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Comparative and Population Genomics Platforms for Fungi and Oomycetes
곰팡이와 난균류를 위한 비교유전체 및 집단유전체 분석 시스템 구축

DC Field Value Language
dc.contributor.advisor이용환-
dc.contributor.author최재영-
dc.date.accessioned2017-07-13T17:37:34Z-
dc.date.available2017-07-13T17:37:34Z-
dc.date.issued2014-02-
dc.identifier.other000000017428-
dc.identifier.urihttp://hdl.handle.net/10371/120977-
dc.description학위논문 (박사)-- 서울대학교 대학원 : 협동과정 농업생물공학전공, 2014. 2. 이용환.-
dc.description.abstractFungal genomes have been extensively sequenced mainly aided by next-generation sequencing technologies. Currently, more than 300 fully-sequenced fungal genomes are available in public domain, facilitating comparative and evolutionary genomics at the kingdom-wide level. Recently, the 1,000 Fungal Genomes Project (http://1000.fungalgenomes.org/) was launched to sequence the species especially focused on taxa which are rarely sequenced, hence providing foundation for deciphering underpinnings of fungal evolution and diversity. The emerging technologies and a number of genomes from fungi, animals and plants would provide an opportunity for exhaustive comparative genomics. In order to fully take advantage of such an opportunity, comprehensive and systematic genomics solution had an immediate need.
As a solution, Comparative Fungal Genomics Platform (CFGP
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dc.description.abstracthttp://cfgp.snu.ac.kr/) was publicly open with 65 genomes belonging to 58 fungal and Oomycete species in 2007. The first release provided six bioinformatics tools, including a novel tool entitled BLASTMatrix that enables search homologous genes to queries in multiple species simultaneously. CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools. Since then, CFGP has grown to archive 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants, and 105 animals. In addition, the number of tools in Favorite increased to 27. As a result, CFGP 2.0 was released with the considerable update and development. The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions. The user interface of BLASTMatrix was also improved to facilitate subsequent analyses of retrieved data. A newly developed genome browser, Seoul National University Genome Browser (SNUGB-
dc.description.abstracthttp://genomebrowser.snu.ac.kr/), was integrated into CFGP 2.0 to support graphical presentation of diverse genomic contexts. Based on the standardized genome warehouse of CFGP 2.0, gene family analysis platforms including Fungal Secretome Database (FSD-
dc.description.abstracthttp://fsd.snu.ac.kr/) and Fungal Plant Cell Wall-degrading Enzyme Database (FPDB-
dc.description.abstracthttp://pcwde.riceblast.snu.ac.kr/) were constructed.
Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed the FSD. A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/Oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species.
Plant cell wall-degrading enzymes (PCWDEs) play significant roles throughout the fungal life including acquisition of nutrients and decomposition of plant cell walls. In addition, many of PCWDEs are also utilized by biofuel and pulp industries. In order to develop a comparative genomics platform focused in fungal PCWDEs and provide a resource for evolutionary studies, FPDB was constructed (http://pcwde.riceblast.snu.ac.kr/). In order to archive genes encoding PCWDEs, 22 sequence profiles were constructed and searched on 328 genomes of fungi, Oomycetes, plants and animals. A total of 6,682 putative genes encoding PCWDEs were predicted, showing differential distribution by their life styles, host ranges and taxonomy. Genes known to be involved in fungal pathogenicity, including polygalacturonase (PG) and pectin lyase, were enriched in plant pathogens. Furthermore, crop pathogens had more PCWDEs than those of rot fungi, implying that the PCWDEs analysed in this study are more needed for invading plant hosts than wood-decaying processes. Evolutionary analysis of PGs in 34 selected genomes revealed that gene duplication and loss events were mainly driven by taxonomic divergence and partly contributed by those events in species-level, especially in plant pathogens.
Understanding intra-species diversity of the rice blast fungus, Magnaporthe oryzae, is important, since the reference strain 70-15 is a lab strain. In order to set a multiple reference genomes and study genomic differences among field isolates, a world-wide collection of 37 M. oryzae genomes were sequenced. The repeat-masked genome size, the number of predicted genes and domain profile were similar to each other, but they showed differential distribution of structural variations and Zn(II)2Cys6, CCHC and C2H2 transcription factor families. The average size of assembled genomes was 36.41 Mb and the number of predicted genes was 13,403, on average. The size of core genome for M. oryzae was estimated as 8,262 genes, and the size of pan-genome was predicted to contain 20,655 genes. In order to provide a genomics platform focused on M. oryzae, a web-based system, Magnaporthe Atlas (http://www.magnaporthe.org/) was developed by implementing genome assembly, gene prediction, gene family annotation, SNUGB module and Favorite extension.
Collectively, CFGP 2.0, FSD and FPDB would serve as comprehensive fungal genomics platforms which were also used for analyzing 38 M. oryzae genomes. Comparative analysis on multiple M. oryzae genomes showed genomic characteristics at population scale, thus providing a foundation for further comparative and evolutionary genomics studies.
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dc.description.tableofcontentsABSTRACT i
CONTENTS v
LIST OF TABLES ix
LIST OF FIGURES xii

