BOGOR
2010
DAFTAR PUSTAKA
Aidawati N. 2006. Keanekaragaman Begomovirus pada Tomat dan Serangga Vektornya, Bemicia tabaci Gennadius (Hemiptera: Aleyrodidae), serta Pengujian Ketahanan Genotipe Tomat Terhadap Strain Begomovirus [disertasi]. Bogor: Sekolah Pascasarjana, Institut Pertanian Bogor.
Aidawati N, Hidayat P, Hidayat SH, Suseno R, Sujiprihati S. 2007. Response of various tomato genotypes to Begomovirus infection and its improved diagnostic. Hayati J Biosci14:93-97.
Agrios GN. 2005.Plant Pathology.Elsevier Academic Press.723-756 p.
Ala-Poikela M, Svenson E, Rojas A, Horko T, Paulin L, Valkonen JPT, Kvarnheden A. 2005. Genetic diversity and mixed infections of begomoviruses infecting tomato, pepper and cucurbit crops in Nicaragua.
Plant Pathol54:448-4459.
Ambrozevicius LP, Calegario RF, Fontes EPB, Carvalho MG, Zerbini FM. 2002. Genetic diversity of begomovirus infecting tomato and associated weeds in Southeastern Brazil.Fitopatol Brasil27:372-377.
Astier S, Albouy J, Maury Y, Robaglia C, Lecoq H. 2001. Principles of Plant Virology, Genom, Pathogenicity,Virus Ecology. Science Publishers. 390- 395.
Bos L. 1990. Pengantar Virologi Tumbuhan. Gadjah Mada University Press. Yogyakarta. hlm 20-28.
Briddon RW, Robertson I, Markham PG, Stanley J. 2004. Occurrence of Sout African cassava mosaic virus (SACMV) in Zimbabwe. Plant Pathol
53(2):233-234.
Clavarie JM, Notradame J. 2003. Bioinformatics for Dummies. Wiley Publishing Inc.
Czosnek H, Ber R, Navot N, Zamir D, Antignus Y, Cohen S. 1988. Detection of tomato yellow leaf curl virus in lysates of plants and insects by hybridization with a viral DNA probe.Plant Dis72:949-951.
Doyle JJ, Doyle JL. 1990. Isolation of Plant DNA from Fresh Tissue. Focus
12:13-15.
Fauziah R. 2010. Karakterisasi Beberapa Genotipe Cabai (Capsicum spp.) dan Mekanisme Ketahanannya Terhadap Begomovirus Penyebab Penyakit Daun Keriting Kuning [tesis]. Bogor: Sekolah Pascasarjana, Institut Pertanian Bogor.
Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA. 2005. Virus Taxonomy Classification and Nomenclature of Viruses. Virology Division International Union of Microbiological Societies. London and USA: Elsevier Inc. 309-325 p.
Fermentas. 2006.QuickProtocol™GeneJET™ Plasmid Miniprep Kit. Amersham Pharmacia Biotech.
Glick BR, Pasternak JJ. 1998. Molecular biotechnology: principle and applications of recombinant DNA. 2nd edition.United States of America: American Society for Microbiology.
Gilbertson RL, Faria JC, Ahlquist P, Maxwel DP. 1993. Genetic diversity in geminivirus causing bean mosaic disease.Phytophatology83:709-715. Gilbertson RL, Hidayat SH, Martinez RT, Leong SA, Faria JC, Morales F,
Maxwell DP. 1991. Differentiation of Bean Infecting Geminiviruses by Nucleic Acid Hybridization Probes and Aspects ofBean Golden Mosaicin Brazil.Plant Dis75:336-342.
Ganefianti ED. 2010. Genetik Ketahanan Cabai terhadap Begomovirus Penyebab Penyakit Daun Keriting Kuning dan Arah Pemuliaannya [disertasi]. Bogor: Sekolah Pascasarjana, Institut Pertanian Bogor.
Hidayat SH, Chatchawankanpanich O, Rusli E, Aidawati N. 2006. Begomovirus
associated with pepper yellow leaf curl virus in West Java, Indonesia.
Indon Microbiol11(2):87-89.
Hull R. 2002.Matthews’ Plant Virology. 4thEdition. San Diego: Academic Press. ICTVdB Management. 2006. Begomovirus. In: ICTVdB - The Universal Virus
Database, version 4. Büchen-Osmond, C. (Ed), New York, USA. ColumbiaUniversity.http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/00.02 9.0.03.htm. [28 April 2008].
Kalshoven LGS. 1981.Pests of Crops in Indonesia. Jakarta: PT. Ikhtiar baru Van Hoeve.
