請用此 Handle URI 來引用此文件：
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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 伊藤剛 | zh_TW |
| dc.contributor.advisor | Takeshi Itoh | en |
| dc.contributor.author | 劉亞澤 | zh_TW |
| dc.contributor.author | Joenilo II Esperas Paduhilao | en |
| dc.date.accessioned | 2025-07-02T16:12:24Z | - |
| dc.date.available | 2025-07-03 | - |
| dc.date.copyright | 2025-07-02 | - |
| dc.date.issued | 2025 | - |
| dc.date.submitted | 2025-06-24 | - |
| dc.identifier.citation | Aho, A. V., Kernighan, B. W., & Weinberger, P. (2024). The AWK Programming Language. Pearson Education (US).
Aimi, T., Kano, S., Wang, Q., & Morinaga, T. (2001). Molecular Cloning of Three Genes Encoding G Protein Alpha Subunits in the White Root Rot Fungus, Rosellinia necatrix. Bioscience, Biotechnology, and Biochemistry, 65(3), 678–682. https://doi.org/10.1271/bbb.65.678 Akakpo, R., Carpentier, M., Ie Hsing, Y., & Panaud, O. (2020). The impact of transposable elements on the structure, evolution and function of the rice genome. New Phytologist, 226(1), 44–49. https://doi.org/10.1111/nph.16356 Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., Genereux, D., Johnson, J., Marinescu, V. D., Alföldi, J., Harris, R. S., Lindblad-Toh, K., Haussler, D., Karlsson, E., Jarvis, E. D., … Paten, B. (2020). Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature, 587(7833), 246–251. https://doi.org/10.1038/s41586-020-2871-y Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., Bidwell, S. L., Clark, K., Davis, E. W., Smith-White, B., Hlavina, W., Pruitt, K. D., Schneider, V. A., & Murphy, T. D. (2023). Rapid and sensitive detection of genome contamination at scale with FCS-GX [Preprint]. Bioinformatics. https://doi.org/10.1101/2023.06.02.543519 Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., Warren, W. C., Magrini, V., McGrath, S. D., Li, Y. I., Wilson, R. K., & Eichler, E. E. (2019). Characterizing the Major Structural Variant Alleles of the Human Genome. Cell, 176(3), 663-675.e19. https://doi.org/10.1016/j.cell.2018.12.019 Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J., & Edwards, D. (2020). Plant pan-genomes are the new reference. Nature Plants, 6(8), 914–920. https://doi.org/10.1038/s41477-020-0733-0 Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological), 57(1), 289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x Bessho-Uehara, K., Masuda, K., Wang, D. R., Angeles-Shim, R. B., Obara, K., Nagai, K., Murase, R., Aoki, S., Furuta, T., Miura, K., Wu, J., Yamagata, Y., Yasui, H., Kantar, M. B., Yoshimura, A., Kamura, T., McCouch, S. R., & Ashikari, M. (2023). Regulator of Awn Elongation 3 , an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication. Proceedings of the National Academy of Sciences, 120(4), e2207105120. https://doi.org/10.1073/pnas.2207105120 Bian, P., Li, J., Zhou, S., Wang, X., Gong, M., Guo, X., Cai, Y., Yang, Q., Fu, J., Li, R., Huang, S., Luo, F., Shah, A. M., Lenstra, J. A., Mwacharo, J. M., Li, R., Ren, G., Wang, X., Li, C., … Wang, X. (2024). A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation. Molecular Biology and Evolution, 41(12), msae251. https://doi.org/10.1093/molbev/msae251 Bolognini, D., Sanders, A., Korbel, J. O., Magi, A., Benes, V., & Rausch, T. (2020). VISOR: A versatile haplotype-aware structural variant simulator for short- and long-read sequencing. Bioinformatics, 36(4), 1267–1269. https://doi.org/10.1093/bioinformatics/btz719 Bonenfant, Q., Noé, L., & Touzet, H. (2023). Porechop_ABI: Discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming. Bioinformatics Advances, 3(1), vbac085. https://doi.org/10.1093/bioadv/vbac085 Buchfink, B., Reuter, K., & Drost, H.-G. (2021). Sensitive protein alignments at tree-of-life scale using DIAMOND. Nature Methods, 18(4), 366–368. https://doi.org/10.1038/s41592-021-01101-x Caicedo, A. L., Williamson, S. H., Hernandez, R. D., Boyko, A., Fledel-Alon, A., York, T. L., Polato, N. R., Olsen, K. M., Nielsen, R., McCouch, S. R., Bustamante, C. D., & Purugganan, M. D. (2007). Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice. PLoS Genetics, 3(9), e163. https://doi.org/10.1371/journal.pgen.0030163 Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10(1), 421. https://doi.org/10.1186/1471-2105-10-421 Chen, Q., Li, W., Tan, L., & Tian, F. (2021). Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding. Molecular Plant, 14(1), 9–26. https://doi.org/10.1016/j.molp.2020.12.006 Chen, Y., Nie, F., Xie, S.-Q., Zheng, Y.-F., Dai, Q., Bray, T., Wang, Y.-X., Xing, J.-F., Huang, Z.-J., Wang, D.-P., He, L.-J., Luo, F., Wang, J.-X., Liu, Y.-Z., & Xiao, C.-L. (2021). Efficient assembly of nanopore reads via highly accurate and intact error correction. Nature Communications, 12(1), 60. https://doi.org/10.1038/s41467-020-20236-7 Cheng, L., Wang, N., Bao, Z., Zhou, Q., Guarracino, A., Yang, Y., Wang, P., Zhang, Z., Tang, D., Zhang, P., Wu, Y., Zhou, Y., Zheng, Y., Hu, Y., Lian, Q., Ma, Z., Lassois, L., Zhang, C., Lucas, W. J., … Huang, S. (2025). Leveraging a phased pangenome for haplotype design of hybrid potato. Nature. https://doi.org/10.1038/s41586-024-08476-9 Choi, J. Y., & Purugganan, M. D. (2018). Multiple Origin but Single Domestication Led to Oryza sativa. G3 Genes|Genomes|Genetics, 8(3), 797–803. https://doi.org/10.1534/g3.117.300334 Choi, J. Y., Zaidem, M., Gutaker, R., Dorph, K., Singh, R. K., & Purugganan, M. D. (2019). The complex geography of domestication of the African rice Oryza glaberrima. PLOS Genetics, 15(3), e1007414. https://doi.org/10.1371/journal.pgen.1007414 Civáň, P., Craig, H., Cox, C. J., & Brown, T. A. (2015). Three geographically separate domestications of Asian rice. Nature Plants, 1(11), 15164. https://doi.org/10.1038/nplants.2015.164 Cooper, L., Elser, J., Laporte, M.-A., Arnaud, E., & Jaiswal, P. (2024). Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology. Nucleic Acids Research, 52(D1), D1548–D1555. https://doi.org/10.1093/nar/gkad1028 Copetti, D., Zhang, J., El Baidouri, M., Gao, D., Wang, J., Barghini, E., Cossu, R. M., Angelova, A., Maldonado L., C. E., Roffler, S., Ohyanagi, H., Wicker, T., Fan, C., Zuccolo, A., Chen, M., Costa De Oliveira, A., Han, B., Henry, R., Hsing, Y., … Wing, R. A. (2015). RiTE database: A resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 16(1), 538. https://doi.org/10.1186/s12864-015-1762-3 Crysnanto, D., Leonard, A., & Pausch, H. (2022). Comparison of methods for building pangenome graphs [Application/pdf]. https://doi.org/10.3929/ETHZ-B-000566083 Crysnanto, D., Leonard, A. S., Fang, Z.-H., & Pausch, H. (2021). Novel functional sequences uncovered through a bovine multiassembly graph. Proceedings of the National Academy of Sciences, 118(20), e2101056118. https://doi.org/10.1073/pnas.2101056118 Dale, R. K., Pedersen, B. S., & Quinlan, A. R. (2011). Pybedtools: A flexible Python library for manipulating genomic datasets and annotations. Bioinformatics, 27(24), 3423–3424. https://doi.org/10.1093/bioinformatics/btr539 De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: Visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666–2669. https://doi.org/10.1093/bioinformatics/bty149 Doerr, D. (2021). GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure [Computer software]. https://github.com/marschall-lab/GFAffix Du, H., Yu, Y., Ma, Y., Gao, Q., Cao, Y., Chen, Z., Ma, B., Qi, M., Li, Y., Zhao, X., Wang, J., Liu, K., Qin, P., Yang, X., Zhu, L., Li, S., & Liang, C. (2017). Sequencing and de novo assembly of a near complete indica rice genome. Nature Communications, 8(1), 15324. https://doi.org/10.1038/ncomms15324 Du, Z.