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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 林仲彥(Chung-Yen Lin) | |
| dc.contributor.author | Yi-Ching Lin | en |
| dc.contributor.author | 林宜靜 | zh_TW |
| dc.date.accessioned | 2021-05-17T09:15:24Z | - |
| dc.date.available | 2012-08-16 | |
| dc.date.available | 2021-05-17T09:15:24Z | - |
| dc.date.copyright | 2012-08-16 | |
| dc.date.issued | 2012 | |
| dc.date.submitted | 2012-08-10 | |
| dc.identifier.citation | Adams MD (2000) The Genome Sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252: 1651-1656. 3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29. 4. Brady P, Elizur A, Williams R, Cummins SF, Knibb W (2012) Gene expression profiling of the cephalothorax and eyestalk in Penaeus monodon during ovarian maturation. Int J Biol Sci 8: 328-343. 5. Cheng W, Chen SM, Wang FI, Hsu PI, Liu CH, Chen JC (2003) Effects of temperature, pH, salinity and ammonia on the phagocytic activity and clearance efficiency of giant freshwater prawn Macrobrachium rosenbergii to Lactococcus garvieae. Aquaculture 219: 111-121. 6. Cheng W, Liu CH, Kuo CM (2003) Effects of dissolved oxygen on hemolymph parameters of freshwater giant prawn, Macrobrachium rosenbergii (de Man). Aquaculture 220: 843-856. 7. Chevreux B (2005) MIRA: An Automated Genome and EST Assembler: German Cancer Research Center Heidelberg. 8. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WEG, Wetter T, Suhai S (2004) Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. Genome Res 14: 1147-1159. 9. Clavero-Salas A, Sotelo-Mundo RR, Gollas-Galvan T, Hernandez-Lopez J, Peregrino-Uriarte AB, Muhlia-Almazan A, Yepiz-Plascencia G (2007) Transcriptome analysis of gills from the white shrimp Litopenaeus vannamei infected with white spot syndrome virus. Fish Shellfish Immunol 23: 459-472. 10. Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Frohlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kultz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL (2011) The ecoresponsive genome of Daphnia pulex. Science 331: 555-561. 11. Dong B, Xiang JH (2007) Discovery of genes involved in defense/immunity functions in a haemocytes cDNA library from Fenneropenaeus chinensis by ESTs annotation. Aquaculture 272: 208-215. 12. FAO (2010-2012) Fisheries and Aquaculture Department. 13. Foster CA, Howse HD (1978) A morphological study on gills of the brown shrimp, Penaeus aztecus. Tissue Cell 10: 77-92. 14. Gross PS, Bartlett TC, Browdy CL, Chapman RW, Warr GW (2001) Immune gene discovery by expressed sequence tag analysis of hemocytes and hepatopancreas in the Pacific White Shrimp, Litopenaeus vannamei, and the Atlantic White Shrimp, L. setiferus. Dev Comp Immunol 25: 565-577. 15. Huang da W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13. 16. Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57. 17. Huang da W, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, Lempicki RA (2007) DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res 35: W169-175. 18. Jain M, Shrager J, Harris EH, Halbrook R, Grossman AR, Hauser C, Vallon O (2007) EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome. Nucleic Acids Res 35: 2074-2083. 19. Jongeneel CV (2000) Searching the expressed sequence tag (EST) databases: panning for genes. Brief Bioinform 1: 76-92. 20. Jung H, Lyons RE, Dinh H, Hurwood DA, McWilliam S, Mather PB (2011) Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery. PLoS ONE 6: e27938. 21. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30. 22. Khatri P, Drăghici S (2005) Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21: 3587-3595. 23. Leekitcharoenphon P, Taweemuang U, Palittapongarnpim P, Kotewong R, Supasiri T, Sonthayanon B (2010) Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species. BMC Res Notes 3: 295. 24. Leelatanawit R, Sittikankeaw K, Yocawibun P, Klinbunga S, Roytrakul S, Aoki T, Hirono I, Menasveta P (2009) Identification, characterization and expression of sex-related genes in testes of the giant tiger shrimp Penaeus monodon. Comp Biochem Physiol A Mol Integr Physiol 152: 66-76. 