HUBUNGAN KEKERABATAN CUCUMBER GREEN MOTTLE MOSAIC VIRUS (CGMMV) BERDASARKAN KESAMAAN SEKUEN COAT PROTEIN GENE MENGGUNAKAN BIOINFORMATIKA

Bioinformatika merupakan salah satu cabang ilmu pengetahuan yang menerapkan teknologi informasi untuk mengolah dan menganalisis data-data biologi berupa sekuen nukleotida, protein maupun database lainnya. Pada penelitian ini, bioinformatika digunakan dalam menganalisis sekuen nukleotida coat protein (cp) gene pada berbagai isolat Cucumber green mottle mosaic virus (CGMMV). CGMMV adalah salah satu virus anggota genus Tobamovirus yang dapat menginfeksi tanaman anggota famili Cucurbitaceae. Tujuan penelitian ini adalah untuk mengetahui hubungan kekerabatan cp gene antara berbagai isolat CGMMV tersebut menggunakan bioinformatika. Penelitian ini menggunakan metode browsing pada GenBank dalam situs National Center for Biotechnology Information (NCBI) dan analisis data menggunakan software BLAST dalam situs DNA Data Bank of Japan (DDBJ), serta Align dan ClustalW dalam situs European Bioinformatics Institute (EBI) secara online. Data biologi yang dianalisis adalah sekuen nukleotida cp gene dari 13 isolat CGMMV dan satu isolat Kyuri green mottle mosaic virus (KGMMV) sebagai outgroup. Hasil analisis data menunjukkan bahwa dua pasang isolat CGMMV, yaitu CGMMV- Zucchini dan CGMMV-China serta CGMMV-LHP dan CGMMV-NS, memiliki indeks similaritas tertinggi (100%). Sedangkan indeks similaritas terendah (90.9%) dimiliki oleh pasangan isolat CGMMV-Rajasthan dan CGMMV-GR5. Berdasarkan indeks similaritas tersebut, diperoleh hubungan kekerabatan antara 13 isolat CGMMV yang dapat dikelompokkan menjadi tiga grup, yaitu grup Asia Timur, Asia Selatan dan Eropa

Hubungan Kekerabatan Cucumber Green Mottle Mosaic Virus (CGMMV) Berdasarkan Kesamaan Sekuen Coat Protein Gene Menggunakan Bioinformatika

Bioinformatics is science that applies information technology to manage and analyze biological data, such as sequences of nucleotide, protein or other database. Bioinformatics data could be used to find out the similarity or genetic relationships and protein structure of an organism. In this research, bioinformatics was applied to analyze nucleotide sequences of coat protein (CP) gene among 13 isolate of Cucumber green mosaic viruses (CGMMV). CGMMV is virus belongs to the genus Tobamovirus that infects the plants belong to family Cucurbitaceae. Each isolate of CGMMV has a conserved CP gene with different nucleotide sequence. The purposes of this research was to find the genetic relationships among 13 isolates of CGMMV based on CP gene using bioinformatics. Data were acquired by browsing to GeneBank on National Center for Biotechnology Information (NCBI)site. Nucleotide sequences of CP gene from 13 isolates of CGMMV and one isolate of Kyuri green mottle mosaic virus (KGMMV) as aoutgroup were analyzed by BLAST software on DNA Data Bank of Japan (DDBJ) site, and align by ClustalW software on European Bioniformatics Institute (EBI) site. Results of data analysis showed that two pairs of CGMMV isolates, that is CGMMV-Zucchini with CGMMV-China and CGMMV-LPH with CGMMV-NS have the highest similarity index (100%). However, the lowest similarity index (90,9%) was found between CGMMV-Rajasthan and CGMMV-GRS. Accoring to the similarity index, genetic relationship among 13 isolates of CGMMV coul be devided into three groups, that is East Asia, South Asia and Europe groups

HUBUNGAN KEKERABATAN CUCUMBER GREEN MOTTLE MOSAIC VIRUS (CGMMV) BERDASARKAN KESAMAAN SEKUEN COAT PROTEIN GENE MENGGUNAKAN BIOINFORMATIKA

Bioinformatika merupakan salah satu cabang ilmu pengetahuan yang menerapkan teknologi informasi untuk mengolah dan menganalisis data-data biologi berupa sekuen nukleotida, protein maupun database lainnya. Pada penelitian ini, bioinformatika digunakan dalam menganalisis sekuen nukleotida coat protein (cp) gene pada berbagai isolat Cucumber green mottle mosaic virus (CGMMV). CGMMV adalah salah satu virus anggota genus Tobamovirus yang dapat menginfeksi tanaman anggota famili Cucurbitaceae. Tujuan penelitian ini adalah untuk mengetahui hubungan kekerabatan cp gene antara berbagai isolat CGMMV tersebut menggunakan bioinformatika. Penelitian ini menggunakan metode browsing pada GenBank dalam situs National Center for Biotechnology Information (NCBI) dan analisis data menggunakan software BLAST dalam situs DNA Data Bank of Japan (DDBJ), serta Align dan ClustalW dalam situs European Bioinformatics Institute (EBI) secara online. Data biologi yang dianalisis adalah sekuen nukleotida cp gene dari 13 isolat CGMMV dan satu isolat Kyuri green mottle mosaic virus (KGMMV) sebagai outgroup. Hasil analisis data menunjukkan bahwa dua pasang isolat CGMMV, yaitu CGMMV- Zucchini dan CGMMV-China serta CGMMV-LHP dan CGMMV-NS, memiliki indeks similaritas tertinggi (100%). Sedangkan indeks similaritas terendah (90.9%) dimiliki oleh pasangan isolat CGMMV-Rajasthan dan CGMMV-GR5. Berdasarkan indeks similaritas tersebut, diperoleh hubungan kekerabatan antara 13 isolat CGMMV yang dapat dikelompokkan menjadi tiga grup, yaitu grup Asia Timur, Asia Selatan dan Eropa.</p

