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Molecular characterization of whole genome duplication in Panax ginseng
DC Field | Value | Language |
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dc.contributor.advisor | 양태진 | - |
dc.contributor.author | 김남훈 | - |
dc.date.accessioned | 2017-07-13T17:39:15Z | - |
dc.date.available | 2017-07-13T17:39:15Z | - |
dc.date.issued | 2015-08 | - |
dc.identifier.other | 000000067313 | - |
dc.identifier.uri | https://hdl.handle.net/10371/121008 | - |
dc.description | 학위논문 (박사)-- 서울대학교 대학원 : 식물생산과학부(작물생명과학), 2015. 8. 양태진. | - |
dc.description.abstract | Panax ginseng, belonging to Araliaceae, has been used as medicinal plant for centuries. Even though medicinal effect of ginseng is well-studied, the genomic information of ginseng is very limitedly available. Genome of P. ginseng has been considered to be experienced two rounds of whole genome duplication (WGD) based on expressed sequence tag (EST) sequences. However, there was no sign of the WGD at the genomic sequence level, except that multiple band patterns have been consistently observed during PCR amplification even though we used unique gene sequences in P. ginseng. Here, I tried to define the genome duplication at the sequence level. First, I analyzed the sequences of multiple bands derived from unique EST-SSR markers and at second, I deeply investigated four paralogous gene-rich genome blocks using whole genome draft sequence of P. ginseng. Re-amplification and sequencing of the individual bands for EST-SSR markers revealed that two bands around the expected size were genuine amplicons derived from two paralogous loci. Sequences derived from the two loci showed high similarity including the same primer-binding site, but each locus could be distinguished by the based on SSR copy number variations and additional SNPs or InDels. The comparison of the paralogous blocks in the draft sequence revealed that sequences are highly conserved between two recent duplicated paralagous scaffolds although there was some InDels derived from transposable elements. However, paleo duplicated paraloguous blocks showed little conservation only in genic regions. The paralogous gene pairs were identified and molecular clocks were calculated in four genome blocks. I estimated that first WGD happened at around 25.8 million years ago (MYA) which is common phenomena in all Panax species, and another recent WGD happened at around 2.54 MYA between P. ginseng and P. quinfuefolius only. Since high sequence homology between recent WGD blocks interrupts the amplification of single band in marker development, I developed the strategy of designing sequence tagged site (STS) primers, one for dCAPS based on single nucleotide polymorphism (SNP) site between cultivars, and another complementary primer for locus-specific primer based on SNP between paralogs. Genetic mapping using two STS markers derived from recent paralog blocks, Block 1 and Block 2, showed different segregation pattern in F2 population between Yunpoong and Chunpoong, which indicates that two recent duplicated paralog blocks are located independently at chromosomal locus and those were derived from WGDs. This study provide the first insight for WGD-derived genome structure in sequence level. The information and finding will be helpful for further ginseng genomics study for improving draft sequence quality and chromosome anchoring of scaffolds, and genetic mapping. | - |
dc.description.tableofcontents | GENERAL ABSTRACT I
LIST OF TABLES VII LIST OF FIGURES VIII LIST OF ABBREVIATIONS IX GENERAL INTRODUCTION 1 REFERENCES 3 CHAPTER I 6 Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tag-simple sequence repeat bands in Panax ginseng Meyer ABSTACT 7 INTRODUCTION 8 MATERIAL AND METHODS 10 Sample preparation and preliminary PCR 10 Sequencing of each individual band among multiple bands 10 Sequence analysis and design of locus-specific primer for gm47n marker 11 RESULTS 12 Separation and re-amplification of individual bands 12 Sequence comparison of Band-A and Band-B 14 Locus-specific PCR amplification for the gm47n marker 18 DISCUSSION 21 PCR amplification of two paralogous loci derived from genome duplication in P. ginseng 21 Sequence variation between paralogous bands 22 Additional artifact bands are caused by coexistence of two paralogous bands 22 Development of locus-specific markers and future application 23 REFERENCES 25 CHAPTER II 29 Micro-collinearity within Panax ginseng genome sequences resulted from two rounds of whole genome duplication ABSTRACT 30 INTRODUCTION 32 MATERIAL AND METHODS 34 Plant material and extraction of DNA and RNA 34 Genome sequencing, assembly and repeat masking 35 Transcriptome sequencing and assembly 35 Selection of homoeologous scaffolds and comparative analysis 36 Gene annotation and expression profiling of homoeologous scaffolds 36 Development of STS markers in micro-collinearity blocks 37 RESULTS 39 Genome sequence and transcriptome assembly. 39 Identification of homoeologous scaffolds from draft sequence. 42 Annotation of the homoeologous scaffold sequences 46 Comparative analysis of the homoeologous scaffold sequences 48 Paralogous gene pairs and its divergence in four paralogous blocks 59 Expression profiles of paralogous gene pairs. 62 Designing locus-specific SNP markers 66 DICUSSIONS 69 REFERENCES 75 APPENDIX 81 ABSTRACT IN KOREAN 92 | - |
dc.format | application/pdf | - |
dc.format.extent | 6231011 bytes | - |
dc.format.medium | application/pdf | - |
dc.language.iso | en | - |
dc.publisher | 서울대학교 대학원 | - |
dc.subject | Panax ginseng genome | - |
dc.subject | whole genome duplication | - |
dc.subject | paralog | - |
dc.subject.ddc | 633 | - |
dc.title | Molecular characterization of whole genome duplication in Panax ginseng | - |
dc.type | Thesis | - |
dc.description.degree | Doctor | - |
dc.citation.pages | ix, 93 | - |
dc.contributor.affiliation | 농업생명과학대학 식물생산과학부 | - |
dc.date.awarded | 2015-08 | - |
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