25. Lehnert SA, Wilson KJ, Byrne K, Moore SS (1999) Tissue-specific expressed sequence tags from the black tiger shrimp Penaeus monodon. Mar Biotechnol 1: 465-476. 26. Leu JH, Chang CC, Wu JL, Hsu CW, Hirono I, Aoki T, Juan HF, Lo CF, Kou GH, Huang HC (2007) Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon. BMC Genomics 8: 120. 27. Leu JH, Chen SH, Wang YB, Chen YC, Su SY, Lin CY, Ho JM, Lo CF (2011) A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp. Mar Biotechnol (NY) 13: 608-621. 28. Liao IC, Huang TL (1969) A preliminary report on artificial propagation of Penaeus monodon(Fabricius). Joint Commission on Rural Reconstruction (JCRR) Fisheries Series 8: 67-71. 29. McQuilton P, St Pierre SE, Thurmond J (2012) FlyBase 101--the basics of navigating FlyBase. Nucleic Acids Res 40: D706-714. 30. Nagaraj SH, Gasser RB, Ranganathan S (2007) A hitchhiker's guide to expressed sequence tag (EST) analysis. Brief Bioinform 8: 6-21. 31. O'Leary NA, Trent HF, 3rd, Robalino J, Peck ME, McKillen DJ, Gross PS (2006) Analysis of multiple tissue-specific cDNA libraries from the Pacific whiteleg shrimp, Litopenaeus vannamei. Integr Comp Biol 46: 931-939. 32. Pongsomboon S, Wongpanya R, Tang S, Chalorsrikul A, Tassanakajon A (2008) Abundantly expressed transcripts in the lymphoid organ of the black tiger shrimp, Penaeus monodon, and their implication in immune function. Fish Shellfish Immunol 25: 485-493. 33. Pontius JU, Wagner L, Schuler GD (2002) UniGene: a unified view of the transcriptome. In: McEntyre J, Ostell J, editors. Bethesda (MD): National Center for Biotechnology Information (US). 34. Preechaphol R, Leelatanawit R, Sittikankeaw K, Klinbunga S, Khamnamtong B, Puanglarp N, Menasveta P (2007) Expressed sequence tag analysis for identification and characterization of sex-related genes in the giant tiger shrimp Penaeus monodon. J Biochem Mol Biol 40: 501-510. 35. Preston N (1985) The combined effects of temperature and salinity on hatching success and the survival, growth, and development of the larval stages of Metapenaeus bennettae (Racek & Dall). Journal of Experimental Marine Biology and Ecology 85: 57-74. 36. Primavera JH (1998) Tropical shrimp farming and its sustainability. In: Silva SSD, editor. Tropical Mariculture. San Diego: Academic Press. pp. 257-289. 37. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-301. 38. Rivals I, Personnaz L, Taing L, Potier MC (2007) Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics 23: 401-407. 39. Robalino J, Almeida JS, McKillen D, Colglazier J, Trent HF, Chen YA, Peck MET, Browdy CL, Chapman RW, Warr GW, Gross PS (2007) Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge. Physiological Genomics 29: 44-56. 40. Rojtinnakorn J, Hirono I, Itami T, Takahashi Y, Aoki T (2002) Gene expression in haemocytes of kuruma prawn, Penaeus japonicus, in response to infection with WSSV by EST approach. Fish Shellfish Immunol 13: 69-83. 41. Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends in Plant Science 8: 321-329. 42. Sathiyamoorthy S, In JG, Gayathri S, Kim YJ, Yang DC (2010) Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. Mol Biol Rep 37: 3465-3472. 43. Selvam DG, Mujeeb Rahiman KM, Mohamed Hatha AA (2012) An investigation into occasional white spot syndrome virus outbreak in traditional paddy cum prawn fields in India. ScientificWorldJournal 2012: 340830. 44. Stojmirovic A, Yu YK (2010) Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics 26: 2752-2759. 45. Supungul P, Klinbunga S, Pichyangkura R, Hirono I, Aoki T, Tassanakajon A (2004) Antimicrobial peptides discovered in the black tiger shrimp Penaeus monodon using the EST approach. Dis Aquat Organ 61: 123-135. 46. Supungul P, Klinbunga S, Pichyangkura R, Jitrapakdee S, Hirono I, Aoki T, Tassanakajon A (2002) Identification of immune-related genes in hemocytes of black tiger shrimp (Penaeus monodon). Mar Biotechnol (NY) 4: 487-494. 