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Genome Divergence between Vigna angularis & Vigna nakashimae
DC Field | Value | Language |
---|---|---|
dc.contributor.advisor | Suk Ha Lee | - |
dc.contributor.author | 쿠쉬부 | - |
dc.date.accessioned | 2017-07-14T06:30:20Z | - |
dc.date.available | 2017-07-14T06:30:20Z | - |
dc.date.issued | 2014-02 | - |
dc.identifier.other | 000000018287 | - |
dc.identifier.uri | https://hdl.handle.net/10371/125646 | - |
dc.description | 학위논문 (석사)-- 서울대학교 대학원 : 식물생산과학부(작물생명과학전공), 2014. 2. Suk Ha Lee. | - |
dc.description.abstract | The Azuki bean, Vigna angularis (2n=2x=22), is one of the important legume crop grown in the world. Comparing the genome of domesticated (Vigna angularis) and undomesticated (Vigna nakashimae) forms of Azuki bean can facilitate crop improvement. We used the Next-generation massively parallel DNA sequencing technologies which provide ultrahigh throughput at a substantially lower unit data cost. However, the data generated is very short read length sequences and constructing de novo assembly from it is extremely challenging. Here, we describe a novel method for finding genome divergence between the domesticated and the wild variety of Azuki bean. We de novo sequenced and assembled the Vigna angularis and Vigna nakashimae genome, achieving an N50 contig size of approximately 11 and 7 kilo base pairs (kbp) respectively. The genome size of Azuki bean is estimated to be around 545 mega-bases (Mb). We predicted 45,985 protein-coding genes in Vigna angularis, 70% more than that of Arabidopsis, approximately similar to poplar and soybean. For Vigna nakashimae we predicted 38,965 protein-coding genes which is 40% more than Arabidopsis and approximately similar to potato. Vigna angularis diverged from Vigna nakashimae approximately 1.9 million years ago. The data obtained from structural translocations and gene categories from the evolutionary relationship between Vigna angularis and Vigna nakashimae suggest that these genes can be a probable cause for the domestication of Azuki bean. The development of this de novo short read assembly method creates new opportunities for building reference genome and carrying out accurate analyses of unexplored genomes in a cost effective manner as well as overcomes the limitations of the re-sequencing method for discovering structural translocations. | - |
dc.description.tableofcontents | CONTENTS
ABSTRACT …………………………………………………………… i CONTENTS …………………………………………………………… iii LIST OF TABLES …………………………………………………….. v LIST OF FIGURES …………………………………………………… vi INTRODUCTION …………………………………………………….. 1 LITERATURE REVIEW Next Generation Sequencing Technology ………..……………….. 4 De Novo Assembly ….……………………………….……………. 7 Structural Variation ...……………………………………………… 8 Synonymous Substitutions, Non-Synonymous Substitutions and Evolutionary Time …………….………………………………….. 10 MATERIALS AND METHODS De Novo Sequencing ………………………………………………. 11 De Novo Assembly ………………………………………………... 11 Ab initio gene prediction ………………………………………….. 12 Homology search ………………………………………………….. 12 Synteny and Evolutionary relationship ……………………………. 13 Structural Translocations ………………………………………….. 14 Divergence Time …………………………………………………... 14 Specific Gene Categories …….……………. …………………….. 15 RESULTS Overview of De Novo Sequencing and Assembly …….…..….….. 16 Estimating Genome Size ……..………………………...…………. 19 Ab initio gene prediction and Homology search ….……..….…….. 20 Syntenic Regions …………………………..……………………… 20 Evolutionary Relationship ………………..……………………….. 21 Divergence Time …………………………………………………... 25 Structural Translocations and Synteny Pairs ……………………… 25 Specific Gene Categories …….……………. …………………….. 33 DISCUSSION …………………………………………………………. 40 REFERENCES.…………………………………………..………......... 44 ABSTRACT IN KOREAN ……………………………………………. 49 LIST OF TABLES Table 1. Some important tools for analysis of NGS data 6 Table 2. Sequencing status of 2 deep sequenced accession 17 Table 3. ABySS Genome Assembly results 18 Table 4. Ab-initio Gene Prediction result 22 Table 5. Syntenic region between Vigna angularis and Vigna nakashimae 23 Table 6. Structural Translocations and Synteny Pairs between Vigna angularis and Vigna nakashimae 27 Table 7. Peak 1: Specific gene category – Retained 34 Table 8. Peak 2: Specific gene category – Retained 37 Table 9. Peak 3: Specific gene category - Diverged 39 LIST OF FIGURES Figure 1. Distribution of Ka/Ks for the gene pair in order to find the evolutionary changes between Vigna angularis and Vigna nakashimae. 24 Figure 2. Frequency distribution for the synonymous substitution rate, for estimating the divergence time between Vigna angularis and Vigna nakashimae. 26 Figure 3. Synteny pairs and Structural Translocation between Vigna angularis and Vigna nakashimae. 32 | - |
dc.format | application/pdf | - |
dc.format.extent | 2265718 bytes | - |
dc.format.medium | application/pdf | - |
dc.language.iso | en | - |
dc.publisher | 서울대학교 대학원 | - |
dc.subject | Vigna angularis | - |
dc.subject | Vigna nakashimae | - |
dc.subject | structural translocations | - |
dc.subject | dom estication | - |
dc.subject | genome divergence | - |
dc.subject | Next-generation sequencing. | - |
dc.subject.ddc | 633 | - |
dc.title | Genome Divergence between Vigna angularis & Vigna nakashimae | - |
dc.type | Thesis | - |
dc.description.degree | Master | - |
dc.citation.pages | 60 | - |
dc.contributor.affiliation | 농업생명과학대학 식물생산과학부(작물생명과학전공) | - |
dc.date.awarded | 2014-02 | - |
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