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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 陳立涵(Li-Han Chen) | |
| dc.contributor.author | Ya-Ting Wang | en |
| dc.contributor.author | 王雅婷 | zh_TW |
| dc.date.accessioned | 2023-03-20T00:14:46Z | - |
| dc.date.copyright | 2022-08-02 | |
| dc.date.issued | 2022 | |
| dc.date.submitted | 2022-07-28 | |
| dc.identifier.citation | 1 Nash, C. E. & Shehadeh, Z. H. Review of breeding and propagation techniques for grey mullet, Mugil cephalus L. (1980). 2 Whitfield, A., Panfili, J. & Durand, J.-D. A global review of the cosmopolitan flathead mullet Mugil cephalus Linnaeus 1758 (Teleostei: Mugilidae), with emphasis on the biology, genetics, ecology and fisheries aspects of this apparent species complex. Reviews in Fish Biology and Fisheries 22, 641-681 (2012). 3 FAO. Mugil cephalus Linnaeus,1758, <https://www.fao.org/fishery/en/aqspecies/3050/en> (2022). 4 Kumaran, R., Ravi, V., Gunalan, B., Murugan, S. & Sundramanickam, A. Estimation of proximate, amino acids, fatty acids and mineral composition of mullet (Mugil cephalus) of Parangipettai, Southeast Coast of India. Advances in Applied Science Research 3, 2015-2019 (2012). 5 I Chiu Liao, E. M. L. Mullet and Its Aquaculture. (2022). 6 Shen, K.-N., Chang, C.-W. & Durand, J.-D. Spawning segregation and philopatry are major prezygotic barriers in sympatric cryptic Mugil cephalus species. Comptes Rendus Biologies 338, 803-811 (2015). 7 Institute., F. R. 烏魚品系, <https://kmweb.coa.gov.tw/subject/subject.php?id=3278> (2009). 8 Kalogeropoulos, N., Nomikos, T., Chiou, A., Fragopoulou, E. & Antonopoulou, S. Chemical composition of greek avgotaracho prepared from mullet (Mugil cephalus): nutritional and health benefits. Journal of agricultural and food chemistry 56, 5916-5925 (2008). 9 Byadgi, O. et al. Transcriptome analysis of grey mullet (Mugil cephalus) after challenge with Lactococcus garvieae. Fish & Shellfish Immunology 58, 593-603 (2016). 10 Shimahara, Y. et al. Genotypic and phenotypic analysis of fish pathogen, Nocardia seriolae, isolated in Taiwan. Aquaculture 294, 165-171 (2009). 11 Chang, H.-Y., Lai, J.-M. & Wang, J.-H. The minimum inhibitory concentration of antibiotics against Nocardia seriolae isolation from diseased fish in Taiwan. Taiwan Veterinary Journal 42, 81-84 (2016). 12 Su, F.-J. & Chen, M.-M. Protective Efficacy of Novel Oral Biofilm Vaccines against Lactococcus garvieae Infection in Mullet, Mugil cephalus. Vaccines 9, 844 (2021). 13 Rao, S., Byadgi, O., Pulpipat, T., Wang, P. C. & Chen, S. C. Efficacy of a formalin‐inactivated Lactococcus garvieae vaccine in farmed grey mullet (Mugil cephalus). Journal of Fish Diseases 43, 1579-1589 (2020). 14 Maekawa, S., Yoshida, T., Wang, P. C. & Chen, S. C. Current knowledge of nocardiosis in teleost fish. Journal of fish diseases 41, 413-419 (2018). 15 KARIYA, T., KUBOTA, S., NAKAMURA, Y. & KIRA, K. Nocardial infection in cultured yellowtails (Seriola quinqueruiata and S. purpurascens)—I Bacteriological study. Fish Pathology 3, 16-23 (1968). 16 Wang, P. C. et al. Nocardia seriolae infection in the three striped tigerfish, Terapon jarbua (Forsskål). Journal of fish diseases 32, 301-310 (2009). 17 Byadgi, O., Chen, C.-W., Wang, P.-C., Tsai, M.-A. & Chen, S.-C. De novo transcriptome analysis of differential functional gene expression in largemouth bass (Micropterus salmoides) after challenge with Nocardia seriolae. International journal of molecular sciences 17, 1315 (2016). 18 Miyoshi, Y. & Suzuki, S. A PCR method to detect Nocardia seriolae in fish samples. Fish Pathology 38, 93-97 (2003). 19 Reynolds, J., Moyes, R. B. & Breakwell, D. P. Differential staining of bacteria: acid fast stain. Current protocols in microbiology 15, A. 3H. 1-A. 3H. 5 (2009). 20 Itano, T., Kawakami, H., Kono, T. & Sakai, M. Experimental induction of nocardiosis in yellowtail, Seriola quinqueradiata Temminck & Schlegel by artificial challenge. Journal of Fish Diseases 29, 529-534 (2006). 