-Z., He, J.-B., & Jiao, W.-B. (2025). Plant graph-based pangenomics: Techniques, applications, and challenges. aBIOTECH. https://doi.org/10.1007/s42994-025-00206-7 Eizenga, J. M., Novak, A. M., Sibbesen, J. A., Heumos, S., Ghaffaari, A., Hickey, G., Chang, X., Seaman, J. D., Rounthwaite, R., Ebler, J., Rautiainen, M., Garg, S., Paten, B., Marschall, T., Sirén, J., & Garrison, E. (2020). Pangenome Graphs. Annual Review of Genomics and Human Genetics, 21(1), 139–162. https://doi.org/10.1146/annurev-genom-120219-080406 Ellinghaus, D., Kurtz, S., & Willhoeft, U. (2008). LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9(1), 18. https://doi.org/10.1186/1471-2105-9-18 Emms, D. M., & Kelly, S. (2019). OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biology, 20, 1–14. https://doi.org/10.1186/s13059-019-1832-y Fang, B., & Edwards, S. V. (2024). Fitness consequences of structural variation inferred from a House Finch pangenome. Proceedings of the National Academy of Sciences, 121(47), e2409943121. https://doi.org/10.1073/pnas.2409943121 Feng, D.-F., & Doolittle, R. F. (1987). Progressive sequence alignment as a prerequisitetto correct phylogenetic trees. Journal of Molecular Evolution, 25(4), 351–360. https://doi.org/10.1007/BF02603120 Fisher, R. A. (1970). Statistical methods for research workers. In Breakthroughs in statistics: Methodology and distribution (pp. 66–70). Springer. Fitch, W. M. (1971). Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology. Systematic Zoology, 20(4), 406–416. https://doi.org/10.2307/2412116 Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020). RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences, 117(17), 9451–9457. https://doi.org/10.1073/pnas.1921046117 Fuentes, R. R., Chebotarov, D., Duitama, J., Smith, S., De La Hoz, J. F., Mohiyuddin, M., Wing, R. A., McNally, K. L., Tatarinova, T., Grigoriev, A., Mauleon, R., & Alexandrov, N. (2019). Structural variants in 3000 rice genomes. Genome Research, 29(5), 870–880. https://doi.org/10.1101/gr.241240.118 Fuller, D. Q., Qin, L., Zheng, Y., Zhao, Z., Chen, X., Hosoya, L. A., & Sun, G.-P. (2009). The Domestication Process and Domestication Rate in Rice: Spikelet Bases from the Lower Yangtze. Science, 323(5921), 1607–1610. https://doi.org/10.1126/science.1166605 Fuller, D. Q., Van Etten, J., Manning, K., Castillo, C., Kingwell-Banham, E., Weisskopf, A., Qin, L., Sato, Y.-I., & Hijmans, R. J. (2011). The contribution of rice agriculture and livestock pastoralism to prehistoric methane levels: An archaeological assessment. The Holocene, 21(5), 743–759. https://doi.org/10.1177/0959683611398052 Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D. M., Burzynski-Chang, E. A., Fish, T. L., Stromberg, K. A., Sacks, G. L., Thannhauser, T. W., Foolad, M. R., Diez, M. J., Blanca, J., Canizares, J., Xu, Y., Van Der Knaap, E., Huang, S., Klee, H. J., … Fei, Z. (2019). The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 51(6), 1044–1051. https://doi.org/10.1038/s41588-019-0410-2 Garrison, E. (2020). Fastix [Computer software]. https://github.com/ekg/fastix Garrison, E., & Guarracino, A. (2023). Unbiased pangenome graphs. Bioinformatics, 39(1), btac743. https://doi.org/10.1093/bioinformatics/btac743 Garrison, E., Guarracino, A., Heumos, S., Villani, F., Bao, Z., Tattini, L., Hagmann, J., Vorbrugg, S., Marco-Sola, S., Kubica, C., Ashbrook, D. G., Thorell, K., Rusholme-Pilcher, R. L., Liti, G., Rudbeck, E., Golicz, A. A., Nahnsen, S., Yang, Z., Mwaniki, M. N., … Prins, P. (2024). Building pangenome graphs. Nature Methods, 21(11), 2008–2012. https://doi.org/10.1038/s41592-024-02430-3 Garrison, E., Kronenberg, Z. N., Dawson, E. T., Pedersen, B. S., & Prins, P. (2022). A spectrum of free software tools for processing the VCF variant call format: Vcflib, bio-vcf, cyvcf2, hts-nim and slivar. PLOS Computational Biology, 18(5), e1009123. https://doi.org/10.1371/journal.pcbi.1009123 Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., Paten, B., & Durbin, R. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology, 36(9), 875–879. https://doi.org/10.1038/nbt.4227 GFA Specification Community. (2025). GFA1 Specification. https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md Golicz, A. A., Bayer, P. E., Barker, G. C., Edger, P. P., Kim, H., Martinez, P. A., Chan, C. K. K., Severn-Ellis, A., McCombie, W. R., Parkin, I. A. P., Paterson, A. H., Pires, J. C., Sharpe, A. G., Tang, H., Teakle, G. R., Town, C. D., Batley, J., & Edwards, D. (2016). The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications, 7(1), 13390. https://doi.org/10.1038/ncomms13390 Gorbunova, V., & Levy, A. A. (1999). How plants make ends meet: DNA double-strand break repair. Trends in Plant Science, 4(7), 263–269. https://doi.org/10.1016/S1360-1385(99)01430-2 Greene, D., Richardson, S., & Turro, E. (2017). ontologyX: A suite of R packages for working with ontological data. Bioinformatics, 33(7), 1104–1106. https://doi.org/10.1093/bioinformatics/btw763 Gremme, G., Steinbiss, S., & Kurtz, S. (2013). GenomeTools: A comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(3), 645–656. https://doi.org/10.1109/TCBB.2013.68 Groza, C., Schwendinger-Schreck, C., Cheung, W. A., Farrow, E. G., Thiffault, I., Lake, J., Rizzo, W. B., Evrony, G., Curran, T., Bourque, G., & Pastinen, T. (2024). Pangenome graphs improve the analysis of structural variants in rare genetic diseases. Nature Communications, 15(1), 657. https://doi.org/10.1038/s41467-024-44980-2 Gu, B., Zhou, T., Luo, J., Liu, H., Wang, Y., Shangguan, Y., Zhu, J., Li, Y., Sang, T., Wang, Z., & Han, B. (2015). An-2 Encodes a Cytokinin Synthesis Enzyme that Regulates Awn Length and Grain Production in Rice. Molecular Plant, 8(11), 1635–1650. https://doi.org/10.1016/j.molp.2015.08.001 Guan, C., Liu, Y., Li, Z., Zhang, Y., Liu, Z., Zhu, Q., Zhang, P., Shen, X., Fang, J., Li, J., Zhang, Q., Guan, Q., Luo, Z., Yang, Y., & Zhao, T. (2025). Haplotype-resolved and chromosome-level reference genome assembly of Diospyros deyangensis provides insights into the evolution and juvenile growth of persimmon. Horticulture Research, 12(4), uhaf001. https://doi.org/10.1093/hr/uhaf001 Guarracino, A., Heumos, S., Nahnsen, S., Prins, P., & Garrison, E. (2022). ODGI: Understanding pangenome graphs. Bioinformatics, 38(13), 3319–3326. https://doi.org/10.1093/bioinformatics/btac308 Guarracino, A., Mwaniki, N., Marco-Sola, S., & Garrison, E. (2021). wfmash: Whole-chromosome pairwise alignment using the hierarchical wavefront algorithm [Computer software]. https://github.com/waveygang/wfmash Guo, D., Li, Y., Lu, H., Zhao, Y., Kurata, N., Wei, X., Wang, A., Wang, Y., Zhan, Q., Fan, D., Zhou, C., Lu, Y., Tian, Q., Weng, Q., Feng, Q., Huang, T., Zhang, L., Gu, Z., Wang, C., … Han, B. (2025). A pangenome reference of wild and cultivated rice. Nature. https://doi.org/10.1038/s41586-025-08883-6 Guo, J., Xu, C., Wu, D., Zhao, Y., Qiu, Y., Wang, X., Ouyang, Y., Cai, B., Liu, X., Jing, S., Shangguan, X., Wang, H., Ma, Y., Hu, L., Wu, Y., Shi, S., Wang, W., Zhu, L., Xu, X., … He, G. (2018). Bph6 encodes