Publications
Detailed Information
Genome structure and evolution of Panax ginseng C. A. Meyer
| DC Field | Value | Language |
|---|---|---|
| dc.contributor.advisor | 양태진 | - |
| dc.contributor.author | 최홍일 | - |
| dc.date.accessioned | 2017-07-13T17:40:43Z | - |
| dc.date.available | 2017-07-13T17:40:43Z | - |
| dc.date.issued | 2013-02 | - |
| dc.identifier.other | 000000009318 | - |
| dc.identifier.uri | https://hdl.handle.net/10371/121035 | - |
| dc.description | 학위논문 (박사)-- 서울대학교 대학원 : 식물생산과학부 작물생명과학전공, 2013. 2. 양태진. | - |
| dc.description.abstract | Ginseng (Panax ginseng C. A. Meyer) has been known as a valuable medicinal herb for thousands of years in East Asia. Although medicinal components and their functions of ginseng have been widely investigated, it could be regarded as an underdeveloped crop in genetics and genomics research areas. This study was conducted to elucidate genome structure and evolution in ginseng by analyses of expressed sequence tags (ESTs) and bacterial artificial chromosome (BAC) sequences. The EST analysis based on the calculation of synonymous substitutions per synonymous site (Ks) in paralog and ortholog pairs revealed that two rounds of polyploidy events occurred in the common ancestor of ginseng and American ginseng (P. quinquefolius L.) and subsequent divergence of the two species. The sequence analysis of repeat-rich BAC clones characterized the major component of the ginseng genome, long terminal repeat retrotransposons (LTR-RTs). Ty3/Gypsy-like elements were more predominant than Ty1/Copia. High abundance of the LTR-RTs were revealed by whole genome shotgun (WGS) read mapping and fluorescence in situ hybridization (FISH) analysis. Particularly, the PgDel1 elements played major roles in expanding heterochromatic regions as well as remodeling euchromatic regions. The PgDel2 elements showed biased intensity of FISH signals on half the total chromosomes, which demonstrate the alloploidy-like nature of ginseng. Insertion time of the LTR-RTs indicated that LTR-RTs may proliferate after the recent polyploidy event in the ginseng genome. These results suggest that the ginseng genome of the present day has been expanded and evolved by two rounds of polyploidy events and accumulation of LTR-RTs. | - |
| dc.description.tableofcontents | GENERAL ABSTRACT i
CONTENTS iii LIST OF TABLES vi LIST OF FIGURES vii ABBREVIATION USED viii GENERAL INTRODUCTION 1 REFERENCES 4 CHAPTER I. Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags ABSTRACT 8 INTRODUCTION 9 MATERIALS AND METHODS 12 Plant material, construction of cDNA library and normalization 12 Generation, collection and assembly of ESTs 13 Functional annotation of ginseng uniESTs 13 Identification of paralogs and orthologs 14 Estimation of Ks values and elimination of redundant Ks values 14 RESULTS 16 Construction of cDNA library 16 Generation, collection, and assembly of ESTs 16 Functional annotation of the uniEST set of ginseng 18 Identification of paralogs and orthologs 21 Peaks in the Ks distribution 23 DISCUSSION 30 Two rounds of genome duplications are found in both ginseng and American ginseng 30 American ginseng recently diverged from ginseng by migration 31 Estimation of molecular clocks for evolutionary events 33 REFERENCES 36 CHAPTER II. Repeat-rich bacterial artificial chromosome (BAC) sequences and fluorescence in situ hybridization (FISH) unveil major heterochromatic components and alloploid-like genome structure in Panax ginseng ABSTRACT 43 INTRODUCTION 45 MATERIALS AND METHODS 48 Selection of BAC clones, sequencing and assembly 48 Sequence analysis and annotation 48 Phylogenetic analysis of LTR-RTs 49 Insertion time estimation of LTR-RTs 50 Utilization of whole genome shotgun sequences 50 Fluorescence in situ hybridization analysis 52 RESULTS 54 Selection and sequencing of three repeat-rich BAC clones 54 Sequence annotation of repeat-rich BAC sequences 56 Characterization and classification of LTR-RTs 61 LTR-RT derivatives 66 Other repetitive elements 66 Genome proportion of LTR-RTs in ginseng 67 Distribution of LTR-RTs in ginseng genome 72 The unique gene structure in 5J07 76 Duplicated copies of non-repetitive regions in ginseng genome 78 DISCUSSION 81 LTR-RTs and genome size expansion in ginseng 81 PgDel elements and remodeling of euchromatic regions in ginseng genome 82 PgDel2 and alloploidy-like nature of ginseng genome 83 Evolution of ginseng genome 84 REFERENCES 88 ABSTRACT IN KOREAN 96 | - |
| dc.format | application/pdf | - |
| dc.format.extent | 2215391 bytes | - |
| dc.format.medium | application/pdf | - |
| dc.language.iso | en | - |
| dc.publisher | 서울대학교 대학원 | - |
| dc.subject | Bacterial artificial chromosome (BAC) | - |
| dc.subject | ginseng (Panax ginseng C. A. Meyer) genome | - |
| dc.subject | expressed sequence tag (EST) | - |
| dc.subject | fluorescence in situ hybridization (FISH) | - |
| dc.subject | long terminal repeat retrotransposon (LTR-RT) | - |
| dc.subject | polyploidy | - |
| dc.subject.ddc | 633 | - |
| dc.title | Genome structure and evolution of Panax ginseng C. A. Meyer | - |
| dc.type | Thesis | - |
| dc.description.degree | Doctor | - |
| dc.citation.pages | viii, 97 | - |
| dc.contributor.affiliation | 농업생명과학대학 식물생산과학부(작물생명과학전공) | - |
| dc.date.awarded | 2013-02 | - |
- Appears in Collections:
- Files in This Item:
Item View & Download Count
Items in S-Space are protected by copyright, with all rights reserved, unless otherwise indicated.