Sekuen DNA Parsial Dari Gen GAPDH Pada Sirsak (Annona muricata L.)
Abstract
Abstrak
Gen glyceraldehyde-3-phosphate dehydrogenase (GAPDH) merupakan salah satu gen referensi yang sering bertindak sebagai kontrol internal pada analisis ekspresi gen di beberapa spesies tumbuhan. Penelitian ini bertujuan menganalisis sekuen gen GAPDH parsial pada sirsak (Annona muricata L.). Metode meliputi persiapan sampel tanaman, isolasi DNA total menggunakan Genomic DNA mini kit Plant (Geneaid), amplifikasi gen GAPDH dengan teknik polymerase chain reaction (PCR), elektroforesis pada 1% gel agarose dan analisis data sekuen DNA. Studi ini telah memperoleh sekuen DNA dari gen GAPDH parsial sirsak sepanjang 961 pb. Sekuen tersebut memiliki kemiripan sekitar 68,93–84,35% dengan sekuen mRNA gen GAPDH pada beberapa spesies tumbuhan. Sekuen ini diprediksi terdiri dari 5 ekson dan 4 intron. Total ekson diprediksi terdiri dari 429 pb. Sekuen ini adalah yang pertama kali dilaporkan dari genus Annona dan juga dari famili Annonaceae. Sekuen ini dapat dimanfaatkan untuk analisis ekspresi gen pada sirsak dan dapat menjadi dasar untuk mengisolasi gen GAPDH spesies lain di dalam genus Annona dan famili Annonaceae.
Abstract
GAPDH (glyceraldehyde-3-phosphate dehydrogenase) gene is one of reference genes that is frequently became an internal control in any plant species. This study reports a DNA sequence of parsial GAPDH gene on soursop (Annona muricata L.). Methods included sample preparation, total DNA isolation using Genomic DNA mini kit Plant (Geneaid), amplification of GAPDH gene using PCR (polymerase chain reaction) technique, electrophoresis using 1% agarose gel and data analysis. This study had been obtained the DNA sequence of soursop partial GAPDH gene sizing 961 bp. The sequence had 68.93–84.35% similarity to GAPDH mRNA of some plants species. The soursop partial GAPDH gene was predicted consisting of 5 exons and 4 introns. The total exons length was 429 bp. The sequence is the first reported from Annona genus and also Annonaceae family. The sequence can be used for gene expression in soursop and also can be used to isolate GAPDH gene of other species in Annona genus and Annonaceae family.
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Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acid Research, 25(17), 3389-3402.
Aman, S., Haq, N. U., Ahmed, S., & Shakeel, S. N. (2017). Identifications and validations of reference genes for gene expression data normalization of Chenopodium album. International Journal of Agriculture and Biololgy, 19(4), 761-770.
Basa, B., Solti, A., Sarvari, E., & Tamas, L. (2009). Housekeeping gene selection in poplar plants under Cd-stress: Comparative study for real-time PCR normalisation. Functional Plant Biology, 36(12), 1079-1087.
Bao, W., Qu, Y., Shan, X., & Wan, Y. (2016). Screening and validation of housekeeping genes of the root and cotyledon of Cunninghamia lanceolata under abiotic stresses by using quantitative real-time PCR. International Journal of Molecular Sciences, 17(8), 1198. doi: 10.3390/ijms17081198www.
Coria-Te´llez, A.V., Montalvo-Go´nzalez, E., Yahia, E. M., & Obledo-Va´zquez, E. N. (2018). Annona muricata: A comprehensive review on its traditional medicinal uses, phytochemicals, pharmacological activities, mechanisms of action and toxicity. Arabian Journal of Chemistry, 11(5), 662-691.
Fassler, J., & Cooper, P. (2008). BLAST help. Bethesda (MD): National Center for Biotechnology Information (US).
Gantasala, N. P., Papolu, P. K., Thakur, P. K., Kamaraju, D., Sreevathsa, R., & Rao, U. (2013). Selection and validation of reference genes for quantitative gene expression studies by real-time PCR in eggplant (Solanum melongena L). BMC Research Notes, 6(1), 312.
Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
Hong, S. Y., Seo, P. J., Yang, M. S., Xiang, F., & Park, C. M. (2008). Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. BMC Plant Biology, 8(1), 112. doi:10.1186/1471-2229-8-112.
