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DNA Super-barcoding and Authentication of Species in Araliaceae Family : DNA 슈퍼바코딩 및 인증 아라리과과의 종의 수

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dc.contributor.advisorTae-Jin Yang-
dc.contributor.author보녹린앙-
dc.date.accessioned2022-06-08T06:41:40Z-
dc.date.available2024-04-18T05:51:11Z-
dc.date.issued2022-
dc.identifier.other000000171074-
dc.identifier.urihttps://hdl.handle.net/10371/181214-
dc.identifier.urihttps://dcollection.snu.ac.kr/common/orgView/000000171074ko_KR
dc.description학위논문(박사) -- 서울대학교대학원 : 농업생명과학대학 식물생산과학부, 2022.2. Tae-Jin Yang.-
dc.description.abstractThe Araliaceae family includes 50 genera and around 1500 species worldwide. Overharvesting and adulteration of high-value medicinal plants from this family, particularly Panax species, have caused trouble in supply systems. The whole plastid genome (plastome) and 45S nuclear ribosomal DNA (nrDNA) sequences, referred to as super-barcodes, have emerged as a promising approach for correctly identifying plant species, a vital first step in the authentication system for combating economically motivated adulteration (EMA). This dissertation was conducted to assess the efficiency of these super-barcodes in classifying Araliaceae species and identifying specific barcoding loci for Panax species authentication.
Eleven newly characterized complete plastomes and 64 previously reported complete plastomes were included, representing 56 species from 26 genera in the Araliaceae family and Centella asiatica (Apiaceae). The maximum likelihood (ML) tree was constructed from 75 plastome sequences and showed the monophyly of 25 genera with 100% bootstrap support. The genus Aralia was polyphyletic. The relaxed molecular clock estimation based on the 78 plastid genes indicated that subsequent speciation occurred within the Araliaceae genera from 8.04 to 0.67 million years ago (MYA) during the Middle Miocene and Pliocene. The collection of 74 complete plastomes revealed 43,458 variants. The 45S nrDNA sequences of 22 Araliaceae species showed 97.5 to 100% identities with 383 variants. Critical examination of plastome and 45S nrDNA super-barcoding data would provide new insights to improve knowledge of the evolutionary history of Araliaceae species. Furthermore, based on the phylogenetic tree, a total of fifteen SNPs in the plastid coding gene sequences were selected and successfully developed Kompetitive allele-specific PCR (KASP) markers, enabling clear identification among three genera: Panax, Aralia, and Eleutherococcus.
Panax species native to Vietnam are designated as endangered species due to illegal harvesting and EMA from related species. Conservation of Panax species in Vietnam is hindered by a lack of genetic resources and molecular techniques. Seven P. vietnamensis individuals, representing three varieties: var vietnamensis, var. fuscidiscus, and var. langbianesis, were collected from Vietnamese habitats to generate NGS data for assemblies of whole plastome and 45S nrDNA sequences. The ML phylogenetic trees of the complete plastomes and 45S nrDNA indicated nine major Panax clades. The plastomes of P. vietnamensis var. vietnamensis and var. langbianesis were almost identical and clustered within the P. vietnamensis clade. However, P. vietnamensis var. fuscidiscus formed a distinct clade with P. zingiberensis, which was sister to the clade of P. vietnamensis. Significant intraspecific variation and phylogenetic incongruence within the P. japonicus clade and within the P. vietnamensis var. fuscidiscus and P. zingiberensis clade suggested an ambiguous species delimitation. Sixteen Panax-specific SNPs were developed as KASP markers, a high throughput SNP genotyping platform, which were highly accurate in the authentication of 114 Panax individuals collected from Vietnam.
In conclusion, the two investigations demonstrated the effectiveness of the DNA super-barcoding approach through the use of whole plastome and 45S nrDNA sequences. The results of this study widened the field of phylogenetic analysis and species identification in the Araliaceae family. Furthermore, the markers developed through the analysis of Panax species entire plastome and 45S nrDNA sequences will aid in the detection of counterfeit ginseng in Vietnam's ginseng industry.
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dc.description.tableofcontentsGENERAL ABSTRACT i
LIST OF TABLES vi
LIST OF FIGURES vii
LIST OF ABBREVIATIONS viii
GENERAL INTRODUCTION 1
REFERENCES 4
CHAPTER I 9
Exploration of DNA super-barcoding for the Araliaceae family
ABSTRACT 10
INTRODUCTION 11
MATERIAL AND METHODS 14
RESULTS 17
The size and structure of Araliaceae plastome and 45S nrDNA 17
Variations of plastomes and 45S nrDNA sequences in Araliaceae 24
Phylogenetic study 27
Substitution rates of plastomes and estimation of divergence time 30
SNP markers associated with the important genera 34
DISCUSSION 38
CONCLUSIONS 43
REFERENCES 44
CHAPTER II 51
Authentication of Panax collections in Vietnam and Southern China based on multi plastomes and 45S nrDNA
ABSTRACT 52
INTRODUCTION 53
MATERIAL AND METHODS 56
RESULTS 61
Assembly and annotation of the plastome and 45S nrDNA sequences of seven P. vietnamensis varieties 61
Sequences variant distribution in Panax plastomes and 45S nrDNA 62
Phylogenetic analysis 65
The matrix of pairwise SNP differences () and the ML phylogenetic analysis of Panax plastomes 67
Nucleotide substitutions in plastid genomes of Panax species 69
Clade-specific SNPs analysis in Panax genus 71
Development and validation of KASP and dCAPS markers 73
Authentication of Panax collections in Vietnam and Southern China 78
DISCUSSION 80
CONCLUSIONS 84
REFERENCES 85
APPENDIX 97
ACKNOWLEDGEMENT 109
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dc.format.extent121-
dc.language.isoeng-
dc.publisher서울대학교 대학원-
dc.subjectAraliaceae, Panax species, Next-generation sequencing (NGS), Plastome, 45S nrDNA-
dc.subject.ddc633-
dc.titleDNA Super-barcoding and Authentication of Species in Araliaceae Family-
dc.title.alternativeDNA 슈퍼바코딩 및 인증 아라리과과의 종의 수-
dc.typeThesis-
dc.typeDissertation-
dc.contributor.AlternativeAuthorVO NGOC LINH GIANG-
dc.contributor.department농업생명과학대학 식물생산과학부-
dc.description.degree박사-
dc.date.awarded2022-02-
dc.identifier.uciI804:11032-000000171074-
dc.identifier.holdings000000000047▲000000000054▲000000171074▲-
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