Title Page
Abstract
Contents
1. Introduction 10
1.1. Pinewood nematode as a global threat to forest ecosystems 10
1.2. Previous study about pinewood nematode 11
1.3. Pinewood nematode in South Korea 12
1.4. Pinewood nematode and its relative species 13
1.5. Purpose of this study 14
2. Materials and Methods 16
2.1. Isolate collection and individual selection 16
2.2. Whole genome sequencing 17
2.3. Sequenced reads mapping and quality filtering 18
2.4. Variant calling and filtering 18
2.5. Genotype refinement 19
2.6. Principal component analysis 19
2.7. Genetic distance and Fst calculation[이미지참조] 20
2.8. Phylogenetic tree analysis 20
2.9. Subpopulation detection 20
3. Results 22
3.1. Individual-level whole genome sequencing of pinewood nematode 22
3.2. Genome-wide variant identification and individual-level genotyping 24
3.3. Genetic profile of B. xylophilus in South Korea and multiple introductions into the Korean Peninsula 26
3.4. Genetic diversity of Korean B. xylophilus lineages 36
3.5. Comparison of genetic diversity between B. xylophilus and B. mucronatus 49
4. Discussion 54
References 58
국문 초록 70
Appendices 72
Appendix 1. Summary of B. xylophilus and B. mucronatus samples used in this study. 72
Appendix 2. Summary of sequenced B. xylophilus and B. mucronatus samples. 77
Table 1. The Number of produced variants for each diversity panel. 25
Table 2. Fst of each population set.[이미지참조] 33
Table 3. The distribution of derived allele frequencies for KL01 and KL02. 38
Figure 1. Mapped read depth plot of 7 B. xylophilus individuals. 23
Figure 2. Distribution of bi-allelic SNPs throughout 6 chromosomes. 29
Figure 3. PCA plot of B. xylophilus samples. 30
Figure 4. Sampling sites of B. xylophilus in South Korea. 32
Figure 5. Heatmap plot of F₂ distance between lineages. 33
Figure 6. Phylogenetic tree constructed with 14 B. xylophilus lineages. C14 was set to root. 34
Figure 7. PCA plot of the Korean lineage individuals. 39
Figure 8. Heatmap of pairwise heatmap rate for the Korean lineage individuals. 43
Figure 9. Heatmap of rare variant sharing rate for the Korean lineage individuals. 45
Figure 10. Heatmap of genotype similarity rate for the Korean lineage individuals. 47
Figure 11. Boxplot of heterozygosity of each species. 50
Figure 12. PCA plot of B. mucronatus samples. 51
Figure 13. PCA plot of B. mucronatus individuals in each type. 52