CHAPTER 1. CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes
ABSTRACT 2
INTRODUCTION 3
MATERIALS AND METHODS 7
I. System design 7
II. Mining orthologues 7
III. Expanded genome data warehouse 8
ENHANCED UTILITY AND NEW FEATURES 10
I. Improved user interface 10
II. Taxonomy browser 10
III. SNUGB 12
IV. New bioinformatics tools added to the Favorite Browser. 12
V. Orthologue browsing function. 12
FUNCTIONAL/EVOLUTIONARY GENOMICS PLATFORMS DEVELOPED BASED ON THE STANDARDIZED GENOME WAREHOUSE OF CFGP 2.0 15
FUTURE DIRECTIONS 17
LITERATURE CITED 18
SUPPLEMENT DATA 25

CHAPTER 2. Fungal Secretome Database: an integrated platform for annotation of fungal secretomes
ABSTRACT 43
INTRODUCTION 44
RESULTS 47
I. Evaluation of the pipeline for predicting secretory proteins 47
II. System structure of the FSD 54
CONTENT AND DISCUSSION 55
I. Secretory proteins in 158 fungal/Oomycete genomes 55
II. Effectors encoded by fungal/Oomycete and Plasmodium genomes 70
UTILITY 73
I. FSD web interfaces 73
II. The personalized virtual space, Favorite, supports in-depth analyses in the FSD 74
CONCLUSION 80
LITERATURE CITED 81

CHAPTER 3. Fungal Plant Cell Wall-degrading Enzyme Database: a platform for comparative and evolutionary genomics in fungi and Oomycetes
ABSTRACT 107
INTRODUCTION 108
MATERIALS AND METHODS 113
I. Collection of protein sequences for construction of sequence profiles 113
II. Collection of proteome sequences 113
III. A constructed pipeline for genes encoding PCWDEs 113
IV. Elimination of redundancy 114
V. Preparation of evaluation data sets 114
VI. Reconciliation analysis 115
RESULTS AND DISCUSSIONS 118
I. Evaluation of the pipeline 118
II. Identification of genes encoding PCWDEs 119
III. Differential distribution of PCWDEs by life styles 124
IV. Differential distribution of PCWDEs among plant-associated fungi 125
V. Tracking evolutionary history of PGs 128
UTILITY 130
I. Web interfaces 130
II. Cross-link with the CFGP 2.0 for further analysis 130
CONCLUSION 132
LITERATURE CITED 133
SUPPLEMENT DATA 139

CHAPTER 4. Comparative genome analysis of a world-wide population of Magnaporthe oryzae isolates
ABSTRACT 142
INTRODUCTION 143
MATERIALS AND METHODS 147
I. Origin of M. oryzae isolates 147
II. Sequencing, genome assembly and gene prediction 150
III. Construction of phylogeny 151
IV. Assessment of repetitive sequences 152
V. Calling method for structural variations 152
VI. Pairwise comparison of the genomes 153
VII. Strategy for defining core and pan-genome 153
VIII. Gene family annotation 155
IX. Development of a web-based genomics portal, Magnaporthe Atlas 155
RESULTS AND DISCUSSIONS 158
I. General features of 38 M. oryzae genomes 158
II. Prediction of repetitive elements revealed genomic complexity in M. oryzae genomes 167
III. Distribution and sequence analysis of avirulence genes 172
IV. Structural variations of M. oryzae genomes against the reference strain 70-15 180
V. Distribution of gene families among M. oryzae genomes 187
VI. Genome conservation measured by pairwise comparison of shared genes and average nucleotide identity 191
VII. Core genome of M. oryzae 196
VIII. Orphan genes of M. oryzae 202
IX. Pan-genome of M. oryzae 204
X. M. oryzae KJ201 reflects the genes shared by 35 field isolates better than 70-15 207
XI. Development of a web-based genomics platform for M. oryzae 211
CONCLUSION 213
LITERATURE CITED 214
SUPPLEMENT DATA 226
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dc.formatapplication/pdf-
dc.format.extent4709256 bytes-
dc.format.mediumapplication/pdf-
dc.language.isoen-
dc.publisher서울대학교 대학원-
dc.subjectbioinformatics platform-
dc.subjectcomparative genomics-
dc.subjectsecretome-
dc.subjectplant cell wall-degrading enzyme-
dc.subjectMagnarporthe oryzae-
dc.subjectgenome sequences-
dc.subjectcore genome-
dc.subjectpan-genome-
dc.subject.ddc660-
dc.titleComparative and Population Genomics Platforms for Fungi and Oomycetes-
dc.title.alternative곰팡이와 난균류를 위한 비교유전체 및 집단유전체 분석 시스템 구축-
dc.typeThesis-
dc.contributor.AlternativeAuthorJaeyoung Choi-
dc.description.degreeDoctor-
dc.citation.pagesxiv, 235-
dc.contributor.affiliation농업생명과학대학 협동과정 농업생물공학전공-
dc.date.awarded2014-02-
Appears in Collections:
College of Agriculture and Life Sciences (농업생명과학대학)Program in Agricultural Biotechnology (협동과정-농업생물공학전공)Theses (Ph.D. / Sc.D._협동과정-농업생물공학전공)
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