have occurred between plants and fungi by using phylogenomic analysis of the proteomes of diverse plants, fungi, and other organisms. To explain what the Horizontal Gene Transfer is, I first need to talk about the Vertical Gene Transfer . The Vertical Gene Transfer refers to the passage of genes from one generation to the next through sexual or asexual production. However, Horizontal Gene Transfer doesnt require such reproduction process and involves the movement of genetic materials across species barriers. Although most genes transferred through HGT probably fail to function, probably because the recipient organism degrade the genes, dies because of mutations caused by the introduction, or lacks the ability to turn on the genes, in some cases the introduced genes can survive and be fixed in the recipient genome, especially when the introduced genes help the recipient organism survive under harmful conditions, such as the presence of antibiotics, or allows the recipient to utilize certain substrates as nutrients.Basically, HGT is a mechanism that provides opportunities for rapid genome innovation. It appears that HGT is a common mechanism of genome evolution in prokaryotes, but the roles and frequencies of HGT in eukaryotes have not yet been extensively studied. However, the rapid increase in genome sequencing has opened up opportunities for studying HGT in the evolution of eukaryotes.I would like to introduce two examples of HGTs in Eukaryotes. First example is plant pathogenic fungus, Fusarium oxysporum. Certain strains of the asexual species F. oxysporum have Lineage-specific (LS) chromosomes. These chromosomes cover about one-quarter of the genome, and many genes in the LS chromosomes are highly related to pathogenecity. The presence of these chromosomes allow the strains carrying them pathogenic to a particular host plant. Horizontal transfers of some of these chromosomes from a tomato pathogenic strain to a nonpathogenic strain have been experimentally demonstrated in the laboratory, and the recipient strains became pathogenic to tomato. Second example is the cartenoids biosynthe by