21 Huang, S. Isolation and characterization of the pathogenic bacterium, Nocardia seriolae, from female broodstock of Striped Mullet, Mugil cephalus. J Fish Res 12, 61-69 (2004). 22 Wang, G. L., Yuan, S. P. & Jin, S. Nocardiosis in large yellow croaker, Larimichthys crocea (Richardson). Journal of fish diseases 28, 339-345 (2005). 23 Shimahara, Y., Huang, Y.-F., Tsai, M.-A., Wang, P.-C. & Chen, S.-C. Immune response of largemouth bass, Micropterus salmoides, to whole cells of different Nocardia seriolae strains. Fisheries Science 76, 489-494 (2010). 24 Kudo, T., Hatai, K. & Seino, A. Nocardia seriolae sp. nov. causing nocardiosis of cultured fish. International Journal of Systematic and Evolutionary Microbiology 38, 173-178 (1988). 25 Chen, S. C. et al. Nocardiosis in sea bass, Lateolabrax japonicus, in Taiwan. Journal of Fish Diseases 23, 299-307 (2000). 26 Yasuike, M. et al. Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species. PloS one 12, e0173198 (2017). 27 Wang, R. et al. Studies on nocardiasis infected farming Trachinotus ovatus. Transactions of Oceanology and Limnology 1, 52-58 (2010). 28 Jiang, Y., Li, Y., Zhou, S. & Li, A. Isolation and identification of Nocardia, a pathogen of nocardiosis in largemouth bass, Micropterus salmoides. Acta Scientiarum Naturalium Universitatis Sunyatseni 51, 76-81 (2012). 29 Chen, J. et al. Immunogenicity and efficacy of two DNA vaccines encoding antigenic PspA and TerD against Nocardia seriolae in hybrid snakehead. Fish & Shellfish Immunology 106, 742-754 (2020). 30 Plouffe, D. A., Hanington, P. C., Walsh, J. G., Wilson, E. C. & Belosevic, M. Comparison of select innate immune mechanisms of fish and mammals. Xenotransplantation 12, 266-277 (2005). 31 Uribe, C., Folch, H., Enríquez, R. & Moran, G. Innate and adaptive immunity in teleost fish: a review. Veterinarni Medicina 56, 486 (2011). 32 Cabillon, N. A. R. & Lazado, C. C. Mucosal barrier functions of fish under changing environmental conditions. Fishes 4, 2 (2019). 33 Gomez, D., Sunyer, J. O. & Salinas, I. The mucosal immune system of fish: the evolution of tolerating commensals while fighting pathogens. Fish & shellfish immunology 35, 1729-1739 (2013). 34 Boltaña, S., Roher, N., Goetz, F. W. & MacKenzie, S. A. PAMPs, PRRs and the genomics of gram negative bacterial recognition in fish. Developmental & Comparative Immunology 35, 1195-1203 (2011). 35 Liu, H. et al. Molecular insights of a novel fish Toll-like receptor 9 homologue in Nibea albiflora to reveal its function as PRRs. Fish & Shellfish Immunology 118, 321-332 (2021). 36 Haugland, G. T. et al. Phagocytosis and respiratory burst activity in lumpsucker (Cyclopterus lumpus L.) leucocytes analysed by flow cytometry. PloS one 7, e47909 (2012). 37 Haugland, G. T., Rønneseth, A. & Wergeland, H. I. Flow cytometry analyses of phagocytic and respiratory burst activities and cytochemical characterization of leucocytes isolated from wrasse (Labrus bergylta A.). Fish & Shellfish Immunology 39, 51-60 (2014). 38 Magnadóttir, B. Innate immunity of fish (overview). Fish & shellfish immunology 20, 137-151 (2006). 39 Bassity, E. & Clark, T. G. Functional identification of dendritic cells in the teleost model, rainbow trout (Oncorhynchus mykiss). PloS one 7, e33196 (2012). 40 Firdaus-Nawi, M. & Zamri-Saad, M. Major Components of Fish Immunity: A Review. Pertanika Journal of Tropical Agricultural Science 39 (2016). 41 Saurabh, S. & Sahoo, P. Lysozyme: an important defence molecule of fish innate immune system. Aquaculture research 39, 223-239 (2008). 42 Secombes, C. & Wang, T. in Infectious disease in aquaculture 3-68 (Elsevier, 2012). 43 Kordon, A. O., Pinchuk, L. & Karsi, A. Adaptive Immune System in Fish. Turkish Journal of Fisheries and Aquatic Sciences 22 (2021). 44 Smith, N. C., Rise, M. L. & Christian, S. L. A comparison of the innate and adaptive immune systems in cartilaginous fish, ray-finned fish, and lobe-finned fish. Frontiers in immunology, 2292 (2019). 