47. Tassanakajon A, Klinbunga S, Paunglarp N, Rimphanitchayakit V, Udomkit A, Jitrapakdee S, Sritunyalucksana K, Phongdara A, Pongsomboon S, Supungul P, Tang S, Kuphanumart K, Pichyangkura R, Lursinsap C (2006) Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database. Gene 384: 104-112. 48. Yamano K, Unuma T (2006) Expressed sequence tags from eyestalk of kuruma prawn, Marsupenaeus japonicus. Comp Biochem Physiol A Mol Integr Physiol 143: 155-161. 49. Xiang J, Wang B, Li F, Liu B, Zhou Y, Tong W (2008) Generation and analysis of 10,443 ESTs from cephalothorax of Fenneropenaeus Chinensis. The 2nd International Conference on Bioinformatics and Biomedical Engineering, Shanghai, China. p. 74–80. 50. 王瑜琦 (2007) 白蝦免疫相關基因之表現及其受口服葡聚多醣的影響. 高雄市: 國立中山大學. 209 p. 51. 鄭金華 (2007) 無特定病原(SPF)白蝦繁養殖模式之開發與產業應用. 農業生技產業季刊. pp. 48-59. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/6623 | - |
| dc.description.abstract | 南美白蝦 ( Litopenaeus vannamei ) 在蝦類養殖的地位日趨重要，進行其基因轉錄體的研究可了解該物種的基因組成，有助於對蝦生理、遺傳、育種、與病理研究等基礎領域，以因應對蝦繁養殖上所面臨的問題。EST (Expressed Sequence Tag) 是cDNA的部分定序序列，可提供轉錄基因的序列資訊及相對表現數量，對於尚未完成完整基因體的物種，藉由EST定序能得到大量蛋白質基因的資訊。本研究蒐集公開資料庫上的白蝦ESTs序列，共161,241筆資料，利用與白蝦在分類上相近且完成完整基因體定序解析資訊的水蚤 (Daphnia pulex) 及果蠅 (Drosophila melanogaster) 為參考，利用序列的同源關係，設計序列分析流程，組裝得到16,886筆contigs及20,515筆singletons，共37,401筆重組序列；經過資料庫比對的序列註解程序後，超過40%的重組序列可在non-redundant protein database及Pfam database找到相似的序列或模組特徵。
在原始EST序列資料中，92%的是來自眼柄、鰓、血細胞、肝胰臟、淋巴器官及神經索，此六個組織的EST數量皆超過20,000筆。上述重組序列，以其 EST來源組織的EST數為基因表現量，代表六個組織的基因表現概況。分析這六個組織以重組序列的Gene Ontology 註解資訊，發現眼柄、肝胰臟及淋巴器官的表現基因功能分類有較明顯集中（enrichment）的傾向，挑選其中差異較大的眼柄及肝胰臟，進一步分析兩組織的重組序列組成在KEGG pathway 的配置方式，是否有集中程度的差異。綜合 KEGG pathway 與 GO term 的分析結果顯示，兩組織間都有共同表現的重組序列，大多是參與轉譯過程的基因，眼柄組織特有序列較集中表現actin及myosin兩個基因，肝胰臟組織的特有序列，則是表現血藍素 (hemocyanin)。本研究提供不同的序列組裝策略，運用重組序列之註解了解組織特異性，其結果能幫助我們對白蝦的基因更加了解，過程得到的資料也可提供後續研究者作為研究之參考。 參考網站：http://ips.sinica.edu.tw/lv | zh_TW |
| dc.description.abstract | The Pacific white shrimp, Litopenaeus vannamei, has became a more important animal in shrimp aquaculture. Although its genome has not been fully sequenced, this economically important species has attracted researchers for building a rich source of ESTs for benefiting both the basic biology and the applied science. Expressed Sequence Tags (ESTs), are short sequences derived from a batch-wise partial sequencing result of cDNA library, which may represents the relative expression level of transcripts in the library. It is an effective approach to get numerous sequences of protein coding genes of a species without previous knowing about the genome context. In this study, we collected 161,241 ESTs of white shrimp from public database. Reference sequences from two taxonomically closed species Daphnia pulex and Drosophila melanogaster were used for selecting subset for de novo assembling. Totally, 37,401 assembled sequences, including 16,886 contigs and 20,515 singletons, were obtained. Over 40% of the assemblies could be matched to homolog sequences in non-redundant protein database and/or protein domain feature in Pfam database. Six tissues including eyestalk, gills, hemocyte, hepatopancreas, lymphoid organ and nerve cord are the major tissue source of this collection. Assemblies were annotated and the expression level of each assembled contig/ singleton in each tissue was calculated by the number of ESTs contributed to this contig/singleton. Enrichment analyses were further applied to detect Gene Ontology terms, and KEGG pathway for describing the unique function of each tissue. For example, the unique expressing subset of hepatopancreas is related to hemocyanin in KEGG pathway enrichment analysis result, while the unique subset in eyestalk represent actin and myosin genes. In summary, this study provides an alternative strategy of assembling EST and the data produced from this research can assist any studies about white shrimp in the future.
