Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar
Theobroma cacao L. is an important Indonesian estate crop, which suffers from biotic and abiotic stresses. TcOSM, which encodes osmotin as a response to pathogens and environmental stresses, is, therefore, a focus of interest in this research, aiming to characterize TcOSM in an Indonesian local caca...
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| Format: | Article |
| Language: | English |
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Universitas Gadjah Mada, Yogyakarta
2020-12-01
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| Series: | Indonesian Journal of Biotechnology |
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| Online Access: | https://jurnal.ugm.ac.id/ijbiotech/article/view/53937 |
| _version_ | 1828041221640028160 |
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| author | Imam Bagus Nugroho Fahrurrozi Fahrurrozi |
| author_facet | Imam Bagus Nugroho Fahrurrozi Fahrurrozi |
| author_sort | Imam Bagus Nugroho |
| collection | DOAJ |
| description | Theobroma cacao L. is an important Indonesian estate crop, which suffers from biotic and abiotic stresses. TcOSM, which encodes osmotin as a response to pathogens and environmental stresses, is, therefore, a focus of interest in this research, aiming to characterize TcOSM in an Indonesian local cacao cultivar. Bioinformatics queries for putative TcOSM were performed against the reference genome of a Criollo-type cacao cultivar. Based on nucleotide sequence determination, our results revealed two genes, TcOSM1 and TcOSM2, which have the highest similarity (≥ 90\%) to the cacao reference genes. Heterozygosity was detected in the TcOSM1-encoding gene, which contained two overlapping peaks in Sanger-sequencing chromatograms. One of the alleles resulted from a single nucleotide change (G to A), leading to a same-sense mutation that did not substitute corresponding alanine residue. Homology modeling using Phyre2 and structural alignment (superimposition) was conducted to examine the influence of genetic variations in TcOSM sequences upon the global protein structures. The result showed no significant changes (RMSD ≤ 0.206 Å, TM-score > 0.5) in tertiary protein structures. Altogether, this research succeeded in characterizing TcOSM while providing a fundamental study for future cacao biotechnology endeavors. |
| first_indexed | 2024-04-10T17:07:10Z |
| format | Article |
| id | doaj.art-46b10ab331b04a86903b5449d1bcafd0 |
| institution | Directory Open Access Journal |
| issn | 0853-8654 2089-2241 |
| language | English |
| last_indexed | 2024-04-10T17:07:10Z |
| publishDate | 2020-12-01 |
| publisher | Universitas Gadjah Mada, Yogyakarta |
| record_format | Article |
| series | Indonesian Journal of Biotechnology |
| spelling | doaj.art-46b10ab331b04a86903b5449d1bcafd02023-02-06T03:00:10ZengUniversitas Gadjah Mada, YogyakartaIndonesian Journal of Biotechnology0853-86542089-22412020-12-01252849410.22146/ijbiotech.5393728811Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivarImam Bagus Nugroho0Fahrurrozi Fahrurrozi1Indonesian Research Institute for Biotechnology and Bioindustry (IRIBB), Jalan Taman Kencana No 1, Bogor, Jawa Barat 16128, IndonesiaIndonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km. 46, Cibinong, Jawa Barat 16119, IndonesiaTheobroma cacao L. is an important Indonesian estate crop, which suffers from biotic and abiotic stresses. TcOSM, which encodes osmotin as a response to pathogens and environmental stresses, is, therefore, a focus of interest in this research, aiming to characterize TcOSM in an Indonesian local cacao cultivar. Bioinformatics queries for putative TcOSM were performed against the reference genome of a Criollo-type cacao cultivar. Based on nucleotide sequence determination, our results revealed two genes, TcOSM1 and TcOSM2, which have the highest similarity (≥ 90\%) to the cacao reference genes. Heterozygosity was detected in the TcOSM1-encoding gene, which contained two overlapping peaks in Sanger-sequencing chromatograms. One of the alleles resulted from a single nucleotide change (G to A), leading to a same-sense mutation that did not substitute corresponding alanine residue. Homology modeling using Phyre2 and structural alignment (superimposition) was conducted to examine the influence of genetic variations in TcOSM sequences upon the global protein structures. The result showed no significant changes (RMSD ≤ 0.206 Å, TM-score > 0.5) in tertiary protein structures. Altogether, this research succeeded in characterizing TcOSM while providing a fundamental study for future cacao biotechnology endeavors.https://jurnal.ugm.ac.id/ijbiotech/article/view/53937bioinformaticheterozygosityhomology modelinglocal cacao cultivarpathogenesis-related proteins |
| spellingShingle | Imam Bagus Nugroho Fahrurrozi Fahrurrozi Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar Indonesian Journal of Biotechnology bioinformatic heterozygosity homology modeling local cacao cultivar pathogenesis-related proteins |
| title | Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar |
| title_full | Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar |
| title_fullStr | Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar |
| title_full_unstemmed | Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar |
| title_short | Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar |
| title_sort | cloning and in silico analysis revealed a genetic variation in osmotin encoding genes in an indonesian local cacao cultivar |
| topic | bioinformatic heterozygosity homology modeling local cacao cultivar pathogenesis-related proteins |
| url | https://jurnal.ugm.ac.id/ijbiotech/article/view/53937 |
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