45 Press, C. M. & Evensen, Ø. The morphology of the immune system in teleost fishes. Fish & shellfish immunology 9, 309-318 (1999). 46 Lin, W. et al. Long-term crowding stress causes compromised nonspecific immunity and increases apoptosis of spleen in grass carp (Ctenopharyngodon idella). Fish & shellfish immunology 80, 540-545 (2018). 47 Zwollo, P., Haines, A., Rosato, P. & Gumulak-Smith, J. Molecular and cellular analysis of B-cell populations in the rainbow trout using Pax5 and immunoglobulin markers. Developmental & Comparative Immunology 32, 1482-1496 (2008). 48 Zwollo, P. Dissecting teleost B cell differentiation using transcription factors. Developmental & Comparative Immunology 35, 898-905 (2011). 49 Tanekhy, M. et al. Expression of cytokine genes in head kidney and spleen cells of Japanese flounder (Paralichthys olivaceus) infected with Nocardia seriolae. Veterinary immunology and immunopathology 134, 178-183 (2010). 50 Nayak, S. K., Shibasaki, Y. & Nakanishi, T. Immune responses to live and inactivated Nocardia seriolae and protective effect of recombinant interferon gamma (rIFN γ) against nocardiosis in ginbuna crucian carp, Carassius auratus langsdorfii. Fish & shellfish immunology 39, 354-364 (2014). 51 Von Bubnoff, A. Next-generation sequencing: the race is on. Cell 132, 721-723 (2008). 52 Behjati, S. & Tarpey, P. S. What is next generation sequencing? Archives of Disease in Childhood-Education and Practice 98, 236-238 (2013). 53 Grada, A. & Weinbrecht, K. Next-generation sequencing: methodology and application. The Journal of investigative dermatology 133, e11 (2013). 54 Goodwin, S., McPherson, J. D. & McCombie, W. R. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 17, 333-351 (2016). 55 Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews genetics 10, 57-63 (2009). 56 Marguerat, S. & Bähler, J. RNA-seq: from technology to biology. Cellular and molecular life sciences 67, 569-579 (2010). 57 Sudhagar, A., Kumar, G. & El-Matbouli, M. Transcriptome analysis based on RNA-Seq in understanding pathogenic mechanisms of diseases and the immune system of fish: a comprehensive review. International journal of molecular sciences 19, 245 (2018). 58 Mu, Y. et al. Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection. BMC genomics 11, 1-14 (2010). 59 Wang, Y.-D. et al. Transcriptome analysis of the effect of Vibrio alginolyticus infection on the innate immunity-related complement pathway in Epinephelus coioides. Bmc Genomics 15, 1-15 (2014). 60 Katz, D. S. The streak plate protocol. Microbe Library (2008). 61 Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014). 62 Angelini, R. M. D. M. et al. De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits. BMC genomics 19, 1-21 (2018). 63 Haas, B. TransDecoder, <https://github.com/TransDecoder/TransDecoder> (2018). 64 Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic acids research 47, D309-D314 (2019). 65 Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic acids research 39, W29-W37 (2011). 66 Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659 (2006). 67 Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210-3212 (2015). 68 Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC bioinformatics 4, 1-14 (2003). 69 Consortium, G. O. The Gene Ontology (GO) database and informatics resource. Nucleic acids research 32, D258-D261 (2004). 70 Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research 28, 27-30 (2000). 71 Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature methods 9, 357-359 (2012). 72 Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12, 1-16 (2011). 73 Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 15, 1-21 (2014). 74 Shen, Y., Wang, D., Zhao, J. & Chen, X. Fish red blood cells express immune genes and responses. Aquaculture and Fisheries 3, 14-21 (2018). 75 Muller, W. A. Mechanisms of leukocyte transendothelial migration. Annual review of pathology 6, 323 (2011). 