an exocyst-localized protein and confers broad resistance to planthoppers in rice. Nature Genetics, 50(2), 297–306. https://doi.org/10.1038/s41588-018-0039-6 Gutaker, R. M., Groen, S. C., Bellis, E. S., Choi, J. Y., Pires, I. S., Bocinsky, R. K., Slayton, E. R., Wilkins, O., Castillo, C. C., Negrão, S., Oliveira, M. M., Fuller, D. Q., Guedes, J. A. d’Alpoim, Lasky, J. R., & Purugganan, M. D. (2020). Genomic history and ecology of the geographic spread of rice. Nature Plants, 6(5), 492–502. https://doi.org/10.1038/s41477-020-0659-6 Harlan, J. R., De Wet, J. M., & Stemler, A. B. (1976). Plant domestication and indigenous African agriculture. Origins of African Plant Domestication, 3–19. https://doi.org/10.1515/9783110806373.3 He, H., Leng, Y., Cao, X., Zhu, Y., Li, X., Yuan, Q., Zhang, B., He, W., Wei, H., Liu, X., Xu, Q., Guo, M., Zhang, H., Yang, L., Lv, Y., Wang, X., Shi, C., Zhang, Z., Chen, W., … Shang, L. (2024). The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice. Nature Communications, 15(1), 7291. https://doi.org/10.1038/s41467-024-51854-0 He, W., Li, X., Qian, Q., & Shang, L. (2025). The developments and prospects of plant super-pangenomes: Demands, approaches, and applications. Plant Communications, 6(2), 101230. https://doi.org/10.1016/j.xplc.2024.101230 Hickey, G., Heller, D., Monlong, J., Sibbesen, J. A., Sirén, J., Eizenga, J., Dawson, E. T., Garrison, E., Novak, A. M., & Paten, B. (2020). Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biology, 21(1), 35. https://doi.org/10.1186/s13059-020-1941-7 Hickey, G., Monlong, J., Ebler, J., Novak, A. M., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Abel, H. J., Antonacci-Fulton, L. L., Asri, M., Baid, G., Baker, C. A., Belyaeva, A., Billis, K., Bourque, G., Buonaiuto, S., Carroll, A., Chaisson, M. J. P., Chang, P.-C., … Paten, B. (2023). Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology. https://doi.org/10.1038/s41587-023-01793-w Hou, M., & Pang, S. (2024). Plant Pan-Genomics: Opportunities, Advances, and Challenges. Journal of Data Science and Intelligent Systems. https://doi.org/10.47852/bonviewJDSIS42023107 Howe, K. L., Contreras-Moreira, B., De Silva, N., Maslen, G., Akanni, W., Allen, J., Alvarez-Jarreta, J., Barba, M., Bolser, D., Cambell, L., & others. (2020). Ensembl Genomes 2020—Enabling non-vertebrate genomic research. Nucleic Acids Research, 48(D1), D689–D695. https://doi.org/10.1093/nar/gkz890 Hu, H., Li, R., Zhao, J., Batley, J., & Edwards, D. (2024). Technological Development and Advances for Constructing and Analyzing Plant Pangenomes. Genome Biology and Evolution, 16(4), evae081. https://doi.org/10.1093/gbe/evae081 Hu, J., Fan, J., Sun, Z., & Liu, S. (2020). NextPolish: A fast and efficient genome polishing tool for long-read assembly. Bioinformatics, 36(7), 2253–2255. https://doi.org/10.1093/bioinformatics/btz891 Hu, J., Wang, Z., Sun, Z., Hu, B., Ayoola, A. O., Liang, F., Li, J., Sandoval, J. R., Cooper, D. N., Ye, K., Ruan, J., Xiao, C.-L., Wang, D., Wu, D.-D., & Wang, S. (2024). NextDenovo: An efficient error correction and accurate assembly tool for noisy long reads. Genome Biology, 25(1), 107. https://doi.org/10.1186/s13059-024-03252-4 Huang, X., Kurata, N., Wei, X., Wang, Z.-X., Wang, A., Zhao, Q., Zhao, Y., Liu, K., Lu, H., Li, W., Guo, Y., Lu, Y., Zhou, C., Fan, D., Weng, Q., Zhu, C., Huang, T., Zhang, L., Wang, Y., … Han, B. (2012). A map of rice genome variation reveals the origin of cultivated rice. Nature, 490(7421), 497–501. https://doi.org/10.1038/nature11532 Huang, Y., Zhao, S., Fu, Y., Sun, H., Ma, X., Tan, L., Liu, F., Sun, X., Sun, H., Gu, P., Xie, D., Sun, C., & Zhu, Z. (2018). Variation in the regulatory region of FZP causes increases in secondary inflorescence branching and grain yield in rice domestication. The Plant Journal, 96(4), 716–733. https://doi.org/10.1111/tpj.14062 Ikeda, K., Sunohara, H., & Nagato, Y. (2004). Developmental Course of Inflorescence and Spikelet in Rice. Breeding Science, 54(2), 147–156. https://doi.org/10.1270/jsbbs.54.147 International Rice Genome Sequencing Project, & Sasaki, T. (2005). The map-based sequence of the rice genome. Nature, 436(7052), 793–800. https://doi.org/10.1038/nature03895 Itoh, H., Yamashita, H., Wada, K. C., & Yonemaru, J. (2024). Real-time emulation of future global warming reveals realistic impacts on the phenological response and quality deterioration in rice. Proceedings of the National Academy of Sciences, 121(21), e2316497121. https://doi.org/10.1073/pnas.2316497121 Jacquemin, J., Bhatia, D., Singh, K., & Wing, R. A. (2013). The International Oryza Map Alignment Project: Development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Current Opinion in Plant Biology, 16(2), 147–156. https://doi.org/10.1016/j.pbi.2013.02.014 Jain, M., Tyson, J. R., Loose, M., Ip, C. L. C., Eccles, D. A., O’Grady, J., Malla, S., Leggett, R. M., Wallerman, O., Jansen, H. J., Zalunin, V., Birney, E., Brown, B. L., Snutch, T. P., Olsen, H. E., & MinION Analysis and Reference Consortium. (2017). MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry. F1000Research, 6, 760. https://doi.org/10.12688/f1000research.11354.1 Jang, J., Jung, J., Lee, Y. H., Lee, S., Baik, M., & Kim, H. (2023). Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies. Scientific Data, 10(1), 560. https://doi.org/10.1038/s41597-023-02453-z Jayakodi, M., Lu, Q., Pidon, H., Rabanus-Wallace, M. T., Bayer, M., Lux, T., Guo, Y., Jaegle, B., Badea, A., Bekele, W., Brar, G. S., Braune, K., Bunk, B., Chalmers, K. J., Chapman, B., Jørgensen, M. E., Feng, J.-W., Feser, M., Fiebig, A., … Stein, N. (2024). Structural variation in the pangenome of wild and domesticated barley. Nature, 636(8043), 654–662. https://doi.org/10.1038/s41586-024-08187-1 Jin, I.-D. (1986). On the formation and development of abscission layer in rice plants, Oryza sativa L. Japanese Journal of Crop Science, 55(4), 451–457. https://doi.org/10.1626/jcs.55.451 Jing, C.-Y., Zhang, F.-M., Wang, X.-H., Wang, M.-X., Zhou, L., Cai, Z., Han, J.-D., Geng, M.-F., Yu, W.-H., Jiao, Z.-H., Huang, L., Liu, R., Zheng, X.-M., Meng, Q.-L., Ren, N.-N., Zhang, H.-X., Du, Y.-S., Wang, X., Qiang, C.-G., … Ge, S. (2023). Multiple domestications of Asian rice. Nature Plants, 9(8), 1221–1235. https://doi.org/10.1038/s41477-023-01476-z Kawahara, Y., De La Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., Zhou, S., Childs, K. L., Davidson, R. M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S. S., Kim, J., Numa, H., … Matsumoto, T. (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice, 6(1), 4. https://doi.org/10.1186/1939-8433-6-4 Khush, G. S. & Virk. (2005). IR varieties and their impact. International Rice Research Institute. Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology, 37(5), 540–546. https://doi.org/10.1038/s41587-019-0072-8 Komatsu, M., Chujo, A., Nagato, Y., Shimamoto, K., & Kyozuka, J. (2003). FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets. Development, 130(16), 3841–3850. https://doi.org/10.1242/dev.00564 Konishi, S., Izawa, T., Lin, S. Y., Ebana, K., Fukuta, Y., Sasaki, T., & Yano, M. (2006). An SNP caused loss of seed shattering during rice domestication. Science, 312(5778), 1392–1396. https://doi.org/10.1126/science.1126410 Koo, H., Lee, G.-W., Ko, S.-R., Go, S., Kwon, S.-Y., Kim, Y.-M., & Shin, A.-Y. (2023). Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms. Scientific Data, 10(1), 713. https://doi.org/10.1038/s41597-023-02631-z Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017). Canu: Scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation. Genome Research, 27(5), 722–736. https://doi.org/10.1101/gr.215087.116 Kruskal, W. H., & Wallis, W. A. (1952). Use of ranks in one-criterion variance analysis. Journal of the American Statistical Association, 47(260), 583–621. https://doi.org/10.1080/01621459.1952.10483441 Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PLOS ONE, 12(5), e0177459. https://doi.org/10.1371/journal.pone.0177459 Lee, C., Grasso, C., & Sharlow, M. F. (2002). Multiple sequence alignment using partial order graphs. Bioinformatics, 18(3), 452–464. https://doi.org/10.1093/bioinformatics/18.3.452 Lee, S.-K., Song, M.-Y., Seo, Y.-S., Kim, H.-K., Ko, S., Cao, P.-J., Suh, J.-P., Yi, G., Roh, J.-H., Lee, S., An, G., Hahn, T.-R., Wang, G.-L., Ronald, P., & Jeon, J.-S. (2009). Rice Pi5 -Mediated Resistance to Magnaporthe oryzae Requires the Presence of Two Coiled-Coil–Nucleotide-Binding–Leucine-Rich Repeat Genes. Genetics, 181(4), 1627–1638. https://doi.org/10.1534/genetics.108.099226 Leinonen, R., Sugawara, H., Shumway, M., & on behalf of the International Nucleotide Sequence Database Collaboration. (2011). The Sequence Read Archive. Nucleic Acids Research, 39(Database), D19–D21. https://doi.org/10.1093/nar/gkq1019 Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2023). Graph construction method impacts variation representation and analyses in a bovine super-pangenome. Genome Biology, 24(1), 124. https://doi.org/10.1186/s13059-023-02969-y Lewin, H. A., Robinson, G. E., Kress, W. J., Baker, W. J., Coddington, J., Crandall, K. A., Durbin, R., Edwards, S. V., Forest, F., Gilbert, M. T. P., Goldstein, M. M., Grigoriev, I. V., Hackett, K. J., Haussler, D., Jarvis, E. D., Johnson, W. E., Patrinos, A., Richards, S., Castilla-Rubio, J. C., … Zhang, G. (2018). Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences, 115(17), 4325–4333. https://doi.org/10.1073/pnas.1720115115 Li, B., Yang, Q., Yang, L., Zhou, X., Deng, L., Qu, L., Guo, D., Hui, R., Guo, Y., Liu, X., Wang, T., Fan, L., Li, M., & Yan, M. (2023). A gap-free reference genome reveals structural variations associated with flowering time in rapeseed ( Brassica napus ). Horticulture Research, 10(10), uhad171. https://doi.org/10.1093/hr/uhad171 Li, C., Zhou, A., & Sang, T. (2006). Rice Domestication by Reducing Shattering. Science, 311(5769), 1936–1939. https://doi.org/10.1126/science.1123604 Li, H. (n.d.). Minigraph GitHub Repository [Computer software]. https://github.com/lh3/minigraph Li, H. (2018). Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094–3100. https://doi.org/10.1093/bioinformatics/bty191 Li, H. (2024). Gfatools [Computer software]. https://github.com/lh3/gfatools Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp324 Li, H., Feng, X., & Chu, C. (2020). The design and construction of reference pangenome graphs with minigraph. Genome Biology, 21(1), 265. https://doi.org/10.1186/s13059-020-02168-z Li, K., Jiang, W., Hui, Y., Kong, M., Feng, L.-Y., Gao, L.-Z., Li, P., & Lu, S. (2021). Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution. Molecular Plant, 14(10), 1745–1756. https://doi.org/10.1016/j.molp.2021.06.017 Li, L., Stoeckert, C. J., & Roos, D. S. (2003). OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research, 13(9), 2178–2189. https://doi.org/10.1101/gr.1224503 Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., Buonaiuto, S., Chang, X. H., Cheng, H., Chu, J., Colonna, V., Eizenga, J. M., Feng, X., Fischer, C., Fulton, R. S., … Paten, B. (2023). A draft human pangenome reference. Nature, 617(7960), 312–324. https://doi.org/10.1038/s41586-023-05896-x Liu, Y., Wu, H., Chen, H., Liu, Y., He, J., Kang, H., Sun, Z., Pan, G., Wang, Q., Hu, J., Zhou, F., Zhou, K., Zheng, X., Ren, Y., Chen, L., Wang, Y., Zhao, Z., Lin, Q., Wu, F., … Wan, J. (2015). A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice. Nature Biotechnology, 33(3), 301–305. https://doi.org/10.1038/nbt.3069 Liu, Z., Wang, N., Su, Y., Long, Q., Peng, Y., Shangguan, L., Zhang, F., Cao, S., Wang, X., Ge, M., Xue, H., Ma, Z., Liu, W., Xu, X., Li, C., Cao, X., Ahmad, B., Su, X., Liu, Y., … Zhou, Y. (2024). Grapevine pangenome facilitates trait genetics and genomic breeding. Nature Genetics, 56(12), 2804–2814. https://doi.org/10.1038/s41588-024-01967-5 Liu, Z., Yang, F., Wan, H., Deng, C., Hu, W., Fan, X., Wang, J., Yang, M., Feng, J., Wang, Q., Yang, N., Cai, L., Liu, Y., Tang, H., Li, S., Luo, J., Zheng, J., Wu, L., Yang, E., … Yang, W. (2024). Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement. Plant Communications, 101131. https://doi.org/10.1016/j.xplc.2024.101131 Long, Q., Cao, S., Huang, G., Wang, X., Liu, Z., Liu, W., Wang, Y., Xiao, H., Peng, Y., & Zhou, Y. (2024). Population comparative genomics discovers gene gain and loss during grapevine domestication. Plant Physiology, 195(2), 1401–1413. https://doi.org/10.1093/plphys/kiae039 Long, W., He, Q., Wang, Y., Wang, Y., Wang, J., Yuan, Z., Wang, M., Chen, W., Luo, L., Luo, L., Xu, W., Li, Y., Li, W., Yan, L., Cai, Y., Du, H., & Xie, H. (2024). Genome evolution and diversity of wild and cultivated rice species. Nature Communications, 15(1), 9994. https://doi.org/10.1038/s41467-024-54427-3 Lorig-Roach, R., Meredith, M., Monlong, J., Jain, M., Olsen, H., McNulty, B., Porubsky, D., Montague, T., Lucas, J., Condon, C., Eizenga, J. M., Juul, S., McKenzie, S., Simmonds, S. E., Park, J., Asri, M., Koren, S., Eichler, E., Axel, R., … Paten, B. (2024). Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Research, genome;gr.278268.123v1. https://doi.org/10.1101/gr.278268.123 Luo, J., Liu, H., Zhou, T., Gu, B., Huang, X., Shangguan, Y., Zhu, J., Li, Y., Zhao, Y., Wang, Y., Zhao, Q., Wang, A., Wang, Z., Sang, T., Wang, Z., & Han, B. (2013). An-1 Encodes a Basic Helix-Loop-Helix Protein That Regulates Awn Development, Grain Size, and Grain Number in Rice. The Plant Cell, 25(9), 3360–3376. https://doi.org/10.1105/tpc.113.113589 Lv, S., Wu, W., Wang, M., Meyer, R. S., Ndjiondjop, M.-N., Tan, L., Zhou, H., Zhang, J., Fu, Y., Cai, H., & others. (2018). Genetic control of seed shattering during African rice domestication. Nature Plants, 4(6), 331–337. https://doi.org/10.1038/s41477-018-0164-3 Ma, J., & Bennetzen, J. L. (2004). Rapid recent growth and divergence of rice nuclear genomes. Proceedings of the National Academy of Sciences, 101(34), 12404–12410. https://doi.org/10.1073/pnas.0403715101 Ma, J., Lei, C., Xu, X., Hao, K., Wang, J., Cheng, Z., Ma, X., Ma, J., Zhou, K., Zhang, X., Guo, X., Wu, F., Lin, Q., Wang, C., Zhai, H., Wang, H., & Wan, J. (2015). Pi64 , Encoding a Novel CC-NBS-LRR Protein, Confers Resistance to Leaf and Neck Blast in Rice. Molecular Plant-Microbe Interactions®, 28(5), 558–568. https://doi.org/10.1094/MPMI-11-14-0367-R Mahon, P., & Bateman, A. (2000). The PA domain: A protease‐associated domain. Protein Science, 9(10), 1930–1934. https://doi.org/2023102900015600942 Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018). MUMmer4: A fast and versatile genome alignment system. PLOS Computational Biology, 14(1), e1005944. https://doi.org/10.1371/journal.pcbi.1005944 Mavromatis, K., Land, M. L., Brettin, T. S., Quest, D. J., Copeland, A., Clum, A., Goodwin, L., Woyke, T., Lapidus, A., Klenk, H. P., Cottingham, R. W., & Kyrpides, N. C. (2012). The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation. PLoS ONE, 7(12), e48837. https://doi.org/10.1371/journal.pone.0048837 McClintock, B. (1984). The Significance of Responses of the Genome to Challenge. Science, 226(4676), 792–801. https://doi.org/10.1126/science.15739260 Meyer, R. S., Choi, J. Y., Sanches, M., Plessis, A., Flowers, J. M., Amas, J., Dorph, K., Barretto, A., Gross, B., Fuller, D. Q., Bimpong, I. K., Ndjiondjop, M.