台中在來 1 號（TN1）是IR8 “奇蹟稻” 的姊妹品種，它開啟了水稻綠色革命（GR）。 TN1 和 IR8 均為低腳烏尖 (Dee-geo-woo-gen, DGWG) 栽培種的直系子代。因此，我們對 TN1 的基因體進行了測序和組裝。它由 PacBio 和 Illumina 二個平台組合測序。基因體主要由 Canu 使用 PacBio 長讀序資料重新組裝。以 R498為參考的基因體，參考RaGOO引導組裝方法輸出染色體水平的組裝，N50 為 33.1 Mb，基因體大小為 409.5 Mb。然後，使用 Illumina 讀值來改善組裝的基因體，包括校正測序錯誤。 TN1 基因體中共預測了 37,526 個基因，其中 24,102 個基因被 Blast2GO鑑定了功能。這種高品質的組裝和註釋與 IR8、MH63 和 IR64 的組裝和註釋，一起用於建立具有 16,999 個核心直向同源組的綠色革命水稻的泛基因體。通過 GR 泛基因體，我們能夠解開 TN1 和 IR8澱粉合成基因的差異，這可能與它們的穀粒產量差異有關。我們還研究了它們的開花基因，以闡明它們對光週期不敏感的基因體基礎。對 TN1 和 IR8 的 sd1（半矮性）基因的分析更正了382 bp 片段的缺失，並通過 Sanger 測序進行驗證。 sd1 基因的外顯子-內含子結構在 TN1和 IR8 之間也不同；前者俱有與日本晴相關的缺失模式，其中外顯子 1 的後半部分至第二外顯子的一部分丟失。但是，在 IR8 sd1 的註釋中並非如此。我們還研究了為什麼 TN1 易受稻熱病影響。以抗稻熱病 Tetep 品種的基因為參考，我們發現 R 基因 Pi-ta 發生突變，使 Pi54 缺失。來自 3,000 水稻基因體測序的栽培品種的單倍型分析，也支持我們的結論。由這兩個基因的解序，我們懷疑 Pi54 的缺失是 TN1 對稻熱病高感性的部分原因。 TN1 的基因體分析提供了對綠色革命早期歷史的瞭解，並可能為提高糧食產量和抗病能力提供線索。

Taichung Native 1 (TN1) served as a prototype in the development of its sister cultivar, the IR8 “miracle rice”, which started the Green Revolution (GR). Both TN1 and IR8 were derived from the Dee-geo-woo-gen cultivar. We therefore sequenced and assembled the genome of TN1. It was sequenced by a combination of PacBio and Illumina platforms. The genome was de novo assembled primarily by Canu using PacBio long reads. The RaGOO reference-guided assembler with the R498 genome as the reference outputted a chromosomal-level assembly, with an N50 of 33.1 Mb and a genome size of 409.5 Mb. The Illumina reads were then used to polish the assembled genome, including correction of sequencing errors. A total of 37,526 genes were predicted in the TN1 genome, in which 24,102 genes were assigned functions by Blast2GO. This high-quality assembly and annotation together with those of IR8, MH63 and IR64 were used to create a GR pangenome that has 16,999 core orthologue groups. Through the GR pangenome, we were able to unravel the difference in the starch synthesis genes of TN1 and IR8, which could be related to the difference in their grain yield. We also studied their flowering genes to elucidate the genetic basis of their photoperiod insensitivity. Analysis of the sd1 (semi-dwarf) gene of TN1 and IR8 revealed a 382-bp deletion, which was validated by Sanger sequencing. The exon-intron structure of the sd1 gene differs between TN1 and IR8. The former has the deletion pattern with respect to Nipponbare, in which the second half of exon 1 is lost up to a portion of the second exon. However, this is not the case in the annotation of IR8 sd1. We also investigated why TN1 is susceptible to the blast disease. Using the genes of the blast resistant Tetep cultivar as the reference, we found that the R gene Pi-ta is mutated and Pi54 is missing. Haplotype analysis of cultivars from the 3,000 Rice Genome Sequencing Project supported our results. Of the two genes, we suspect the loss of Pi54 to be the part of the reason for TN1’s high susceptibility to blast. The TN1 genome provides insights into the early history of the Green Revolution and may provide clues for improving grain yield and resistance against diseases.

Abstract (Chinese)............................................................................................................i
Abstract (English).............................................................................................................ii
Acknowledgement..........................................................................................................iii
Table of Contents.............................................................................................................iv
Publications.......................................................................................................................vi
List of figures.....................................................................................................................vii
List of tables ........................................................................................................................x
List of abbreviations.........................................................................................................xi
Chapter 1 – General Introduction...............................................................................1
1.1 Origin, history and important characteristics of TN1...................................1
1.2 Rice reference genomes..........................................................................................3
1.3 De novo assembly methods...................................................................................6
1.4 Reference-guided assembly...................................................................................8
1.5 Genome annotation...................................................................................................9
1.6 Goals and Specific Aims..........................................................................................10
Chapter 2 – Genome assembly and annotation of the Taichung Native 1 (TN1) genome.................................................................................................................................12
2.1 Abstract..........................................................................................................................12
2.2 Introduction..................................................................................................................12
2.3 Materials and Methods............................................................................................13
2.4 Results.............................................................................................................................19
2.5 Conclusion......................................................................................................................43
2.6 Data availability.............................................................................................................43
2.7 Publication......................................................................................................................43
Chapter 3 – Redefining the genomic deletion in sd1 among semidwarf cultivars and TN1’s blast susceptibility.....................................................................44
3.1 Abstract ...........................................................................................................................44
3.2 Introduction....................................................................................................................44
3.3 Materials and Methods..............................................................................................45
3.4 Results...............................................................................................................................48
3.5 Discussion....................................................................................................................... 59
3.6 Conclusion.......................................................................................................................60
3.7 Publication.......................................................................................................................61
References...............................................................................................................................62
Appendix..................................................................................................................................73
Appendix figures...................................................................................................................73
Appendix tables..................................................................................................................108

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