76 Cook-Mills, J. M. VCAM-1 signals during lymphocyte migration: role of reactive oxygen species. Molecular immunology 39, 499-508 (2002). 77 Elices, M. J. et al. VCAM-1 on activated endothelium interacts with the leukocyte integrin VLA-4 at a site distinct from the VLA-4/fibronectin binding site. Cell 60, 577-584 (1990). 78 Zhao, L. et al. Transcriptomic analysis of the head kidney of Topmouth culter (Culter alburnus) infected with Flavobacterium columnare with an emphasis on phagosome pathway. Fish & Shellfish Immunology 57, 413-418 (2016). 79 Li, S. et al. Expression analysis of Pannexin1 channel gene in response to immune challenges and its role in infection-induced ATP release in tilapia (Oreochromis niloticus). Fish & shellfish immunology 81, 470-475 (2018). 80 YIN, L.-C., LI, C.-L., QIU, X.-Y. & ZHOU, H. Molecular Characterization, 3D Modeling of Grass Carp Autophagy Related 16 Protein Like 1 (ATG16L1). 81 Zaki, M. H., Man, S. M., Vogel, P., Lamkanfi, M. & Kanneganti, T.-D. Salmonella exploits NLRP12-dependent innate immune signaling to suppress host defenses during infection. Proceedings of the National Academy of Sciences 111, 385-390 (2014). 82 Zhou, Q. et al. A chromosome‐level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth. Molecular ecology resources 19, 1322-1332 (2019). 83 Chen, Q. et al. Matrix metalloproteinases: inflammatory regulators of cell behaviors in vascular formation and remodeling. Mediators of inflammation 2013 (2013). 84 Pedersen, M. E., Vuong, T. T., Rønning, S. B. & Kolset, S. O. Matrix metalloproteinases in fish biology and matrix turnover. Matrix Biology 44, 86-93 (2015). 85 Xu, X.-Y. et al. Characterization of MMP-9 gene from grass carp (Ctenopharyngodon idella): an Aeromonas hydrophila-inducible factor in grass carp immune system. Fish & shellfish immunology 35, 801-807 (2013). 86 Jiang, Y. et al. Identification and characterization of matrix metalloproteinase-13 sequence structure and expression during embryogenesis and infection in channel catfish (Ictalurus punctatus). Developmental & Comparative Immunology 34, 590-597 (2010). 87 Gaviria-Agudelo, C., Carter, K., Tareen, N., Pascual, V. & Copley, L. A. Gene expression analysis of children with acute hematogenous osteomyelitis caused by Methicillin-resistant Staphylococcus aureus: Correlation with clinical severity of illness. PloS one 9, e103523 (2014). 88 Ashraf, W. et al. Transcript analysis of P2X receptors in PBMCs of chronic HCV patients: an insight into antiviral treatment response and HCV-induced pathogenesis. Viral Immunology 26, 343-350 (2013). 89 Geng, L., Wang, S., Zhao, Y. & Hu, H. Gene expression profile in mouse bacterial chronic rhinosinusitis. Experimental and therapeutic medicine 17, 3451-3458 (2019). 90 Vallejo, A. N. et al. Cellular pathway (s) of antigen processing and presentation in fish APC: endosomal involvement and cell-free antigen presentation. Developmental immunology 3, 51-65 (1992). 91 Ji, L., Sun, G., Li, X. & Liu, Y. Comparative transcriptome analysis reveals the mechanism of β-glucan in protecting rainbow trout (Oncorhynchus mykiss) from Aeromonas salmonicida infection. Fish & shellfish immunology 98, 87-99 (2020). 92 McLoughlin, K. E. et al. RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis. Frontiers in immunology 5, 396 (2014). 93 Bonello, S. et al. Reactive oxygen species activate the HIF-1α promoter via a functional NFκB site. Arteriosclerosis, thrombosis, and vascular biology 27, 755-761 (2007). 94 Tannahill, G. et al. Succinate is an inflammatory signal that induces IL-1β through HIF-1α. Nature 496, 238-242 (2013). 95 Wang, L. et al. RNA-Seq revealed the impairment of immune defence of tilapia against the infection of Streptococcus agalactiae with simulated climate warming. Fish & Shellfish Immunology 55, 679-689 (2016). 96 Peruzza, L. et al. Transcriptome analysis reveals a complex response to the RGNNV/SJNNV reassortant Nervous Necrosis Virus strain in sea bream larvae. Fish & Shellfish Immunology 114, 282-292 (2021). 