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Transcriptome Profiling and Comparative Analysis of Panax ginseng Adventitious Roots

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dc.contributor.advisorTae-Jin Yang-
dc.contributor.authorJAYAKODI MURUKARTHICK-
dc.date.accessioned2017-07-14T06:29:57Z-
dc.date.available2017-07-14T06:29:57Z-
dc.date.issued2014-02-
dc.identifier.other000000017318-
dc.identifier.urihttp://hdl.handle.net/10371/125639-
dc.description학위논문 (석사)-- 서울대학교 대학원 : 식물생산과학부(작물생명과학전공), 2014. 2. Tae-Jin Yang.-
dc.description.abstractPanax ginseng (C. A. Meyer) is a traditional medicinal plant famous for its strong therapeutic effects. However, genomic resources for P. ginseng are still very limited. In this study, we performed de novo assembly of transcriptomes from adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS). The assemblies were generated from ~85 and ~77 million high-quality Illumina HiSeq reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in TAIR databases. We identified candidate genes involved in ginsenoside biosynthesis: 10 transcripts for farnesyl diphosphate synthase to protopanaxatriol synthase and 21 transcripts for UDP-glycosyltransferase. A large number of transcripts (17%) with different GO designations were uniquely detected in adventitious roots compared to normal ginseng roots. In addition, 10,213 and 7,928 cDNA SSRs were identified as potential molecular markers in CP and CS, respectively. Our assembly of ginseng transcriptomes demonstrates the successful application of genomics approaches to large complex genomes. In addition, we have predicted the long noncoding(lncRNA) based on our CP RNA-Seq data. A total of 11,270 lncRNA were identified. Among them, some were precursors of small RNAs such as microRNAs and siRNAs. The assembly and comparative analysis data have been deposited to our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use. Further, To better understand our ginseng genome (P. ginseng), we used Chunpoong (CP) adventitious root RNA-Seq data to identify lncRNAs of P. gisneng. we found 11,270 long noncoding RNAs which had multiexonic structures. A total of 433 lncRNAs showed significant similarity against publicly available lncRNA database of Arabidopsis, Maize, lncRNA database and Rfam. My study provides a preliminary source for future studies of lncRNA content and function in ginseng.-
dc.description.tableofcontentsABSTRACT 1
INTRODUCTION 3
MATERIALS AND METHODES 5
1 Plant material and RNA isolation 5
2 Illumina sequencing and quality control 6
3 De novo assembly 6
4 Functional annotation and analysis 7
5 Expression profiling 8
6 Identification of candidate transcripts involved in ginsenoside biosynthesis 8
7 SSR identification 8
8 Adventitious root transcriptome (ART) database creation 9
RESULTS 9
1 Adventitious root growth and morphology of two ginseng cultivars 9
2 De novo assembly and validation of Illumina paired-end sequences 9
3 Functional annotation and classification 13
4 Gene expression profiling 15
5 Transcripts showing biased expression between CP and CS adventitious roots 18
6 Identification of candidate genes involved in ginsenoside biosynthesis 22
7 Comparative analysis of the transcriptomes of adventitious and normal roots 26
8 Identification of cDNA-derived SSR markers 27
9 Adventitious root transcriptome database 30
DISCUSSION 31
1 Assembly of Illumina transcriptome sequences 31
2 Comparative analysis of transcriptomes in adventitious roots 33
3 Genes related to ginsenoside biosynthesis 36
4 Comparative analysis of transcriptomes between roots and adventitious roots 36
CONCLUSION 37
REFERENCES 38
CHAPTER 2 Computational prediction of long noncoding RNAs (lncRNAs) in P ginseng
ABSTRACT 49
INTRODUCTION 50
MATERIALS AND METHODES 52
1 Data sources 52
2 The Coding Potential Calculator 53
3 Small RNA database creation 53
RESULTS AND DISCUSSION 53
1 Computational prediction 53
2 Homology based functional search 55
3 Classification of ginseng lncRNAs as small RNA precursors 57
4 Repetitive element content of lncRNAs 59
CONCLUSION 60
REFERENCES 61
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dc.formatapplication/pdf-
dc.format.extent1295579 bytes-
dc.format.mediumapplication/pdf-
dc.language.isoen-
dc.publisher서울대학교 대학원-
dc.subjectMajor in Crop Science and Biotechnology-
dc.subject.ddc633-
dc.titleTranscriptome Profiling and Comparative Analysis of Panax ginseng Adventitious Roots-
dc.typeThesis-
dc.description.degreeMaster-
dc.citation.pages72-
dc.contributor.affiliation농업생명과학대학 식물생산과학부(작물생명과학전공)-
dc.date.awarded2014-02-
Appears in Collections:
College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Plant Science (식물생산과학부)Theses (Master's Degree_식물생산과학부)
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