-N., Hazzouri, K. M., Gregorio, G. B., & Purugganan, M. D. (2016). Domestication history and geographical adaptation inferred from a SNP map of African rice. Nature Genetics, 48(9), 1083–1088. https://doi.org/10.1038/ng.3633 Mi, H., Muruganujan, A., Ebert, D., Huang, X., & Thomas, P. D. (2019). PANTHER version 14: More genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Research, 47(D1), D419–D426. https://doi.org/10.1093/nar/gky1038 Montgomery, S. B., Goode, D. L., Kvikstad, E., Albers, C. A., Zhang, Z. D., Mu, X. J., Ananda, G., Howie, B., Karczewski, K. J., Smith, K. S., Anaya, V., Richardson, R., Davis, J., The 1000 Genomes Project Consortium, MacArthur, D. G., Sidow, A., Duret, L., Gerstein, M., Makova, K. D., … Lunter, G. (2013). The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes. Genome Research, 23(5), 749–761. https://doi.org/10.1101/gr.148718.112 Morrone, D., Jin, Y., Xu, M., Choi, S.-Y., Coates, R. M., & Peters, R. J. (2006). An unexpected diterpene cyclase from rice: Functional identification of a stemodene synthase. Archives of Biochemistry and Biophysics, 448(1–2), 133–140. https://doi.org/10.1016/j.abb.2005.09.001 Murray, S. (2007). Identifying African rice domestication in the middle Niger delta (Mali). Fields of Change: Progress in African Archaeobotany, 53–61. Naito, K., Zhang, F., Tsukiyama, T., Saito, H., Hancock, C. N., Richardson, A. O., Okumoto, Y., Tanisaka, T., & Wessler, S. R. (2009). Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature, 461(7267), 1130–1134. https://doi.org/10.1038/nature08479 Nattestad, M. (2020a). Dot: Interactive dot plot viewer for genome alignments [Computer software]. https://github.com/MariaNattestad/dot Nattestad, M. (2020b). Dot Web Application [Computer software]. https://dot.sandbox.bio Nelson, G. C., Valin, H., Sands, R. D., Havlík, P., Ahammad, H., Deryng, D., Elliott, J., Fujimori, S., Hasegawa, T., Heyhoe, E., Kyle, P., Von Lampe, M., Lotze-Campen, H., Mason d’Croz, D., Van Meijl, H., Van Der Mensbrugghe, D., Müller, C., Popp, A., Robertson, R., … Willenbockel, D. (2014). Climate change effects on agriculture: Economic responses to biophysical shocks. Proceedings of the National Academy of Sciences, 111(9), 3274–3279. https://doi.org/10.1073/pnas.1222465110 Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S. (2011). Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics, 12(6), 443–451. https://doi.org/10.1038/nrg2986 Novak, A. M., Chung, D., Hickey, G., Djebali, S., Yokoyama, T. T., Garrison, E., Narzisi, G., Paten, B., & Monlong, J. (2024). Efficient indexing and querying of annotations in a pangenome graph. https://doi.org/10.1101/2024.10.12.618009 Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S., & Phillippy, A. M. (2016). Mash: Fast genome and metagenome distance estimation using MinHash. Genome Biology, 17(1), 132. https://doi.org/10.1186/s13059-016-0997-x Ou, S., Chen, J., & Jiang, N. (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Research. https://doi.org/10.1093/nar/gky730 Ou, S., & Jiang, N. (2018). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiology, 176(2), 1410–1422. https://doi.org/10.1104/pp.17.01310 Pamilo & Nei. (1988). Relationships between gene trees and species trees. Molecular Biology and Evolution. https://doi.org/10.1093/oxfordjournals.molbev.a040517 Pandey, M. K., Khan, A. W., Singh, V. K., Vishwakarma, M. K., Shasidhar, Y., Kumar, V., Garg, V., Bhat, R. S., Chitikineni, A., Janila, P., Guo, B., & Varshney, R. K. (2017). QTL ‐seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut ( A rachis hypogaea L .). Plant Biotechnology Journal, 15(8), 927–941. https://doi.org/10.1111/pbi.12686 Paradis, E., Claude, J., & Strimmer, K. (2004). APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics, 20(2), 289–290. https://doi.org/10.1093/bioinformatics/btg412 Parmigiani, L., Garrison, E., Stoye, J., Marschall, T., & Doerr, D. (2024). Panacus: Fast and exact pangenome growth and core size estimation. Bioinformatics, 40(12), btae720. https://doi.org/10.1093/bioinformatics/btae720 Paten, B., Earl, D., Nguyen, N., Diekhans, M., Zerbino, D., & Haussler, D. (2011). Cactus: Algorithms for genome multiple sequence alignment. Genome Research, 21(9), 1512–1528. https://doi.org/10.1101/gr.123356.111 Pearson, K. (1900). X. On the criterion that a given system of deviations from the probable in the case of a correlated system of variables is such that it can be reasonably supposed to have arisen from random sampling. The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, 50(302), 157–175. https://doi.org/10.1080/14786440009463897 Pease, J. B., & Hahn, M. W. (2013). MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING: ACCURATE PHYLOGENIES IN LOW-RECOMBINATION REGIONS. Evolution, 67(8), 2376–2384. https://doi.org/10.1111/evo.12118 Peng, S., Khush, G. S., Virk, P., Tang, Q., & Zou, Y. (2008). Progress in ideotype breeding to increase rice yield potential. Field Crops Research, 108(1), 32–38. https://doi.org/10.1016/j.fcr.2008.04.001 Piegu, B., Guyot, R., Picault, N., Roulin, A., Saniyal, A., Kim, H., Collura, K., Brar, D. S., Jackson, S., Wing, R. A., & Panaud, O. (2006). Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis , a wild relative of rice. Genome Research, 16(10), 1262–1269. https://doi.org/10.1101/gr.5290206 Portères, R. (1962). Berceaux agricoles primaires sur le continent africain. The Journal of African History, 3(2), 195–210. https://doi.org/10.1017/S0021853700003030 Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841–842. https://doi.org/10.1093/bioinformatics/btq033 R Core Team. (2024). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. https://www.R-project.org/ Ramírez, V., López, A., Mauch-Mani, B., Gil, M. J., & Vera, P. (2013). An Extracellular Subtilase Switch for Immune Priming in Arabidopsis. PLoS Pathogens, 9(6), e1003445. https://doi.org/10.1371/journal.ppat.1003445 Rautiainen, M., Nurk, S., Walenz, B. P., Logsdon, G. A., Porubsky, D., Rhie, A., Eichler, E. E., Phillippy, A. M., & Koren, S. (2023). Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nature Biotechnology, 41(10), 1474–1482. https://doi.org/10.1038/s41587-023-01662-6 Rice, E. S., Alberdi, A., Alfieri, J., Athrey, G., Balacco, J. R., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O., Fiddaman, S. R., Formenti, G., Frantz, L. A. F., Gilbert, M. T. P., Hearn, C. J., Jarvis, E. D., Klopp, C., Marcos, S., Mason, A. S., … Warren, W. C. (2023). A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biology, 21(1), 267. https://doi.org/10.1186/s12915-023-01758-0 Roach, M. J., Schmidt, S. A., & Borneman, A. R. (2018). Purge Haplotigs: Allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics, 19(1), 460. https://doi.org/10.1186/s12859-018-2485-7 Ruan, J., & Li, H. (2020). Fast and accurate long-read assembly with wtdbg2. Nature Methods, 17(2), 155–158. https://doi.org/10.1038/s41592-019-0669-3 Sacco, M. A., & Moffett, P. (2009). Disease resistance genes: Form and function. In K. Bouarab, N. Brisson, & F. Daayf (Eds.), Molecular plant-microbe interactions (1st ed., pp. 94–141). CABI. https://doi.org/10.1079/9781845935740.0094 Sakai, H., & Itoh, T. (2010). Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis. BMC Genomics, 11(1), 121. https://doi.org/10.1186/1471-2164-11-121 Sakai, H., Lee, S. S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y., Wakimoto, H., Yang, C., Iwamoto, M., Abe, T., Yamada, Y., Muto, A., Inokuchi, H., Ikemura, T., Matsumoto, T., Sasaki, T., & Itoh, T. (2013). Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics. Plant and Cell Physiology, 54(2), e6–e6. https://doi.org/10.1093/pcp/pcs183 Sallaud, C., Lorieux, M., Roumen, E., Tharreau, D., Berruyer, R., Svestasrani, P., Garsmeur, O., Ghesquiere, A., & Notteghem, J.-L. (2003). Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy. Theoretical and Applied Genetics, 106(5), 794–803. https://doi.org/10.1007/s00122-002-1088-9 Sang, T., & Ge, S. (2007). Genetics and phylogenetics of rice domestication. Current Opinion in Genetics & Development, 17(6), 533–538. https://doi.org/10.1016/j.gde.2007.09.005 Sawano, Y., Miyakawa, T., Yamazaki, H., Tanokura, M., & Hatano, K. (2007). Purification, characterization, and molecular gene cloning of an antifungal protein from Ginkgo biloba seeds. Biological Chemistry, 388(3). https://doi.org/10.1515/BC.2007.030 Schneeberger, K., Ossowski, S., Ott, F., Klein, J. D., Wang, X., Lanz, C., Smith, L. M., Cao, J., Fitz, J., Warthmann, N., Henz, S. R., Huson, D. H., & Weigel, D. (2011). Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proceedings of the National Academy of Sciences, 108(25), 10249–10254. https://doi.org/10.1073/pnas.1107739108 Senol Cali, D., Kim, J. S., Ghose, S., Alkan, C., & Mutlu, O. (2019). Nanopore sequencing technology and tools for genome assembly: Computational analysis of the current state, bottlenecks and future directions. Briefings in Bioinformatics, 20(4), 1542–1559. https://doi.org/10.1093/bib/bby017 Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., Sedlazeck, F. J., Marschall, T., Mayes, S., Costa, V., Zook, J. M., Liu, K. J., Kilburn, D., Sorensen, M., Munson, K. M., … Paten, B. (2020). Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology, 38(9), 1044–1053. https://doi.org/10.1038/s41587-020-0503-6 Shang, L., Li, X., He, H., Yuan, Q., Song, Y., Wei, Z., Lin, H., Hu, M., Zhao, F., Zhang, C., Li, Y., Gao, H., Wang, T., Liu, X., Zhang, H., Zhang, Y., Cao, S., Yu, X., Zhang, B., … Qian, Q. (2022). A super pan-genomic landscape of rice. Cell Research, 32(10), 878–896. https://doi.org/10.1038/s41422-022-00685-z Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLOS ONE, 11(10), e0163962. https://doi.org/10.1371/journal.pone.0163962 Shiu, S.-H., & Bleecker, A. B. (2001a). Plant Receptor-Like Kinase Gene Family: Diversity, Function, and Signaling. Science’s STKE, 2001(113). https://doi.org/10.1126/stke.2001.113.re22 Shiu, S.-H., & Bleecker, A. B. (2001b). Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proceedings of the National Academy of Sciences, 98(19), 10763–10768. https://doi.org/10.1073/pnas.181141598 Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19), 3210–3212. https://doi.org/10.1093/bioinformatics/btv351 Sloan, D. B., Wu, Z., & Sharbrough, J. (2018). Correction of Persistent Errors in Arabidopsis Reference Mitochondrial Genomes. The Plant Cell, 30(3), 525–527. https://doi.org/10.1105/tpc.18.00024 Smit, A., Hubley, R., & Green, P. (2015). RepeatMasker Open-4.0. 2013–2015. Seattle, USA. Smith, C. (2014). Encyclopedia of global archaeology. Springer New York. Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J. L., Wei, S., Wang, J., Liao, Y., Wang, M., Jacquemin, J., Becker, C., Kudrna, D., Zhang, J., Londono, C. E. M., … Wing, R. A. (2018). Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics, 50(2), 285–296. https://doi.org/10.1038/s41588-018-0040-0 Storer, J. M., Hubley, R., Rosen, J., Wheeler, T. J., Smit, A. F., & Kent, W. R. (2021). Dfam: The database of repetitive DNA families. Nucleic Acids Research, 49(D1), D104–D110. https://doi.org/10.1093/nar/gkaa1085 Sun, J., Li, R., Chen, C., Sigwart, J. D., & Kocot, K. M. (2021). Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes. Philosophical Transactions of the Royal Society B: Biological Sciences, 376(1825), 20200160. https://doi.org/10.1098/rstb.2020.0160 Sweeney, M., & McCouch, S. (2007). The Complex History of the Domestication of Rice. Annals of Botany, 100(5), 951–957. https://doi.org/10.1093/aob/mcm128 Syauqi, J., Chen, R.-K., Cheng, A.-H., Wu, Y.-F., Chung, C.-L., Lin, C.-C., Chou, H.-P., Wu, H.-Y., Jian, J.-Y., Liao, C.-T., Kuo, C.-C., Chu, S.-C., Tsai, Y.-C., Liao, D.-J., Wu, Y.-P., Abadi, A. L., Sulistyowati, L., & Shen, W.-C. (2022). Surveillance of Rice Blast Resistance Effectiveness and Emerging Virulent Isolates in Taiwan. Plant Disease, 106(12), 3187–3197. https://doi.org/10.1094/PDIS-12-21-2806-RE Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S., DeBoy, R. T., Davidsen, T. M., Mora, M., Scarselli, M., Margarit Y Ros, I., Peterson, J. D., Hauser, C. R., Sundaram, J. P., Nelson, W. C., … Fraser, C. M. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome.” Proceedings of the National Academy of Sciences, 102(39), 13950–13955. https://doi.org/10.1073/pnas.0506758102 The Arabidopsis Genome Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408(6814), 796–815. https://doi.org/10.1038/35048692 The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Adesina, A., Ahmad, S., Bowler-Barnett, E. H., Bye-A-Jee, H., Carpentier, D., Denny, P., Fan, J., Garmiri, P., Gonzales, L. J. D. C., Hussein, A., Ignatchenko, A., Insana, G., Ishtiaq, R., Joshi, V., … Zhang, J. (2025). UniProt: The Universal Protein Knowledgebase in 2025. Nucleic Acids Research, 53(D1), D609–D617. https://doi.org/10.1093/nar/gkae1010 Thomas, P. D., Campbell, M. J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A., & Narechania, A. (2003). PANTHER: A Library of Protein Families and Subfamilies Indexed by Function. Genome Research, 13(9), 2129–2141. https://doi.org/10.1101/gr.772403 Tripathi, L. P., & Sowdhamini, R. (2006). Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC Genomics, 7(1), 200. https://doi.org/10.1186/1471-2164-7-200 Veltman, M. A., Flowers, J. M., Van Andel, T. R., & Schranz, M. E. (2019). Origins and geographic diversification of African rice (Oryza glaberrima). PLOS ONE, 14(3), e0203508. https://doi.org/10.1371/journal.pone.0203508 Villani, F., Guarracino, A., Ward, R. R., Green, T., Emms, M., Pravenec, M., Sharp, B., Prins, P., Garrison, E., Williams, R. W., Chen, H., & Colonna, V. (2025). Pangenome reconstruction in rats enhances genotype-phenotype mapping and variant discovery. iScience, 28(2), 111835. https://doi.org/10.1016/j.isci.2025.111835 Vitte, C., & Panaud, O. (2005). LTR retrotransposons and flowering plant genome size: Emergence of the increase/decrease model. Cytogenetic and Genome Research, 110(1–4), 91–107. https://doi.org/10.1159/000084941 Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., & Earl, A. M. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE, 9(11), e112963. https://doi.org/10.1371/journal.pone.0112963 Wambugu, P. W., Ndjiondjop, M.-N., & Henry, R. (2021). Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. Rice, 14(1), 6. https://doi.org/10.1186/s12284-020-00449-6 Wang, L., Zhao, L., Zhang, X., Zhang, Q., Jia, Y., Wang, G., Li, S., Tian, D., Li, W.-H., & Yang, S. (2019). Large-scale identification and functional analysis of NLR genes in blast resistance in the Tetep rice genome sequence. Proceedings of the National Academy of Sciences, 116(37), 18479–18487. https://doi.org/10.1073/pnas.1910229116 Wang, M., Yu, Y., Haberer, G., Marri, P. R., Fan, C., Goicoechea, J. L., Zuccolo, A., Song, X., Kudrna, D., Ammiraju, J. S. S., Cossu, R. M., Maldonado, C., Chen, J., Lee, S., Sisneros, N., De Baynast, K., Golser, W., Wissotski, M., Kim, W., … Wing, R. A. (2014). The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics, 46(9), 982–988. https://doi.org/10.1038/ng.3044 Wang, T., Duan, S., Xu, C., Wang, Y., Zhang, X., Xu, X., Chen, L., Han, Z., & Wu, T. (2023). Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nature Communications, 14(1), 7377. https://doi.org/10.1038/s41467-023-43270-7 Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., Li, M., Zheng, T., Fuentes, R. R., Zhang, F., Mansueto, L., Copetti, D., Sanciangco, M., Palis, K. C., Xu, J., Sun, C., Fu, B., Zhang, H., Gao, Y., … Leung, H. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557(7703), 43–49. https://doi.org/10.1038/s41586-018-0063-9 Wick, R. R., & Holt, K. E. (2021). Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000Research, 8, 2138. https://doi.org/10.12688/f1000research.21782.4 Wick, R. R., Schultz, M. B., Zobel, J., & Holt, K. E. (2015). Bandage: Interactive visualization of de novo genome assemblies. Bioinformatics, 31(20), 3350–3352. https://doi.org/10.1093/bioinformatics/btv383 Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P., & Schulman, A. H. (2007). A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8(12), 973–982. https://doi.org/10.1038/nrg2165 Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org Wu, J., Zhang, Y., Li, F., Zhang, X., Ye, J., Wei, T., Li, Z., Tao, X., Cui, F., Wang, X., Zhang, L., Yan, F., Li, S., Liu, Y., Li, D., Zhou, X., & Li, Y. (2024). Plant virology in the 21st century in China: Recent advances and future directions. Journal of Integrative Plant Biology, 66(3), 579–622. https://doi.org/10.1111/jipb.13580 Wu, W., Liu, X., Wang, M., Meyer, R. S., Luo, X., Ndjiondjop, M.-N., Tan, L., Zhang, J., Wu, J., Cai, H., & others. (2017). A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nature Plants, 3(6), 1–7. https://doi.org/10.1038/nplants.2017.64 Wu, Y., Zhao, S., Li, X., Zhang, B., Jiang, L., Tang, Y., Zhao, J., Ma, X., Cai, H., Sun, C., & Tan, L. (2018). Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice. Nature Communications, 9(1), 4157. https://doi.org/10.1038/s41467-018-06509-2 Yamaki, S., Miyabayashi, T., Eiguchi, M., Kitano, H., Nonomura, K.-I., & Kurata, N. (2010). Diversity of panicle branching patterns in wild relatives of rice. Breeding Science, 60(5), 586–596. https://doi.org/10.1270/jsbbs.60.586 Yandell, M., & Ence, D. (2012). A beginner’s guide to eukaryotic genome annotation. Nature Reviews Genetics, 13(5), 329–342. https://doi.org/10.1038/nrg3174 Yang, X., Lee, W.-P., Ye, K., & Lee, C. (2019). One reference genome is not enough. Genome Biology, 20(1), 104. https://doi.org/10.1186/s13059-019-1717-0 Yano, R., Li, F., Hiraga, S., Takeshima, R., Kobayashi, M., Toda, K., Umehara, Y., Kajiya-Kanegae, H., Iwata, H., Kaga, A., & Ishimoto, M. (2025). The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars. Nature Genetics. https://doi.org/10.1038/s41588-025-02113-5 Ye, M., Kuai, P., Hu, L., Ye, M., Sun, H., Erb, M., & Lou, Y. (2020). Suppression of a leucine‐rich repeat receptor‐like kinase enhances host plant resistance to a specialist herbivore. Plant, Cell & Environment, 43(10), 2571–2585. https://doi.org/10.1111/pce.13834 Zhai, C., Lin, F., Dong, Z., He, X., Yuan, B., Zeng, X., Wang, L., & Pan, Q. (2011). The isolation and characterization of Pik , a rice blast resistance gene which emerged after rice domestication. New Phytologist, 189(1), 321–334. https://doi.org/10.1111/j.1469-8137.2010.03462.x Zhang, C., Fang, H., Shi, X., He, F., Wang, R., Fan, J., Bai, P., Wang, J., Park, C., Bellizzi, M., Zhou, X., Wang, G., & Ning, Y. (2020). A fungal effector and a rice NLR protein have antagonistic effects on a Bowman–Birk trypsin inhibitor. Plant Biotechnology Journal, 18(11), 2354–2363. https://doi.org/10.1111/pbi.13400 Zhang, L., Zhu, Q., Wu, Z., Ross‐Ibarra, J., Gaut, B. S., Ge, S., & Sang, T. (2009). Selection on grain shattering genes and rates of rice domestication. New Phytologist, 184(3), 708–720. https://doi.org/10.1111/j.1469-8137.2009.02984.x Zhang, Q. J., & Gao, L. Z. (2017). Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species. G3 Genes|Genomes|Genetics, 7(6), 1875–1885. https://doi.org/10.1534/g3.116.037572 Zhang, Q.-J., Zhu, T., Xia, E.-H., Shi, C., Liu, Y.-L., Zhang, Y., Liu, Y., Jiang, W.-K., Zhao, Y.-J., Mao, S.-Y., Zhang, L.-P., Huang, H., Jiao, J.-Y., Xu, P.-Z., Yao, Q.-Y., Zeng, F.-C., Yang, L.-L., Gao, J., Tao, D.-Y., … Gao, L.-Z. (2014). Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proceedings of the National Academy of Sciences, 111(46). https://doi.org/10.1073/pnas.1418307111 Zhang, S., Huang, X., & Han, B. (2021). Understanding the genetic basis of rice heterosis: Advances and prospects. The Crop Journal, 9(3), 688–692. https://doi.org/10.1016/j.cj.2021.03.011 Zhang, X., Liu, C.-G., Yang, S.-H., Wang, X., Bai, F.-W., & Wang, Z. (2022). Benchmarking of long-read sequencing, assemblers and polishers for yeast genome. Briefings in Bioinformatics, 23(3), bbac146. https://doi.org/10.1093/bib/bbac146 Zhang, Y., Fu, J., Wang, K., Han, X., Yan, T., Su, Y., Li, Y., Lin, Z., Qin, P., Fu, C., Deng, X. W., Zhou, D., Yang, Y., & He, H. (2022). The telomere‐to‐telomere gap‐free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding. Plant Biotechnology Journal, 20(9), 1642–1644. https://doi.org/10.1111/pbi.13880 Zhang, Y., Zhao, M., Tan, J., Huang, M., Chu, X., Li, Y., Han, X., Fang, T., Tian, Y., Jarret, R., Lu, D., Chen, Y., Xue, L., Li, X., Qin, G., Li, B., Sun, Y., Deng, X. W., Deng, Y., … He, H. (2024). Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nature Genetics, 56(8), 1750–1761. https://doi.org/10.1038/s41588-024-01823-6 Zhao, K., Xue, H., Li, G., Chitikineni, A., Fan, Y., Cao, Z., Dong, X., Lu, H., Zhao, K., Zhang, L., Qiu, D., Ren, R., Gong, F., Li, Z., Ma, X., Wan, S., Varshney, R. K., Wei, C., & Yin, D. (2025). Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut. Nature Genetics, 57(5), 1250–1261. https://doi.org/10.1038/s41588-025-02170-w Zhao, Q., Feng, Q., Lu, H., Li, Y., Wang, A., Tian, Q., Zhan, Q., Lu, Y., Zhang, L., Huang, T., Wang, Y., Fan, D., Zhao, Y., Wang, Z., Zhou, C., Chen, J., Zhu, C., Li, W., Weng, Q., … Huang, X. (2018). Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nature Genetics, 50(2), 278–284. https://doi.org/10.1038/s41588-018-0041-z Zheng, A., Lin, R., Zhang, D., Qin, P., Xu, L., Ai, P., Ding, L., Wang, Y., Chen, Y., Liu, Y., Sun, Z., Feng, H., Liang, X., Fu, R., Tang, C., Li, Q., Zhang, J., Xie, Z., Deng, Q., … Li, P. (2013). The evolution and pathogenic mechanisms of the rice sheath blight pathogen. Nature Communications, 4(1), 1424. https://doi.org/10.1038/ncomms2427 Zheng, W., Ma, Z., Zhao, M., Xiao, M., Zhao, J., Wang, C., Gao, H., Bai, Y., Wang, H., & Sui, G. (2020). Research and Development Strategies for Hybrid japonica Rice. Rice, 13(1), 36. https://doi.org/10.1186/s12284-020-00398-0 Zheng, X., Zhong, L., Pang, H., Wen, S., Li, F., Lou, D., Ge, J., Fan, W., Wang, T., Han, Z., Qiao, W., Pan, X., Zhu, Y., Wang, J., Tang, C., Wang, X., Zhang, J., Xu, Z., Kim, S. R., … Yang, Q. (2023). Lost genome segments associate with trait diversity during rice domestication. BMC Biology, 21(1), 20. https://doi.org/10.1186/s12915-023-01512-6 | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/97505 | - |