Keller GH, Mark MM. 1992. DNA Probes. United States and Canada: Stockon Press. 1-20 p .
Kitamura K, Murayama A, Ikegami M. 2004. Evidence for recombination among isolates of tobacco eaf curl japan virus and honeysuckle yellow vein mosaic virus. Arch Virol149:1221-1229.
Yan L, Bo S, Xifeng W, Chuanlin Z, Guanghe Z. 2007. Three digoxigenin-labeled cDNA probes for specific detection of natural population of Barley yellow
dwarf viruses in China by dot-blot hybridization. Virol Methods 145:22- 29.
Mehta P, Wyman JA, Nakhla MK, Maxwel DP. 1994. Transmission of tomato yellow leaf curl by Bemicia tabaci (Homoptera; Aleyrodidae). Econ Entomol87:1291-1297.
Meliansyah R. 2010. Peranan Gulma Sebagai Inang Alternatif Geminivirus di Pertanaman Cabai di Jawa [tesis]. Bogor: Sekolah Pascasarjana, Institut Pertanian Bogor.
Monci F, Sánchez-Campos S, Navas-Castillo J, Moriones E. 2002. A Natural Recombinant between the Geminiviruses Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus Exhibits a Novel Pathogenic Phenotype and Is Becoming Prevalent in Spanish Populations. Virology
303(2):317-326
Morin S, Ghanim M, Sobol L, Czosnek H. 2000. The GroEL protein of the whiteflyBemisia tabaciinteracts with the coat protein of transmissible begomovirus in the yeast two-hybrid system.Virology276:404-416.
Prasanna HC, Rai M. 2007. Detection and frequency of recombination in tomato- infecting begomoviruses of South and Southeast Asia.Virology4:111 Pico B. 1999. Improved diagnostic technique for tomato yellow leaf curl virus in
tomato breeding programs.Plant Dis74:248-250.
Polston JE, Anderson PK. 1997. The emergence of whitefly-transmitted geminiviruses in tomato in Western Hemisphere.Plant Dis81:1358-1369. Potter JL, Nakhla MK, Mejia L, Maxwell DP. 2003. PCR and DNA hybridization
methods for specific detection of bean-infecting begomoviruses in the America and Caribbean.Plant Dis87:1205-1212.
Promega. 2007. Technical Manual pGEM-T and pGEM-T Easy Vector Systems. Instruction for Use of Products A1360, A1380, A3600 and A3610. USA: Promega Coorporation.
Qiagen. 2002. QIAquick ® Spin Handbook For QiAquick PCR Purification Kit QIAquick Nucleotide Removal Kit QIAquick Gel Extraction Kit..
QIAGEN. GmbH, Germany.
Roberts IM, Robinson DJ, Harrison BD. 1984. Serological relationship and genome homologies among geminiviruses.Ann App Biol105:483-493. Rohde, C. 1994. Plasmid isolation from bacteria: some fast procedures. Technical
Rojas MR, Gilbertson RL, Russel DR, Maxwell DP. 1993. Use of Degenerate Primers in the Polymerase Chain Reaction to Detect Whitefly-Transmitted Geminiviruses.Plant Dis77:340-347.
Rom M, Antignus Y, Gidoni D, Pilowsky M, Cohen. 1993. Accumulation of tomato yellow leaf curl virus DNA in tolerant and susceptible tomato lines.Plant Dis77:253-257.
Rubio L, Herrero JR, Sarrio J, Guerri J. 2003. A new approach to evaluate relative resistance and tolerance tomato cultivars to geminiviruses causing the tomato yellow leaf curl virus disease in Spain.Plant Pathol52:763-769. Santoso TJ. 2008. Identifikasi Begomovirus Indonesia pada Tomat dan Analisis
Deiverssitas Genetik GenAV1serta Pemanfaatannya untuk Pengembangan Tanaman Tahan Virus [disertasi]. Bogor: Sekolah Pascasarjana, Institut Pertanian Bogor.
Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning a Laboratory Manual. Ed ke-2. New York: Cold Springer Harbor Laboratory Press. Saunders GC, Parkes HC. 1999. Analytical Molecular Biology: Quality and
Validation.The Royal Society of Chemistry. Cambridge, UK.
Sudiono. 2001. Deteksi dan identifikasi virus gemini pada tanaman tomat [tesis]. Bogor: Program Pascasarjana, Institut Pertanian Bogor.
Sudiono, Hidayat SH, Suseno R, Sosromarsono S. 2004. Penggunaan teknik PCR dan RFLP untuk deteksi dan analisis virus gemini pada tanaman tomat yang berasal dari berbagai daerah di Jawa Barat dan Lampung. HPT- Tropika4:89-93.