97 Wu, R., Wang, N., Comish, P. B., Tang, D. & Kang, R. Inflammasome-dependent coagulation activation in sepsis. Frontiers in immunology 12, 684 (2021). 98 Chen, J. & Cosgriff, T. Hemorrhagic fever virus-induced changes in hemostasis and vascular biology. Blood coagulation & fibrinolysis 11, 461-483 (2000). 99 Ding, Y., Ao, J. & Chen, X. Comparative study of interleukin-17C (IL-17C) and IL-17D in large yellow croaker Larimichthys crocea reveals their similar but differential functional activity. Developmental & Comparative Immunology 76, 34-44 (2017). 100 Inoue, Y. et al. Molecular cloning and preliminary expression analysis of banded dogfish (Triakis scyllia) TNF decoy receptor 3 (TNFRSF6B). Fish & shellfish immunology 24, 360-365 (2008). 101 Cheng, X. et al. Identification and modulation of expression of a TNF receptor superfamily member 25 homologue in grass carp (Ctenopharyngodon idella). Aquaculture and Fisheries 5, 28-35 (2020). 102 Hou, Z. et al. Characterization and expression profiling of NOD-like receptor C3 (NLRC3) in mucosal tissues of turbot (Scophthalmus maximus L.) following bacterial challenge. Fish & Shellfish Immunology 66, 231-239 (2017). 103 Laing, K. J., Purcell, M. K., Winton, J. R. & Hansen, J. D. A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish. BMC evolutionary biology 8, 1-15 (2008). 104 Unajak, S. et al. Molecular characterization, expression and functional analysis of a nuclear oligomerization domain proteins subfamily C (NLRC) in Japanese flounder (Paralichthys olivaceus). Fish & Shellfish Immunology 31, 202-211 (2011). 105 Sha, Z. et al. NOD-like subfamily of the nucleotide-binding domain and leucine-rich repeat containing family receptors and their expression in channel catfish. Developmental & Comparative Immunology 33, 991-999 (2009). 106 Sakai, M., Hikima, J.-i. & Kono, T. Fish cytokines: current research and applications. Fisheries Science 87, 1-9 (2021). 107 Wei, X. et al. Fish NF‐κB couples TCR and IL‐17 signals to regulate ancestral T‐cell immune response against bacterial infection. The FASEB Journal 35, e21457 (2021). 108 Alejo, A. & Tafalla, C. Chemokines in teleost fish species. Developmental & Comparative Immunology 35, 1215-1222 (2011). 109 Cartwright, T., Perkins, N. D. & L. Wilson, C. NFKB1: a suppressor of inflammation, ageing and cancer. The FEBS journal 283, 1812-1822 (2016). 110 Caruso, R., Warner, N., Inohara, N. & Núñez, G. NOD1 and NOD2: signaling, host defense, and inflammatory disease. Immunity 41, 898-908 (2014). 111 He, R., Li, Z., Li, S. & Li, A. Development of an immersion challenge model for Streptococcus agalactiae in Nile tilapia (Oreochromis niloticus). Aquaculture 531, 735877 (2021). 112 Food., T. M. S. Grey mullet (Mugil cephalus), <https://www.terramaresf.com/en/grey-mullet-p-10> (2018). 113 S.L., F. C. ICON, <https://www.flaticon.com/premium-icon/syringe_4102463?term=needle&page=1&position=12&page=1&position=12&related_id=4102463&origin=search> (2022). 114 Corp., U.-O. Ficoll- Paque Plus, <http://www.uni-onward.com.tw/pdf/%E7%B4%B0%E8%83%9E%E5%88%86%E9%9B%A2%E6%B6%B2-%E4%BB%8B%E7%B4%B9.pdf> (2022). 115 Cytiva. Ficoll-Paque PLUS density gradient media, <https://www.cytivalifesciences.com/en/us/shop/cell-therapy/media/ficoll-paque-plus-density-gradient-media-p-05824> (2022). | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/86742 | - |
