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Adaptive evolution of polyploid ginseng (Panax ginseng) revealed by genome annotation and comparative transcriptomes
DC Field | Value | Language |
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dc.contributor.advisor | Tae-Jin Yang | - |
dc.contributor.author | 무루칼틱 | - |
dc.date.accessioned | 2018-05-28T16:36:19Z | - |
dc.date.available | 2018-05-28T16:36:19Z | - |
dc.date.issued | 2018-02 | - |
dc.identifier.other | 000000150081 | - |
dc.identifier.uri | https://hdl.handle.net/10371/140810 | - |
dc.description | 학위논문 (박사)-- 서울대학교 대학원 : 농업생명과학대학 식물생산과학부, 2018. 2. Tae-Jin Yang. | - |
dc.description.abstract | and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. Furthermore, eleven novel candidates UDP-glucuronosyltransferase (UGTs) were identified through integrated transcriptome and metabolome data.
Heat and light stress poses an important threat to the growth and sustainable production of ginseng. Efforts have been made to study the effects of high temperature on ginseng physiology, but knowledge of the molecular responses to heat stress is still limited. Thus, in the second chapter, I have compared the transcriptomes (RNA-Seq) of two ginseng cultivars, Chungpoong (CP) and Yunpoong (YP), which are sensitive and resistant to heat stress, respectively, after 1- and 3-week heat treatments. Differential gene expression (DEG) and gene ontology (GO) enrichment along with profiled chlorophyll contents were performed. CP is more sensitive to heat stress than YP, and exhibited a lower chlorophyll content than YP. Moreover, heat stress reduced the chlorophyll content more rapidly in CP compared to YP. A total of 329 heat-responsive genes were identified. Intriguingly, genes encoding chlorophyll ab binding (CAB) proteins, WRKY transcription factors, and fatty acid desaturase (FAD) were predominantly responsive during heat stress and appeared to inhibit photosynthesis. In addition, a genome-wide scan of photosynthetic and sugar metabolic genes revealed reduced transcript levels for ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) under heat stress, especially in CP, possibly attributable to elevated levels of soluble sugars. Long noncoding RNAs (lncRNAs) have been implicated with diverse biological roles including genome regulation, various developmental processes and diseases. In the third chapter, through a systematic pipeline using ~104 billion sequencing RNA reads from various tissues, stages of growth and abiotic stress treatments of P. ginseng, I catalogued 19,495 and identified more than 100 candidate lncRNAs involved in abiotic stress responses to drought, salt, cold, heat and methyl jasmonate (MeJA) and 2,607 involved in specialized unknown function in specific tissues and growth stages of P. ginseng. Further, transposons might have been the contributor for the functional potential of lncRNAs in ginseng. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. In the fourth chapter, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, I developed the Ginseng Genome Database http://ginsengdb.snu.ac.kr/, the first open-access platform to provide comprehensive P. ginseng genomic resources. The current version of this database provides the latest draft genome sequence along with the structural and functional annotations of genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and analysis of genomic data are provided. All data in the database were manually curated and integrated within a user-friendly query page. Overall, this study will enable us to develop new cultivars carrying resistant to biotic/abiotic stresses, tolerant to direct sun light, and improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering. | - |
dc.description.abstract | Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production, and complicated genome structure that hamper its study. Furthermore, the knowledge of molecular responses to various abiotic stresses is still limited in P. ginseng. To facilitate its functional genomics, metabolomics and breeding in P. ginseng, I have performed four independent studies or chapters. With advent of sequencing technologies, the ginseng genome project was initiated in 2011 and the first draft genome assembly was completed in 2016. In first chapter, I annotated a total of 59,352 protein coding genes in tetraploid P. ginseng. Of them, 97% of the genes got functional descriptions. A total of 3, 588 transcription factors and 851 transcription regulators were identified and grouped into 94 families. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots | - |
dc.description.abstract | that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance | - |
dc.description.tableofcontents | GENERAL INTRODUCTION 1
REFERENCES 4 CHAPTER 1. Ginseng genome annotation and genes involved in ginsenoside biosynthetic pathway ABSTRACT 6 INTRODUCTION 7 RESULTS AND DISCUSSION 8 1. Genome assembly 8 2. Genome structural annotation 8 3. Evidence based gene predictions 9 4. Ab initio gene predictions 11 5. Integration of evidences with EVM 11 6. Filtration of non-protein coding genes 12 7. Filtration of transposon genes 13 8. Curation of gene models using PacBio 13 9. Alternative splicing (AS) 15 10. Functional annotation of protein coding genes 15 11. INTERPROSCAN 16 12. Gene Ontology (GO) annotation 17 13. Homology search 18 14. KEGG annotation 19 15. Transcription factor, transcriptional regulator, and protein kinase 20 16. Small RNA (sRNA) annotation 20 17. Ginsenoside biosynthesis 22 18. Gene expression analysis 27 19. Differential expressed gene (DEG) analysis 30 20. GO enrichment of the target DE genes 30 21. Gene family analysis 31 22. Fatty acid desaturase (FAD) 33 23. Chlorophyll ab binding (CAB) 37 CONCLUSION 41 MATERIALS AND METHODES 42 1. De novo sequencing, assembly and quality evaluation 42 2. Transcriptome sequencing and analysis 43 3. Genome annotation 44 4. Identification of genes in ginsenoside biosynthetic pathway 46 5. Identification of FAD and CAB genes 46 6. Phylogenetic analysis 46 7. Estimation of orthologous gene copies using low-coverage WGS 46 REFERENCES 47 CHAPTER 2. Comparative transcriptome analysis of heat stress responsiveness between two contrasting ginseng cultivars 55 ABSTRACT 55 INTRODUCTION 56 MATERIALS AND METHODES 57 1. Plant materials, growth conditions, and heat treatments 57 2. Measurement of chlorophyll content 58 3. Total RNA isolation and RNA-Seq analysis 58 4. Differential gene expression analysis 58 5. Gene family annotation 59 RESULTS AND DISCUSSION 59 1. P. ginseng cultivars CP and YP show different responses to heat 59 2. Identification of heat-responsive genes in P. ginseng 62 3. Comparative expression of genes involved in photosynthesis 67 4. Analysis of sugar metabolic genes 67 CONCLUSION 69 REFERENCES 71 CHAPTER 3. Genome-wide screening of transcriptomes revealed the landscape of long noncoding RNAs in ginseng (Panax ginseng) 75 ABSTRACT 75 INTRODUCTION 76 RESULTS 78 1. Genome-wide characterization of lncRNAs in P. ginseng 78 2. Differential expression analysis 81 3. Co-expression and target interaction analysis 81 4. Conservation analysis 83 5. Single nucleotide polymorphism (SNPs) analysis between Panax species 85 6. Functional repertoire of lncRNAs derived from transposons 87 DISCUSSION 87 MATERIALS AND METHODES 91 1. Datasets used for lncRNA predictions 91 2. Pipeline for lncRNA identification 92 3. Characterization of lncRNAs 93 4. Expression profiling 93 5. Co-expression analysis 94 6. SNP calling 94 7. RNA extraction and quantitative RT-PCR 95 8. Validation of antisense lncRNA by strand-specific quantitative RT-PCR 95 REFERENCES 96 CHAPTER 4. Ginseng Genome Database: An open-access platform for genomics of Panax ginseng 103 ABSTRACT 103 INTRODUCTION 104 CONSTRUCTION AND CONTENT 1. Whole-genome sequencing and assembly and gene models 105 2. Transcriptome data 106 3. Gene families and metabolic pathways 106 4. Genome-scale metabolic network 107 5. Transcription factors 107 6. Genes in the ginsenoside biosynthesis pathway 108 7. Digital gene expression profiles 108 UTILITY AND DISCUSSION 108 1. Database implementation 108 2. Query search 109 3. Sequence retriever 110 4. BLAST 111 5. JBrowse 111 6. Downloads 113 CONCLUSION 113 REFERENCES 114 ABSTRACT IN KOREAN 118 | - |
dc.format | application/pdf | - |
dc.format.extent | 4907555 bytes | - |
dc.format.medium | application/pdf | - |
dc.language.iso | en | - |
dc.publisher | 서울대학교 대학원 | - |
dc.subject | Panax ginseng | - |
dc.subject | genome annotation | - |
dc.subject | long noncoding RNAs | - |
dc.subject | adaptation | - |
dc.subject | database | - |
dc.subject.ddc | 633 | - |
dc.title | Adaptive evolution of polyploid ginseng (Panax ginseng) revealed by genome annotation and comparative transcriptomes | - |
dc.type | Thesis | - |
dc.description.degree | Doctor | - |
dc.contributor.affiliation | 농업생명과학대학 식물생산과학부 | - |
dc.date.awarded | 2018-02 | - |
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