Suharsono, Widyastuti U. 2006. Penuntun Praktikum Pelatihan Teknik Dasar Pengklonan Gen. Bogor: Pusat Penelitian Sumberdaya Hayati dan Bioteknologi (PPSHB), Institut Pertanian Bogor.
Sulandari S, Suseno R, Hidayat SH, Harjosudarmo J, Sosromarsono S. 2006. Deteksi dan kajian kisaran inang penyebab penyakit daun keriting kuning cabai.Hayati13(1):1-6.
Trisno J. 2010. Keanekaragaman Virus dan Peranan Rhizobakteria Indigenus dari Geografis Berbeda dalam Mempengaruhi Perkembangan Penyakit Daun Kuning Keriting Cabai (Capsicum annuum L.) [disertasi]. Padang: Program Pascasarjana, Universitas Andalas.
Van Regenmortel MHV, Faquet CM, Bishop DHL, Carstens E, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Priangle CR, Wickner RB. 2000. Virus Taxonomy Classification and Nomenclature of Viruses.
Seventh Report of The International Committee on Taxonomy of Viruses. San Diego: Academic Press.
Voyles BA. 2002.The Biology of Viruses. 2ndedition. Boston: McGraw Hill. Zhou YC, Noussourou M, Kon T, Rojas MR, Jiang H, Chen LF, Gamby K, Foster
R, Gilbertson RL. 2008. Evidence of local evolution of tomato-infecting begomovirus species in West Africa: characterization of tomato leaf curl Mali virus and tomato yellow leaf crumple virus from Mali. Arch Virol
Lampiran 1 Hasil pengurutan nukleotida gen protein selubungBegomovirushasil amplifikasi PCR
1 ATATTTTATA AGACGAAGCG ACCCGCCGAT TTGGTCATTT CCACTCCCGC CTCGAAGGTA CGTCGCCGTC TGAACTTCGA CACCCCCGCG ATGAGCCGTG
101 CTGCTGCCCC CACTGTCCTC GTCACCAACA GAAGAAGGTC ATGGACCAAC AGGCCCATGT ACCGCAAGCC CAGACTATAC AGAATGTACA GAACCCCTGA
201 TGTACCCAAA GGTTGTGAAG GCCCATGTAA AGTCCAATCG TATGAACAGA GGCACGACAT ATCCCATGTA GGTAAAGTAT TATGTGTTAG TGATGTCACC
301 CGTGGTAATG GGCTTACCCA TCGTGTTGGT AAGAGATTCT GTGTGAAGTC CGTTTATGTA TTGGGTAAAA TATGGATGGA TGAAAATATT AAAACCAAGA
401 ACCATACAAA CACTGTGATG TTTTATCTTG TTCGTGACAG AAGGCCCTTT GGTAGTGCTA TGGATTTTGG ACAGGTGTTT AACATGTATG ATAATGAGCC
501 CAGTACTGCT ACTATCAAGA ACGATCTTCG AGAATCGTTA TCAAGTTTTA AGAAAATTCA CTTCAACAGT CCACAGGTGG TCAATATGCT TCCAAAGGAA
601 CAGTCGTTGG GTCAGGAAAA TTTATGAAGA TTAATAATTA TGTAGTTTAT AATCATCAAG AAGCTGCTAA GTATTGACAA TCATACTGAG AATGCCTTGT
701 TATTGTATAT TGGCTTGTAC TCATGCCAGT AATCCAGTGT ATGCTAACCT TTGAAGATCA GAATCTATTT CTATGATTCT GTCCAAAATA GAAAAATACG
Lampiran 2 Hasil perunutan nukleotida gen protein selubung rekombinan
Begomovirus isolat Ngluwar A
1 TAATTCTAGA TGTCGAAGCG ACCCGCCGAT ATAGTCATTT CCACTCCCGC CTCGAAGGTA CGTCGCCGTC TGAACTTCGA CACCCCCGCG ATGAGCCGTG
101 CTGCTGCCCC CACTGTCCTC GTCACCAACA GAAGAAGGTC ATGGACCAAC AGGCCCATGT ACCGCAAGCC CAGACTATAC AGAATGTACA GAACCCCTGA
201 TGTACCCAAA GGTTGTGAAG GCCCATGTAA AGTCCAATCG TATGAACAGA GGCACGACAT ATCCCATGTA GGTAAAGTAT TATGTGTTAG TGATGTCACC