| dc.description.abstract | none | zh_TW |
| dc.description.abstract | Pangenome graphs have been constructed to analyze the genetic diversity of wild and cultivated rice; however, their applications have been limited to graph characterization and variant calling, with little justification provided for software selection. This study aimed to extend the application of pangenome graphs by estimating genomic gains and losses between wild and cultivated rice through parsimonious inference of graph-encoded variants. To support this objective, a pipeline was developed centered on an appropriate graph builder identified by comparing three widely used software. Initial attempts with Minigraph revealed inaccurate and biased variant calling. In contrast, PGGB achieved perfect recall and was adopted for final graph construction. The resulting pangenome graph contained approximately 400 Mb of non-reference sequences. Core sequences represented only 25% of the graph and encoded genes linked to core biological functions, while the variable category comprised 75% of the graph and contained over 50% repeats. The unmasked fraction of the variable category encoded genes with adaptation-related functions, including members of the protein kinase and NBS-LRR families. While INDEL-based parsimonious inference revealed a balanced distribution of gains and losses across internal branches, mapping SVs showed that the common ancestors of both Asian and African rice lineages experienced more losses than gains. In contrast, gain amplification on external branches was driven by repeats classified in the private category. Removing these elements restored a balanced pattern between gains and losses. These findings demonstrate the potential of pangenome graphs for inferring rice genome evolution and highlight the importance of software selection in pangenome construction. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2025-07-02T16:12:24Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2025-07-02T16:12:24Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | Certificate of Thesis Approval i
Acknowledgement ii ABSTRACT iii Table of Contents iv List of Tables viii List of Figures ix Chapter 1. Introduction 1 Chapter 2. Review of Related Literature 4 2.1 Background of Pangenomes 4 2.2 Strategies in Constructing Pangenomes 5 2.3 Graph-Based Pangenomes 7 2.4 Strategies to Construct Graph-Based Pangenomes 9 2.4.1 Minigraph 9 2.4.2 Minigraph-Cactus 10 2.4.3 PanGenome Graph Builder (PGGB) 12 2.5 Domestication History of Asian Rice 14 2.6 Domestication History of African Rice 17 2.7 Examples of Key Domestication Genes in Asian and African Rice 19 2.8 Genomic Gains and Losses 23 Chapter 3. Materials and Methods 27 3.1 Data Acquisition 27 3.2 Genome assembly 28 3.2.1 Preprocessing Long-Read ONT Sequences 28 3.2.2 Selection of Genome Assembly Pipeline 29 3.2.3 Quality Assessment of Genome Assemblies 30 3.2.5 Repeat Annotation 32 3.3 Pangenome Construction 32 3.3.1 Graph Building Using Minigraph 33 3.3.2 Presence/Absence Matrix of Segments 33 3.3.3 Linearization and Annotating the Pangenome 34 3.3.4 Structural Variations Represented as Bubbles 35 3.3.5 Genomic Gains and Loss Analysis 36 3.4 Simulation of Pangenome Graph Builders 38 3.5 PGGB 41 3.5.1 Parameter Adjustment and Partitioning 41 3.5.2 Pangenome Characterization and Pangenome Growth 42 3.5.3 Repeats and Coding Fractions 43 3.5.4 Protein Family and Domain Characterization 44 3.5.5 Phylogenomic Analysis 44 3.5.6 Variant Analysis 45 3.6 Genomic Gain and Loss Analyses 46 3.6.1 Gain and Loss Annotation 47 3.6.2 Visualization of Graph 48 3.7 Statistical Test 48 3.8 Code Availability 49 Chapter 4. Results 50 4.1 Selection of Genome Assembly Strategy 50 4.2 Genome Assemblies of Wild and Cultivated Rice 53 4.2.1 Repeat Composition of Each Genome Assembly 57 4.3 Graph Building with Minigraph 60 4.3.1 Characterization of Pangenome Graph Generated by Minigraph 62 4.3.2 Pangenome Categories in the Minigraph Output 63 4.3.3 Characterization of Non-reference Segments 68 4.3.4 Detection and Characterization of Structural Variations 74 4.3.5 Genomic Gains and Losses Estimation Using Minigraph 78 4.4 Simulation of Pangenome Graph Builders 79 4.5 Graph Building with PGGB 82 4.5.1 Characterization of Pangenome Graph Generated by PGGB 85 4.5.2 Pangenome Categories 86 4.5.3 Functional Characterization of Core and Variable Categories 88 4.5.4 INDELs and SV Detection 93 4.5.5 Parsimonious and Non-parsimonious Cases 96 4.5.6 Genomic Gains and Losses Estimation using PGGB 99 4.5.7 Functional Characterization of Variants 103 Chapter 5. Discussion 109 5.1 Nextdenovo Outperforms NECAT and WTDBG2 109 5.2 Minigraph Fails to Accurately Call Variants 111 5.3 Variable Categories Mainly Contained Repetitive Sequences and Defense-Related Genes 113 5.4 PGGB Graph Contains More INDELs than SVs 116 5.5 Non-Parsimonious Cases Reflect the Complex History of the Indica Subgroup 116 5.6 Two Scenarios Drawn from Parsimonious Inference Using INDELs and SVs 117 Chapter 6. Conclusions and Perspectives 120 6.1 Conclusions 120 6.2 Limitations and Future Perspectives of the Study 121 References 123 Appendices 144 | - |
| dc.language.iso | en | - |
| dc.subject | 水稻馴化 | zh_TW |
| dc.subject | 泛基因組圖譜 | zh_TW |
| dc.subject | 結構變異 | zh_TW |
| dc.subject | 系統基因組學 | zh_TW |
| dc.subject | Phylogenomics | en |
| dc.subject | Pangenome graph | en |
| dc.subject | Structural variation | en |
| dc.subject | Rice domestication | en |
| dc.title | Genomic Gain and Loss Analyses between Wild and Cultivated Rice Using a Pangenome Graph | zh_TW |
| dc.title | Genomic Gain and Loss Analyses between Wild and Cultivated Rice Using a Pangenome Graph | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 113-2 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 林耀正;小柳香奈子 | zh_TW |
| dc.contributor.oralexamcommittee | Yao-Cheng Lin;Kanako Koyanagi | en |
| dc.subject.keyword | 泛基因組圖譜,結構變異,水稻馴化,系統基因組學, | zh_TW |
| dc.subject.keyword | Pangenome graph,Structural variation,Rice domestication,Phylogenomics, | en |
| dc.relation.page | 154 | - |
| dc.identifier.doi | 10.6342/NTU202501263 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2025-06-25 | - |
| dc.contributor.author-college | 共同教育中心 | - |
| dc.contributor.author-dept | 全球農業科技與基因體科學碩士學位學程 | - |
| dc.date.embargo-lift | 2025-07-03 | - |
| 顯示於系所單位： | 全球農業科技與基因體科學碩士學位學程 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| ntu-113-2.pdf 授權僅限NTU校內IP使用（校園外請利用VPN校外連線服務） | 11.1 MB | Adobe PDF |
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