從田間水稻分離出之稻熱病菌的基因體與演化分析

Genomic and evolutionary analyses of rice pathogen Pyricularia oryzae strains isolated from rice fields

蔡安怡(An-I Tsai)

指導教授 ： 李文雄

國立臺灣大學/生命科學院/基因體與系統生物學學位學程/碩士(2022年)

https://doi.org/10.6342/NTU202201728

摘要

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。

關鍵字

稻熱病 ； 稻熱菌 ； 基因體組裝 ； 演化 ； 效應子 ； 泛基因組

並列摘要

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.

並列關鍵字

Rice blast ； Pyricularia oryzae ； Genome assembly ； Evolution ； Effectors ； Pangenome

參考文獻

1. Skamnioti, P. and S.J. Gurr, Against the grain: safeguarding rice from rice blast disease. Trends in biotechnology, 2009. 27(3): p. 141-150.

2. Sakulkoo, W., et al., A single fungal MAP kinase controls plant cell-to-cell invasion by the rice blast fungus. Science, 2018. 359(6382): p. 1399-1403.

3. Asibi, A.E., Q. Chai, and J.A. Coulter, Rice blast: A disease with implications for global food security. Agronomy, 2019. 9(8): p. 451.

4. Yin, J., et al., Fighting the enemy: How rice survives the blast pathogen’s attack. The Crop Journal, 2021. 9(3): p. 543-552.

5. Sasaki, A., Host-parasite coevolution in a multilocus gene-for-gene system. Proceedings of the Royal Society of London. Series B: Biological Sciences, 2000. 267(1458): p. 2183-2188.