HUBUNGAN KEKERABATAN CUCUMBER GREEN MOTTLE MOSAIC VIRUS ( CGMMV) BERDASARKAN KESAMAAN SEKUEN COAT PROTEIN GENE MENGGUNAKAN BIOINFORMATIKA

Bioinformatika merupakan salah satu cabang ilmu pengetahuan yang menerapkan teknologi informasi untuk mengolah dan menganalisis data-data biologi berupa sekuen nukleotida, protein maupun database lainnya. Pada penelitian ini, bioinformatika digunakan dalam menganalisis sekuen nukleotida coat protein (cp) gene pada berbagai isolat Cucumber green mottle mosaic virus (CGMMV). CGMMV adalah salah satu virus anggota genus Tobamovirus yang dapat menginfeksi tanaman anggota famili Cucurbitaceae. Tujuan penelitian ini adalah untuk mengetahui hubungan kekerabatan cp gene antara berbagai isolat CGMMV tersebut menggunakan bioinformatika. Penelitian ini menggunakan metode browsing pada GenBank dalam situs National Center for Biotechnology Information (NCBI) dan analisis data menggunakan software BLAST dalam situs DNA Data Bank of Japan (DDBJ), serta Align dan ClustalW dalam situs European Bioinformatics Institute (EBI) secara online. Data biologi yang dianalisis adalah sekuen nukleotida cp gene dari 13 isolat CGMMV dan satu isolat Kyuri green mottle mosaic virus (KGMMV) sebagai outgroup. Hasil analisis data menunjukkan bahwa dua pasang isolat CGMMV, yaitu CGMMV-Zucchini dan CGMMV-China serta CGMMV-LHP dan CGMMV-NS, memiliki indeks similaritas tertinggi (100%). Sedangkan indeks similaritas terendah (90.9%) dimiliki oleh pasangan isolat CGMMV- Rajasthan dan CGMMV-GR5. Berdasarkan indeks similaritas tersebut, diperoleh hubungan kekerabatan antara 13 isolat CGMMV yang dapat dikelompokkan menjadi tiga grup, yaitu grup Asia Timur, Asia Selatan dan Eropa.</p

KARAKTERISASI MOLEKULAR COAT PROTEIN GENE PAPAYA RINGSPOT VIRUS PADA TANAMAN PEPAYA (Carica papaya L.) DI INDONESIA

Papaya ringspot virus (PRSV), the member of Potyvirus, is commonly occurred on papaya plants (Carica papaya L.) and caused a serious damage and significant loss in papaya crops troughout the world. These symptoms are mosaic and mottle on leaves, stunted growth, leaf and fruit deformation, and also dark green ringspots on fruits. To date, there is no report about the occurrences of PRSV infecting papaya in Indonesia, but surveys on several papaya fields in The Province of Yogyakarta and Central Java Indonesia during 2011 � 2013 showed the similar symptoms that caused by PRSV. The objective of this research were to find out the occurrences of PRSV infecting papaya in Indonesia and to characterize its coat protein (CP) gene on molecular level. Survey and collecting samples randomly conducted in several papaya fields in Sleman, Bantul, Gunungkidul and Kulonprogo Yogyakarta, and also in Kebumen, Boyolali and Magelang Central Java. Result of serological test by DAS-ELISA indicated that 18 symptomic papaya leaf samples was positive PRSV-infected. Virus particles observation using TEM showed flexuous filament structure of PRSV. Host range analysis with mechanical inoculation showed common symptoms, such as mosaic, necrosis and leaf distortion on Carica papaya and Cucumis melo, and also necrotic local lesion on Chenopodium amaranticolor 6 � 8 weeks after inoculation. Detection of the CP gene of PRSV by RT-PCR revealed + 449 bp in length of DNA fragment on agarose gel electrophoresis. Molecular characterization of partial sequences of the CP gene showed percent identities of 49,51 � 53,92% for PRSV-Kebumen1 and 51,26 � 56,78% for PRSV-Kebumen2. Based on phylogeny tree, its phylogenetic relationship are far enough from other PRSV isolates. Hence, we concluded that the new Indonesia PRSV isolates have evolved by a series of nucleotides mutation

Characterization of a novel virus infected watermelon in Indonesia based on viral particle using electron microscope

Most of the cucurbits diseases in Indonesia are caused by plant viruses. Tobamovirus is one of the viral genera recently infected cucurbits. The members of cucurbits-infecting Tobamovirus are Cucumber green mottle mosaic virus (CGMMV), Kyuri green mottle mosaic virus (KGMMV), Cucumber fruit mottle mosaic virus (CFMMV), Zucchini green mottle mosaic virus (ZGMMV), and Cucumber mottle virus (CuMoV). A research on the occurrence of cucurbits-infecting Tobamovirus in Indonesia was carried out in 2011. Based on the result, a new characteristic of viral particle were found in watermelon. The viral particle was previously identified as CGMMV based on electron microscope investigation revealed presence of rod-shaped and not enveloped virions. The virions were straight about 300 nm long and 28–30 nm in diameter. However, in some electron micrograph shows rare characteristic of the viral particle. The viral particles could joint each other to bend a new form. Two viral particles were able to joint and formed an angle. Moreover, some of viral particles could joint and form a longer viral particle (800-1100 nm), two to four times longer than CGMMV particle, but the both diameter of the virus are similar. These characteristics indicate that the viral particle is a novel virus, different from CGMMV or other Tobamovirus members