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Comparative genome analysis of Ralstonia solanacearum causing potato bacterial wilt in Korea
한국의 세균성 풋마름병 감염 감자에서 분리한 Ralstonia solanacearum의 유전체 해독 및 비교분석

DC Field Value Language
dc.contributor.advisor황인규-
dc.contributor.author조희정-
dc.date.accessioned2018-05-28T16:33:34Z-
dc.date.available2018-05-28T16:33:34Z-
dc.date.issued2018-02-
dc.identifier.other000000150917-
dc.identifier.urihttps://hdl.handle.net/10371/140785-
dc.description학위논문 (박사)-- 서울대학교 대학원 : 농업생명과학대학 농생명공학부, 2018. 2. 황인규.-
dc.description.abstractRalstonia solanacearum, causal agent of bacterial wilt, is one of the most destructive phytopathogen in the world. Soil-borne this bacterium invades plants mainly through the roots, colonizes and proliferates in the xylem, as the results plants wilt by blocking water. R. solanacearum has unusual broad host range over 450 plant species of 50 botanical families. This bacterium distributed worldwide encompassing tropical, subtropical, and temperate region. With these features, this species are very diverse and complex and call as pathogenic Ralstonia solanacearum species complex (RSSC). This study used 93 RSSC isolates collected from potato bacterial wilt (or brown rot) from 1998 to 2003 in Korea. To investigate the host specific factors by comparative genomic analyses, first, their properties were determined by analyzing of phylotype, biovar, and host range. Of the 93 isolates, 71 isolates determined to phylotype I and these divided into eight isolates of biovar 3 and sixty-three isolates of biovar 4. Twenty-two isolates determined to phylotype IV and these were all biovar 2. This phylotype-biovar classification was consistent with phylogenetic trees based on 16S rRNA and egl gene sequences, in which all biovar 3 and 4 isolates clustered to phylotype I, and all biovar 2 isolates clustered to phylotype IV. Korean phylotype IV isolates were distinct from phylotype I isolates pathologically as well as genetically, which was all phylotype IV isolates were nonpathogenic to peppers. In pathogenicity assays for host range determining, there were four pathotypes: (P) only pathogenic on potato, (PT) pathogenic on potato and tomato, (PTE) pathogenic on potato, tomato, and eggplant, and (PTEPe) pathogenic on all tested crops – potato, tomato, eggplant, and pepper. Based on this host range, twenty-five strains were selected and sequenced whole genome. The newly sequenced 25 Korean genomes were structurally compared with previously published nine genome data using ANI values, pair-wise and multiple genome alignment. As the results, genome sequences were usually conserved among the same phylotypes, but more divergent between phylotype I and IV. After that, to investigate candidate genes responsible for host specificity, functional genome comparisons were performed based on the host range by analyzing of pan-genome and type III secretion system effectors (T3Es). The same pathotype strains exhibited considerable gene repertoires for infection of tomato, eggplant, or pepper. In pan-genome analysis, total 127 genes present only in tomato nonpathogenic strains, 8 genes in tomato pathogenic strains, 5 genes from eggplant nonpathogenic strains, 7 genes from eggplant pathogenic strains, one gene from pepper nonpathogenic strains, and 34 genes from pepper pathogenic strains. In T3Es analysis, RipH3 and RipS3 were found only in the tomato pathogenic strains and RipAC were only in the eggplant pathogenic strains. This study showed that the host range of R. solanacearum required comprehensive actions of various virulence factors involving effectors, secretion systems, attachment, and enzymes, etc.-
dc.description.tableofcontentsGENERAL INTRODUCTION 1
LITERATURE CITED 9

CHAPTER I. ANALYSIS OF GENETIC AND PATHOGENIC DIVERSITY OF RALSTONIA SOLANACEARUM CAUSING POTATO BACTERIAL WILT IN KOREA

ABSTRACT 20
INTRODUCTION 22
MATERIALS AND METHODS 25
1. Collection of isolates and culture conditions 25
2. Isolation of genomic DNA 25
3. Phylotype identification 26
4. Biovar determination 27
5. Detection of rsa1 gene 28
6. Phylogenetic analysis of 16S rRNA and partial endoglucanase (egl) gene sequences 28
7. Host range determination 30
RESULTS 32
1. Determination of biovar, phylotype, and rsa1 gene 32
2. Geographical distribution 38
3. Phylogenetic analysis of 16S rRNA and partial endoglucanase (egl) gene sequences 40
4. Host range determination 44
DISCUSSION 48
LITERATURE CITED 53

CHAPTER II. COMPARATIVE GENOME ANALYSIS OF RALSTONIA SOLANACEARUM CAUSING POTATO BACTERIAL WILT IN KOREA

ABSTRACT 60
INTRODUCTION 62
MATERIALS AND METHODS 66
1. Strain selection 66
2. Genome sequencing 69
3. Structural genome comparisons 70
4. COG distribution and Pan-genome Orthologous analysis (POG) 70
5. Effectors prediction 71
6. Genome submission 71
RESULTS 72
1. General genome features 72
2. Structural Genome comparisons: OrthoANI analysis, Pair-wise and Multiple genome alignments 76
3. Clusters of Orthologous Group (COG) distribution 92
4. Functional genome comparison: phylotype-biovar 97
5. Functional genome comparison: host specificity 99
6. Functional genome comparison: T3SS effector 118
DISCUSSION 129
LITERATURE CITED 135
ABSTRACT IN KOREAN 141
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dc.formatapplication/pdf-
dc.format.extent4026450 bytes-
dc.format.mediumapplication/pdf-
dc.language.isoen-
dc.publisher서울대학교 대학원-
dc.subjectRalstonia solanacearum-
dc.subjectpotato bacterial wilt-
dc.subjectpathogen-
dc.subjectdiversity-
dc.subjectphylotype-
dc.subjectcomparative genome-
dc.subjecttype III effector-
dc.subject.ddc630-
dc.titleComparative genome analysis of Ralstonia solanacearum causing potato bacterial wilt in Korea-
dc.title.alternative한국의 세균성 풋마름병 감염 감자에서 분리한 Ralstonia solanacearum의 유전체 해독 및 비교분석-
dc.typeThesis-
dc.description.degreeDoctor-
dc.contributor.affiliation농업생명과학대학 농생명공학부-
dc.date.awarded2018-02-
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College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Agricultural Biotechnology (농생명공학부)Theses (Ph.D. / Sc.D._농생명공학부)
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