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研究生(外文):An-I Tsai
論文名稱(外文):Genomic and evolutionary analyses of rice pathogen Pyricularia oryzae strains isolated from rice fields
指導教授(外文):Wen-Hisung Li
外文關鍵詞:Rice blastPyricularia oryzaeGenome assemblyEvolutionEffectorsPangenome
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稻熱病是一種由病原真菌Pyricularia oryzae引起的植物病害,造成全球每年高達30%的糧食損失而嚴重威脅世界糧食安全。宿主-病原菌間共演化是造成病原菌種內基因多樣性的主因。為了從基因體層面了解致病菌的適應性演化,本研究組裝了兩組高品質基因體,分別為來自1948年與2017年從日本田間稻米所分離出的稻熱病菌菌株P2-b和2029-5-1。與參考基因體70-15 的比較顯示:在P2-b的7條染色體中,有4條染色體具有大範圍染色體位移,而2029-5-1則和參考基因體具有高同線性。為了深入探討種內基因多樣性,研究中也組裝了另外18株由不同時間與地點的田間稻米上所分離出的稻熱病菌株之基因體。根據親緣關係,P2-b和2029-5-1分別屬於不同演化分支群,顯示P2-b和2029-5-1可以作為70-15以外的兩組參考基因體。透過已知效應子基因存在與否作為指標對本研究中的菌株進行分類,階層分群結果顯示稻熱病菌菌株在地理上的快速擴散。此外,藉由推斷當加入新定序之基因組是否能獲取更多未知基因的泛基因組分析,此研究中探討之菌株泛基因組為開放型,是稻熱病菌種內基因體多樣性的證據。總結以上結果,在本研究中所定序組裝並探討的這些由田間稻米所分離出的稻熱病菌株基因體分析顯示種內基因體的快速變化,亦意指著此真菌病原體正在快速演化。
Rice blast, caused by the pathogenic fungus Pyricularia oryzae, is a catastrophic disease threatening world food security resulting in up to 30% of crop losses every year worldwide. Host-pathogen co-evolution is the main driving force of genomic diversity of the pathogen within species. To gain insights into the adaptive evolution, we generated chromosomal-level genome assemblies of P2-b and 2029-5-1, the two strains isolated from Japan in 1948 and 2017, respectively. Compared with the reference genome 70-15, large chromosomal translocations were detected in 4 out of the 7 chromosomes in the P2-b genome while the 2029-5-1 genome is more syntenic to the 70-15 genome and only one translocation was found between the two genomes: from chromosome 1 of 70-15 to 2029-5-1. To explore the genomic diversity within species, we sequenced and assembled the genomes of the other 18 strains isolated from rice fields across time and space. The phylogeny shows that P2-b and 2029-5-1 belong to two distinct clades, suggesting that P2-b and 2029-5-1 can serve as two reference genomes in addition to 70-15. By using the presence/absence of known effectors as an indicator to categorize the strains in this study, hierarchical clustering of the strains shows a scattered geographical distribution of isolated strains, suggesting rapid geographic spreading of strains. Moreover, an open pangenome, in which novel genes would be discovered when new genomes are added to the pangenome analysis, was obtained, providing evidence of high genomic diversity within species. In summary, the assembled genomes of new strains show frequent genomic changes, implying that the fungal pathogen has been undergoing rapid evolution.
口試委員會審定書 i
中文摘要 ii
Introduction 1
Materials and Methods 4
2.1 Genome assemblies 4
2.2 Repeat masking, and gene prediction and annotation 4
2.3 Assessing genome assembly completeness 5
2.4 Whole genome comparison 5
2.5 Pangenome analysis 6
2.6 Phylogenetic analysis 6
2.7 Effector protein finding and prediction 7
Results 8
3.1 Strain selection 8
3.2 Assembly of the P2-b and 2029-5-1 genomes 8
3.3 Genome Assembly of the 18 other strains 11
3.4 Repeat annotation 12
3.5 Gene prediction and annotation 12
3.6 BUSCO evaluation 13
3.7 Comparison of the P2-b and 2029-5-1 genomes with the 70-15 genome 13
3.8 Phylogenies 14
3.9 Pangenome Analysis 15
3.10 Effector Proteins 16
Chapter 4 17
Discussion 17
Figures 20
Fig. 1 The workflow of genome assembly with PacBio long reads and Illumina short reads 20
Fig 2. The geographic distribution of the strains used in this study. 21
Fig 2. The geographic distribution of the strains used in this study. 21
Fig 3. Gene annotation by Blas2GO 22
Fig. 4 The genome comparison of P2-b and 70-15 23
Fig. 5. The genome comparison of 2029-5-1 and 70-15 24
Fig 6. Phylogeny of Pyricularia oryzae isolates 25
Fig 7. Phylogeny of the isolates assembled in this study 26
Fig 8. Pangenome Analysis 27
Fig 9. Presence and Absence of Known Effectors 28
Tables 29
Table 1. Descriptions of the strains used in this study 29
Table 2. Assembly statistics of the P2-b and 2029-5-1 genomes and the reference genome 70-15 30
Table 3. The results of blast match of the smaller scaffolds of 2029-5-1 31
Table 4. Telomere regions detected at the ends of scaffolds of the assembled genomes 32
Table 5. Percentages of repeat types of the assembled genomes 33
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