番茄斑萎病毒屬 (Tospovirus) 為布尼亞病毒科 (Bunyaviridae) 中唯一感染植物的一屬，病毒顆粒直徑大小約80-110 nm，具有脂質外套膜，其內包含三條單股RNA基因體，依其大小分別命名為S、M和L，可轉譯出六種蛋白。S RNA與M RNA具雙極性，而L RNA為負極性。S RNA可轉譯出一個非結構性NSs蛋白，為基因沉默作用之抑制子；以及能與RNA結合的核鞘蛋白 (nucleocapsid protein, NP)。M RNA可轉譯出與病毒在宿主細胞間移動有關的非結構性NSm蛋白，以及兩個外套膜上醣蛋白前驅物 (glycoprotein precursor, GP)。L RNA可轉譯出負責複製與轉錄作用之RNA依賴性RNA聚合酶 (RNA-dependent RNA polymerase, RdRp)。番茄黃輪病毒 (Tomato yellow ring virus, TYRV) 由伊朗的番茄所分離出，花生黃化扇斑病毒 (Peanut chlorotic fan-spot virus, PCFV) 則由臺灣的花生所分離，兩者皆暫定為Tospovirus屬的病毒種 (species)。為了確立此二病毒之分類地位，本研究完成TYRV的M及L RNAs 和 PCFV 的M RNA之定序與分析。TYRV的M RNA含有4786個核苷酸，可轉譯出308個胺基酸 (34.5 kDa) 的NSm蛋白及1310個胺基酸 (128 kDa) 的GP。TYRV的L RNA共有8877個核苷酸，可轉譯出2873個胺基酸 (331 kDa) 的RdRp。PCFV的M RNA含4857個核苷酸，可產生306個胺基酸 (34.3 kDa) 的NSm蛋白及1111個胺基酸 (126.3 kDa) 的GP。TYRV的NSm 和GP與蕎麥輪斑病毒 (Polygonum ringspot virus, PolRSV) 和鳶尾花黃斑病毒 (Iris yellow spot virus, IYSV) 的蛋白分別具有89.9% 與80.1-86.5% 高度的胺基酸相同性 (identity)。PCFV的NSm和GP則與其它tospoviruses的蛋白較疏遠，分別僅有34.6-42.7%與31.1-33.3%的胺基酸相同性。TYRV的RdRp與IYSV的RdRp具有88.7% 的高度胺基酸相同性。序列分析結果顯示 TYRV與IYSV及PolRSV展現高度的親緣同源性，而PCFV則明顯地與其它tospoviruses皆較疏遠。

Tospovirus, the only plant-infecting genus in the family Bunyaviridae, has enveloped virions of 80-110 nm in diameter consisting of three segmented single-stranded RNA genome, denoted S, M and L, for coding six viral proteins. Both S and M RNAs are ambisense and L RNA has a negative polarity. A nonstructural NSs protein, acting as gene-silencing suppressor, and the RNA-binding nucleocapsid protein (NP) are encoded from the S RNA. The M RNA is responsible for coding a nonstructural NSm protein involved in cell-to-cell movement and the precursor of two glycoproteins on the surface of viral envelope. The L RNA codes the RNA-dependent RNA polymerase (RdRp) for replication and transcription. Tomato yellow ring virus (TYRV), isolated from tomato in Iran, and Peanut chlorotic fan-spot virus (PCFV), from peanut in Taiwan, were classified as two tentative species of the genus Tospovirus. To clarify the taxonomic status of these two viruses, the M and L RNAs of TYRV and the M RNA of PCFV were determined and analyzed in this investigation. The M RNA of TYRV has 4786 nucleotides (nt) coding for a NSm protein of 308 amino acids (aa) (34.5 kDa) and a glycoprotein precursor (GP) of 1310 aa (128 kDa). The L RNA of TYRV has 8877 nt encoding an RdRp of 2873 aa (331 kDa). The M RNA of PCFV has 4786 nt encoding a NSm protein of 306 aa (34.3 kDa) and a GP of 1111 aa (126.3 kDa). The NSm and GP proteins of TYRV share high 89.9% and 80.1-86.5% aa identities, respectively, with those of Polygonum ringspot virus (PolRSV) and Iris yellow spot virus (IYSV). However, the NSm and GP proteins of PCFV share low identities of 34.6-42.7% and 31.1-33.3%, respectively, with those of other tospovirus species. The RdRp of TYRV shares the highest aa identity (88.7%) with that of IYSV. Sequence analyses indicate that TYRV and PCFV should be classified as official species of the genus Tospovirus. TYRV is closely related to IYSV and PolRSV, but PCFV is distant from other tospoviruses.

中文摘要………………………………………………………………………………1
Abstract……………………………………………………………………………….2
Literature review…………………………………………………………………….3
Occurrence of tospoviruses…………………………………………………………3
Morphology and genome organization of tospoviruses…………………………….4
Current taxonomic status of tospoviruses…………………………………………..5
Thrips transmission…………………………………………………………………7
Incidence of tospoviruses in Taiwan………………………………………………..8
Studies of PCFV……………………………………………………………………9
Studies of TYRV……………………………………………………………………9
Introduction…………………………………………………………………………11
Materials and methods……………………………………………………………..14
Virus sources and propagation……………………………………………………14
Amplification and cloning of TYRV and PCFV genomes………………………..14
Rapid amplification of cDNA ends (RACE) ……………………………………...15
Sequence analysis…………………………………………………………………15
Analyses of GPs…………………………………………………………………..16
Results……………………………………………………………………………….17
Organization of TYRV M RNA…………………………………………………...17
Sequence comparison of the M RNA of TYRV with those of other tospoviruses...17
Organization of TYRV L RNA…………………………………………………….18
Sequence analysis of TYRV L RNA………………………………………………18
Organization of PCFV M RNA……………………………………………………18
Sequence comparison of the M RNA of PCFV with those of other tospoviruses…19
Molecular characterization of the NSm proteins of TYRV and PCFV……………19
Molecular analysis of the GPs of TYRV and PCFV………………………………20
Phylogenetic relationships of tospoviruses in NSm, GP and RdRp………………20
Discussion……………………………………………………………………………21
References…………………………………………………………………………...25
Tables………………………………………………………………………………...40
Figures……………………………………………………………………………….49
Appendix…………………………………………………………………………….65

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