301 CGTGGTAATG GGCTTACCCA TCGTGTTGGT AAGAGATTCT GTGTGAAGTC CGTTTATGTA TTGGGTAAAA TATGGATGGA TGAAAATATT AAAACCAAGA
401 ACCATACAAA CACTGTGATG TTTTATCTTG TTCGTGACAG AAGGCCCTTT GGTAGTGCTA TGGATTTTGG ACAGGTGTTT AACATGTATG ATAATGAGCC
501 CAGTACTGCT ACTATCAAGA ACGATCTTCG AGAATCGTTA TCAAGTTTTA AGAAAATTCA CTTCAACAGT CCACAGGTGG TCAATATGCT TCCAAAGGAA
601 CAGTCGTTGG GTCAGGAAAA TTTATGAAGA TTAATAATTA TGTAGTTTAT AATCATCAAG AAGCTGCTAA GTATTGACAA TCATACTGAA AATGCCTTGT
701 TATTGTATAT TGGGTTGTAC TCATGCCAGT AATCCCGTGT ATGCTTACTT TTGAAGATCA GAATCTATTT CTATGATTCT GTTCAAAATT AAGAATTCGG
Lampiran 3 Hasil perunutan nukleotida gen protein selubung rekombinan
Begomovirus isolat Ngluwar B
1 TAATTCTAGA TGTCGAAGCG ACCCGCCGAT ATAGTCATTT CCACTCCCGC CTCGAAGGTA CGTCGCCGTC TGAACTTCGA CACCCCCGCG ATGAGCCGTG
101 CTGCTGCCCC CACTGTCCTC GTCACCAACA GAAGAAGGTC ATGGACCAAC AGGCCCATGT ACCGCAAGCC CAGACTATAC AGAATGTACA GAACCCCTGA
201 TGTACCCAAA GGTTGTGAAG GCCCATGTAA AGTCCAATCG TATGAACAGA GGCACGACAT ATCCCATGTA GGTAAAGTAT TATGTGTTAG TGATGTCACC
301 CGTGGTAATG GGCTTACCCA TCGTGTTGGT AAGAGATTCT GTGTGAAGTC CGTTTATGTA TTGGGTAAAA TATGGATGGA TGAAAATATT AAAACCAAGA
401 ACCATACAAA CACTGTGATG TTTTATCTTG TTCGTGACAG AAGGCCCTTT GGTAGTGCTA TGGATTTTGG ACAGGTGTTT AACATGTATG ATAATGAGCC
501 CAGTACTGCT ACTATCAAGA ACGATCTTCG AGAATCGTTA TCAAGTTTTA AGAAAATTCA CTTCAACAGT CCACAGGTGG TCAATATGCT TCCAAAGGAA
601 CAGTCGTTGG GTCAGGAAAA TTTATGAAGA TTAATAATTA TGTAGTTTAT AATCATCAAG AAGCTGCTAA GTATTGACAA TCATACTGAA AATGCCTTGT
701 TATTGTATAT TGGGTTGTAC TCATGCCAGT AATCCCGTGT ATGCTTACTT TTGAAGATCA GAATCTATTT CTATGATTCT GTTCAAAATT AAGAATTCGG
Lampiran 4 Hasil penyejajaran dan kladogram terhadap ketiga sekuen gen protein selubungBegomovirus: rekombinan isolat Ngluwar A (A) dan
rekombinan isolat Ngluwar B (B) dan hasil amplifikasi PCR (C)
A TAATTCTAGATGTCGAAGCGACCCGCCGATATAGTCATTTCCACTCCCGCCTCGAAGGTA 60 B TAATTCTAGATGTCGAAGCGACCCGCCGATATAGTCATTTCCACTCCCGCCTCGAAGGTA 60 C ATATTTTATAAGACGAAGCGACCCGCCGATTTGGTCATTTCCACTCCCGCCTCGAAGGTA 60 *** ** * * ***************** * *************************** A CGTCGCCGTCTGAACTTCGACACCCCCGCGATGAGCCGTGCTGCTGCCCCCACTGTCCTC 120 B CGTCGCCGTCTGAACTTCGACACCCCCGCGATGAGCCGTGCTGCTGCCCCCACTGTCCTC 120 C CGTCGCCGTCTGAACTTCGACACCCCCGCGATGAGCCGTGCTGCTGCCCCCACTGTCCTC 120 ************************************************************ A GTCACCAACAGAAGAAGGTCATGGACCAACAGGCCCATGTACCGCAAGCCCAGACTATAC 180 B GTCACCAACAGAAGAAGGTCATGGACCAACAGGCCCATGTACCGCAAGCCCAGACTATAC 180 C GTCACCAACAGAAGAAGGTCATGGACCAACAGGCCCATGTACCGCAAGCCCAGACTATAC 180 ************************************************************ A AGAATGTACAGAACCCCTGATGTACCCAAAGGTTGTGAAGGCCCATGTAAAGTCCAATCG 240 B