| dc.description.abstract | 烏魚(Mugil cephalus)是台灣經濟價值非常高的養殖物種，其中又以烏魚子最為人所熟知。在烏魚養殖的過程中，可能會因為高密度養殖或是季節變化，使得外來病原入侵。奴卡氏菌(Nocardia seriolae)是其中一種容易感染烏魚的細菌，魚隻會因為感染奴卡氏菌死亡，造成烏魚養殖的損失。為了全面瞭解烏魚被奴卡氏菌感染之後的免疫反應，且制定後續更有效的預防策略，我們透過Illumina轉錄體分析技術，用ex vivo的方式分離烏魚血液中的白血球，並且將烏魚白血球和奴卡氏菌共培養，而後進行轉錄體定序。 在Illumina轉錄體定序(n=3)完成之後，控制組及奴卡氏菌感染組總共6個樣本的序列會進行重新組裝(de novo assembly)，結果總共得到344,329個轉錄本，GC含量、N50、E90N50及平均長度分別為45%、1,738 bp、2,221 bp及928 bp。在經過序列相似度比較與篩選出最完整的相似序列後，總共獲得65,276個unigenes，並有53,620個unigene可注釋基因功能。透過BUSCO的3,640個單拷貝基因進行組裝完整度的評估，總共有74.4%的序列完全覆蓋。比較控制組與奴卡氏菌感染組的基因表現量後，總共得到225個具有表現差異的基因，其中包含140個正調控的基因及85個負調控的基因。比對COG、GO、KEGG及IPA等功能性資料庫，我們從225個表現差異基因中找到免疫相關的基因並且從中揭示出烏魚對抗奴卡氏菌的相關免疫途徑，其中包含IL-17信號通路(IL-17 signaling pathway)、白血球經內皮細胞層遷移(leukocyte transendothelial migration)、NOD-like受體信號通路(NOD-like receptor signaling pathway)。 此外，我們也透過體內實驗(in vivo)的方式進行奴卡氏菌攻毒實驗，使用qPCR實驗驗證轉錄體分析中具有表現差異的重要免疫基因IL17C、MMP-9、MMP-13、PANX1、F3、TNFRSF25、TNFRSF6B、NLRC3。 在本次的研究中，我們透過轉錄體分析的方式，更加了解烏魚在奴卡氏菌入侵後，參與進行調控的免疫基因及途徑，這個研究可以在未來針對奴卡氏菌在烏魚所引起的疾病，制定相關策略並進行預防。 | zh_TW |
| dc.description.abstract | Mugil cephalus (grey mullet) is an important fish species for cultivation in Taiwan. During a long cultivation period, intensive aquaculture or seasonal variations might cause the invasion of the pathogens. Nocardia seriolae is a gram-positive bacteria that might easily infect M. cephalus and cause mortality. Therefore, to comprehensively understand the immune response of M. cephalus after N. seriolae infection and formulate effective strategies in the future, Illumina RNA sequencing technology was applied in our study. RNA sequencing was executed with the leukocytes isolated from M. cephalus blood and co-cultured with N. seriolae. De novo assembly was conducted with six samples from control groups and N. seriolae infection groups. 344,329 transcripts were yielded, GC content, N50, E90N50, and the average length were 45%, 1,738 bp, 2,221 bp, and 928 bp, respectively. A total of 65,276 unigenes were obtained after optimization by TransDecoder and CD-HIT. Moreover, 74.4% of the sequences were completely recovered from the 3640 single-copy orthologs in BUSCO, and EggNOG annotated 53,620 unigenes. 225 differentially expressed genes were discovered, including 140 up-regulated and 85 down-regulated genes, with at least a two-fold difference between control and N. seriolae infection groups. After COG, GO, KEGG, and IPA analysis, we found immune-related genes among 225 differentially expressed genes (DEGs), which revealed the immune-related pathways of M. cephalus after N. seriolae infection, such as IL-17 signaling pathway、leukocyte transendothelial migration、NOD-like receptor signaling pathway. Furthermore, in vivo qPCR was used to confirm the results from RNA sequencing. The crucial DEGs such as IL17C, MMP-9, MMP-13, PANX1, F3, TNFRSF25, TNFRSF6B, and NLRC3 were randomly tested in qPCR. In this study, we assembled the transcriptome of M. cephalus and compared the gene expression profiles among control and N. seriolae infection groups to better understand the immune genes and pathways against bacteria invasion and frame possible strategies to prevent the outbreak of nocardiosis. | en |
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| dc.description.tableofcontents | 口試委員審定書.................................................................... i 致謝..............................................................................ii 中文摘要..........................................................................iii Abstract......................................................................... v Contents ........................................................................ vii Chapter 1 Introduction............................................................1 1-1 Mugil cephalus................................................................1 1-2 Nocardia seriolae and Nocardiosis in aquaculture .............................3 1-3 Teleost immune system ........................................................5 1-4 RNA sequencing................................................................7 1-5 Overview of study ............................................................9 Chapter 2 Research motivation and aims .......................................... 11 Chapter 3 Materials and methods.................................................. 12 3-1 Experimental animal, bacteria and design..................................... 12 3-2 Medium and buffer preparation................................................ 