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Comparative analysis of the complete chloroplast genomes and 45S nrDNAs of six Lonicera species

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dc.contributor.advisor양태진-
dc.contributor.author강신재-
dc.date.accessioned2018-12-03T01:37:57Z-
dc.date.available2019-11-06-
dc.date.issued2018-08-
dc.identifier.other000000152767-
dc.identifier.urihttp://hdl.handle.net/10371/143709-
dc.description학위논문 (석사)-- 서울대학교 대학원 : 농업생명과학대학 식물생산과학부(작물생명과학전공), 2018. 8. 양태진.-
dc.description.abstractThe genus Lonicera belongs to the family Caprifoliaceae and comprises approximately 210 species distributed in East Asia. Many Lonicera species such as L. japonica and L. maackii are ornamental shrub plants, and used as herbal medicines. Despite their usefulness, its genetic, genomics and molecular phylogenetics are rarely reported. Here, we collected six Lonicera species from Medicinal Plant Garden, College of Pharmacy, Seoul National University, and produced 2.7 - 4.1 Gbp of whole genome sequencing (WGS) data. We obtained complete sequences of chloroplast genome and 45S nuclear ribosomal DNA (45S nrDNA) sequences using de novo assembly of Low-Coverage Whole genome sequence (dnaLCW). The chloroplast genome of the six Lonicera species ranged from 154,892 to 155,318 bp and showed high similarities (97.4%) each other. There were 114 genes in L. insularis, L. sachalinensis, L. praeflorens and L. maackii, 113 in L. vesicaria, and 112 in L. japonica. Comparative analysis of chloroplast genome and 45S nrDNA sequences revealed 17~2,261 single nucleotide polymorphisms (SNPs) and 5~278 insertion and deletions (InDels) between species in chloroplast, and a total of 45 SNPs and 4 InDels in 45S nrDNA. Furthermore, 266 large repetitive sequences and 288 simple sequence repeats (SSRs) were detected among six chloroplast genomes. In addition, we found several chloroplast protein-coding genes that showed high Ka/Ks values or highly conserved among six Lonicera species. Four genes, psaJ, rbcL, rps18 and ycf2 genes that showed high Ka/Ks values, might be positively selected in genus Lonicera. On the other hand, four genes in large single copy (LSC), psbI, psbZ, psbL and petZ genes, were highly conserved in six Lonicera species. Estimation of divergence time and phylogenetic relationship of six Lonicera species revealed that L. japonica was diverged first from the common ancestor of six Lonicera species (9.19-10.74 MYA), and L. insularis and L. sachalinensis were recently diverged (0-0.03 MYA). Phylogenetic trees based on chloroplast genomes and 45S nrDNA sequences showed a similar topology that L. insularis and L. sachalinensis were the closest, and they consist a clade with L. maackii. Moreover, phylogenetic analysis with related species in Dipsacales revealed that Lonicera species clustered with genera Patrinia and Kolkwitzia of the same family Caprifoliaceae, as expected. A total of seven molecular markers were developed from polymorphic sites such as SNPs, InDels and copy number variation (CNV) of tandem repeat (TR) in chloroplast genome. We could successfully discriminate six Lonicera species using these developed markers. The chloroplast genome and 45S nrDNA sequences of six Lonicera species along with DNA markers produced in this study will provide valuable information for further genetic diversity studies and authentication of six Lonicera species.-
dc.description.tableofcontentsINTRODUCTION 1

MATERIALS AND METHODS 4

1. Plant materials 4

2. DNA extraction and Whole-Genome shotgun sequencing 4

3. Chloroplast genome and 45S nrDNA assembly 5

4. Gene and structure annotation 5

5. Comparative analysis and Characterization of simple sequence repeats and large sequence repeats 6

6. Development and validation of molecular markers 6

7. Estimation of divergence time and phylogenetic analysis 7

RESULTS 8

1. Complete chloroplast genome and 45S nrDNA sequences of six Lonicera species 8

2. Comparative analysis of chloroplast genomes of six Lonicera species 15

3. Characterization of SSRs and repetitive sequences among six Lonicera species 21

4. Sequence variations of 45S nrDNA sequences of six Lonicera species 30

5. Divergence time estimation and phylogenetic relationship among six Lonicera species 35

6. Phylogenetic relationship within Dipsacales 42

7. Development and validation of chloroplast-based markers 44

DISCUSSION 49

1. Complete chloroplast genome and 45S nrDNA sequences of six Lonciera species derived from low-coverage whole-genome NGS data 49

2. Comparative analysis of chloroplast genome and 45S nrDNA sequences among six Lonicera species 50

3. Repetitive sequences in Lonicera chloroplast genomes 51

4. Divergence and phylogenetic analysis based on chloroplast genome and 45S nrDNA sequences of the Lonicera species 52

5. Development of molecular markers for authentication of six Lonicera species 53

REFERENCES 54

ABSTRACT IN KOREAN 59
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dc.formatapplication/pdf-
dc.format.mediumapplication/pdf-
dc.language.isoko-
dc.publisher서울대학교 대학원-
dc.subject.ddc633-
dc.titleComparative analysis of the complete chloroplast genomes and 45S nrDNAs of six Lonicera species-
dc.typeThesis-
dc.contributor.AlternativeAuthorShin-Jae Kang-
dc.description.degreeMaster-
dc.contributor.affiliation농업생명과학대학 식물생산과학부(작물생명과학전공)-
dc.date.awarded2018-08-
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College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Plant Science (식물생산과학부)Theses (Master's Degree_식물생산과학부)
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