AGAATGTACAGAACCCCTGATGTACCCAAAGGTTGTGAAGGCCCATGTAAAGTCCAATCG 240 C AGAATGTACAGAACCCCTGATGTACCCAAAGGTTGTGAAGGCCCATGTAAAGTCCAATCG 240 ************************************************************ A TATGAACAGAGGCACGACATATCCCATGTAGGTAAAGTATTATGTGTTAGTGATGTCACC 300 B TATGAACAGAGGCACGACATATCCCATGTAGGTAAAGTATTATGTGTTAGTGATGTCACC 300 C TATGAACAGAGGCACGACATATCCCATGTAGGTAAAGTATTATGTGTTAGTGATGTCACC 300 ************************************************************ A CGTGGTAATGGGCTTACCCATCGTGTTGGTAAGAGATTCTGTGTGAAGTCCGTTTATGTA 360 B CGTGGTAATGGGCTTACCCATCGTGTTGGTAAGAGATTCTGTGTGAAGTCCGTTTATGTA 360 C CGTGGTAATGGGCTTACCCATCGTGTTGGTAAGAGATTCTGTGTGAAGTCCGTTTATGTA 360 ************************************************************ A TTGGGTAAAATATGGATGGATGAAAATATTAAAACCAAGAACCATACAAACACTGTGATG 420 B TTGGGTAAAATATGGATGGATGAAAATATTAAAACCAAGAACCATACAAACACTGTGATG 420 C TTGGGTAAAATATGGATGGATGAAAATATTAAAACCAAGAACCATACAAACACTGTGATG 420 ************************************************************
A TTTTATCTTGTTCGTGACAGAAGGCCCTTTGGTAGTGCTATGGATTTTGGACAGGTGTTT 480 B TTTTATCTTGTTCGTGACAGAAGGCCCTTTGGTAGTGCTATGGATTTTGGACAGGTGTTT 480 C TTTTATCTTGTTCGTGACAGAAGGCCCTTTGGTAGTGCTATGGATTTTGGACAGGTGTTT 480 ************************************************************ A AACATGTATGATAATGAGCCCAGTACTGCTACTATCAAGAACGATCTTCGAGAATCGTTA 540 B AACATGTATGATAATGAGCCCAGTACTGCTACTATCAAGAACGATCTTCGAGAATCGTTA 540 C AACATGTATGATAATGAGCCCAGTACTGCTACTATCAAGAACGATCTTCGAGAATCGTTA 540 ************************************************************ A TCAAGTTTTAAGAAAATTCACTTCAACAGTCCACAGGTGGTCAATATGCTTCCAAAGGAA 600 B TCAAGTTTTAAGAAAATTCACTTCAACAGTCCACAGGTGGTCAATATGCTTCCAAAGGAA 600 C TCAAGTTTTAAGAAAATTCACTTCAACAGTCCACAGGTGGTCAATATGCTTCCAAAGGAA 600 ************************************************************ A CAGTCGTTGGGTCAGGAAAATTTATGAAGATTAATAATTATGTAGTTTATAATCATCAAG 660 B CAGTCGTTGGGTCAGGAAAATTTATGAAGATTAATAATTATGTAGTTTATAATCATCAAG 660 C CAGTCGTTGGGTCAGGAAAATTTATGAAGATTAATAATTATGTAGTTTATAATCATCAAG 660 ************************************************************ A AAGCTGCTAAGTATTGACAATCATACTGAAAATGCCTTGTTATTGTATATTGGGTTGTAC 720 B AAGCTGCTAAGTATTGACAATCATACTGAAAATGCCTTGTTATTGTATATTGGGTTGTAC 720 C AAGCTGCTAAGTATTGACAATCATACTGAGAATGCCTTGTTATTGTATATTGGCTTGTAC 720 ***************************** *********************** ****** A TCATGCCAGTAATCCCGTGTATGCTTACTTTTGAAGATCAGAATCTATTTCTATGATTCT 780 B TCATGCCAGTAATCCCGTGTATGCTTACTTTTGAAGATCAGAATCTATTTCTATGATTCT 780 C TCATGCCAGTAATCCAGTGTATGCTAACCTTTGAAGATCAGAATCTATTTCTATGATTCT 780 *************** ********* ** ******************************* A GTTCAAAATTAAGAATTCGGCC---- 802 B GTTCAAAATTAAGAATTCGGCC---- 802 C GTCCAAAATAGAAAAATACGCGGGCA 806 ** ****** * ** * **