12 3-3 Agar preparation............................................................. 13 3-4 Cultivation of Nocardia seriolae............................................. 13 3-5 Animal maintenance........................................................... 13 3-5-1 Mugil cephalus juveniles................................................... 13 3-5-2 Mugil cephalus fry......................................................... 14 3-6 Blood collection and leukocytes isolation of Mugil cephalus juveniles........ 14 3-6-1 Blood collection........................................................... 14 3-6-2 Leukocytes isolation....................................................... 14 3-7 Leukocytes co-culture with Nocardia seriolae ................................ 15 3-8 Immersion challenge of Mugil cephalus fry with Nocardia seriolae ............ 15 3-9 Mugil cephalus immune tissue removed and homogenized......................... 16 3-10 Total RNA isolation ........................................................ 16 3-11 RNA quality assessment...................................................... 16 3-12 Reverse Transcription (RT).................................................. 17 3-13 Library preparation and sequencing.......................................... 17 3-14 De novo transcriptome assembly.............................................. 18 3-14-1 Adapters and low-quality reads removal.................................... 18 3-14-2 De novo assembly and assembly optimization................................ 18 3-14-3 Assessment of assembly completeness ...................................... 19 3-15 Functional unigene annotation and classification ........................... 19 3-16 Identification of DEGs (Differentially expressed genes) and correlation analysis …………………………………………….20 3-17 Real-Time PCR (qPCR)........................................................ 20 3-18 Statistical analysis........................................................ 21 Chapter 4 Results................................................................ 22 4-1 RNA-Seq library sequencing and evaluation of M. cephalus .................... 22 4-2 De novo assembly and optimization of M. cephalus transcriptome............... 22 4-3 De novo assembly completeness and validation ................................ 23 4-4 Gene identification and functional annotation ............................... 23 4-5 Differentially expressed number of genes after N. seriolae challenge......... 24 4-6 Canonical pathways and gene network analysis of differentially expressed genes by IPA........................................................................... 26 4-7 Validation of differentially expressed genes using real-time PCR ............ 27 4-8 Gene expression in KEGG immune-related pathways.............................. 28 Chapter 5 Discussion ............................................................ 29 Chapter 6 Conclusions............................................................ 40 References....................................................................... 72 | |
| dc.language.iso | en | |
| dc.title | 烏魚受奴卡氏菌感染之轉錄體分析 | zh_TW |
| dc.title | Transcriptome analysis of Mugil cephalus after challenge with Nocardia seriolae | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 110-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 李建樂(Chien-Yueh Lee),蔡孟勳(Mong-Hsun Tsai) | |
| dc.subject.keyword | 烏魚,奴卡氏菌,轉錄體,白血球,表現差異基因,免疫反應, | zh_TW |
| dc.subject.keyword | Mugil cephalus,Nocardia seriolae,Transcriptome,Leukocytes,Differential expressed genes,Immune response, | en |
| dc.relation.page | 88 | |
| dc.identifier.doi | 10.6342/NTU202201447 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2022-07-28 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 漁業科學研究所 | zh_TW |
| dc.date.embargo-lift | 2027-07-05 | - |
| 顯示於系所單位： | 漁業科學研究所 | |
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