Reference URL: http://ips.iis.sinica.edu.tw/lv | en |
| dc.description.provenance | Made available in DSpace on 2021-05-17T09:15:24Z (GMT). No. of bitstreams: 1 ntu-101-R97b45011-1.pdf: 1484271 bytes, checksum: 558b0905c9feae1525982425448de007 (MD5) Previous issue date: 2012 | en |
| dc.description.tableofcontents | 謝辭 i
中文摘要 ii ABSTRACT iv 第一章 簡介 1 1.1研究背景 1 1.2研究動機及目的 3 1.3文獻探討 5 1.3.1單一組織的基因表現 5 1.3.2健康蝦體與被病菌感染蝦體的基因表現之比較 8 1.3.3不同組織間的基因表現 11 第二章 材料方法 15 2.1材料介紹 15 2.1.1白蝦(Litopenaeus vannamei)的EST (Expressed Sequence Tags) 15 2.1.2水蚤轉錄基因體 16 2.1.3果蠅蛋白質體 17 2.1.4重組序列之策略及工具 17 2.2白蝦ESTS (Expressed Sequence Tags) 組裝流程 19 2.2.1與水蚤(Daphnia pulex)的序列相似性比較 20 2.2.2以果蠅(Drosophila melanogaster) 的序列輔助建立 21 2.2.3 De novo Assembly 22 2.3對重組序列進行可能的功能註解 23 2.3.1 重組序列與nr及Pfam兩資料庫的相似性比對 23 2.3.2 進行重組序列的Gene Ontology(GO) 註解 24 2.3.3以定序方法研究白蝦基因表現概況（Expression Profiling） 24 2.3.4各組織的基因表現概況 25 2.4組織間表現基因的差異性 25 2.4.1 Digital Differential Display 25 2.4.2 以Gene Ontology 來進行功能性分析 26 2.4.3 Venn diagram & KEGG pathway enrichment analysis 27 2.5建置白蝦EST資料庫 28 2.6資料庫及程式清單 29 第三章 結果 30 3.1白蝦的重組序列 30 3.2註解重組序列 32 3.3組織的基因表現概況 33 3.4組織間表現基因的差異性 39 3.6 KEGG pathway analysis 43 第四章 討論 44 4.1序列組裝之策略 44 4.2重組序列之註解 45 4.3不同組織間重組序列之比較 48 第五章 結論 51 參考文獻 53 | |
| dc.language.iso | zh-TW | |
| dc.title | 以表現標誌序列重組南美白蝦之轉錄基因體並比較不同組織間的基因表現 | zh_TW |
| dc.title | Decipher the transcriptome of Litopenaeus vannamei by assembling ESTs and compare gene expression in different libraries | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 100-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 韓玉山(Yu-San Han),呂健宏(Jiann-Horng Leu) | |
| dc.subject.keyword | 南美白蝦,表現標誌序列,參考基因體,重組,註解, | zh_TW |
| dc.subject.keyword | Litopenaeus vannamei,Expressed Sequence Tags,reference genome,assembly,annotation, | en |
| dc.relation.page | 57 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2012-08-10 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 漁業科學研究所 | zh_TW |
| 顯示於系所單位： | 漁業科學研究所 | |
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