Hou, F., Li, S., Wang, J., Kang, X., Weng, Y., & Xing, G. (2017). Identification and validation of reference genes for quantitative real-time PCR studies in long yellow daylily, Hemerocallis citrina Borani. PLoS ONE, 12(3), e0174933. doi: 10.1371/journal.pone.0174933.
Koressaar, T., Lepamets, M., Kaplinski, L., Raime, K., Andreson, R., & Remm, M.
(2018). Primer3_masker: Integrating masking of template sequence with primer design software. Bioinformatics, 34(11), 1937-1938.
Kosova, A. A, Khodyreva, S. N., & Lavrik, O. I. (2017). Role of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in DNA repair. Biochemistry, 82(6), 643-654. doi: 10.1134/S0006297917060013.
Kozera, B., & Rapacz, M. (2013). Reference genes in real-time PCR. Journal of Applied Genetics, 54(4), 391-406.
Libault, M., Thibivilliers, S., Bilgin, D. D., Radwan, O., Benitez, M., Clough, S. J., & Stacey, G. (2008). Identification of four soybean reference genes for gene expression normalization. The Plant Genome, 1(1), 44-54.
Lim, C. S., Wardell, S. J. T., Kleffmann, T., & Brown, C. M. (2018). The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Research, 46(9), 4575-4591.
Madden, T. (2013). The NCBI handbook, 2nd edition. Bethesda (MD): National Center for Biotechnology Information (US).
Mafra, V., Kubo, K. S., Alves-Ferreira, M., Ribeiro-Alves, M., Stuart, R. M., Boava, L. P., … Machado, M. A. (2012). Reference genes for accurate transcript normalization in citrus genotypes under different experimental conditions. PLoS ONE, 7(2), e31263. doi: 10.1371/journal.pone.0031263.
Meng, H., Yang, Y., Gao, Z-H., & Wei, J-H. (2019). Selection and validation of reference genes for gene expression studies by RT-PCR in Dalbergia odorifera. Scientific Reports, 9(1), 3341. doi: 10.1038/s41598-019-39088-3.
Moghadamtousi, S. Z., Rouhollahi, E., Karimian, H., Fadaeinasab, M., Firoozinia, M., Abdulla, M. A., & Kadir, H.A. (2015a). The chemopotential effect of Annona muricata leaves against azoxymethane-induced colonic aberrant crypt foci in rats and the apoptotic effect of acetogenin annomuricin E in HT-29 cells: A bioassay-guided approach. PLoS ONE, 10(4), e0122288. doi: 10.1371/journal.pone.0122288.
Moghadamtousi, S. Z., Fadaeinasab, M., Nikzad, S., Mohan, G., Ali, H. M., & Kadir, H. A. (2015b). Annona muricata (Annonaceae): A review of its traditional uses, isolated acetogenins and biological activities. International Journal of Molecular Science, 16(7), 15625-15658; doi:10.3390/ijms160715625.
Niu, X., Qi, J., Zhang, G., Xu, J., Tao, A., Fang, P., & Su, J. (2015). Selection of reliable reference genes for quantitative real-time pcr gene expression analysis in Jute (Corchorus capsularis) under stress treatments. Frontiers in Plant Science, 6, 848. doi: 10.3389/fpls.2015.00848.
Pabuayon, I. M., Yamamoto, N., Trinidad, J. L., Longkumer, T., Raorane, M. L., & Kohli, A. (2016). Reference genes for accurate gene expression analyses across different tissues, developmental stages and genotypes in rice for drought tolerance. Rice, 9(1), 32.
Pickart, C. M., & Eddins, M. J. (2004). Ubiquitin: Structures, functions, mechanisms. Biochimica et Biophysica Acta, 1695(1-3), 55-72.
Pinto, A. C., & de Q. (2005). Taxonomy and Botany. In A. C. Pinto, de Q, M. C. R. Cordeiro, S. R. M. De Andrade, F. R. Ferreira, H. A. de C. Filgueiras, R. E. Alves, & D. I. Kinpara (Eds.), Annona species (pp. 3-16). Southampton, United Kingdom: International Centre Underutilised Crops, University of Southampton.
Roslim, D. I., Azrial., Herman., & Lestari, W. (2018). The GAPDH partial gene of durik-durik (Syzygium sp.) from Riau Province of Indonesia. Journal of Physics: Conference Series, 1116, 052055.
Roslim, D. I., Ashfira., Mutiarawati, D., Rosmeilinda, T. F., Aisyah, N., Herman, & Lestari, W. (2019). Isolation of partial housekeeping genes on tuntun angin (Elaeocarpus floribundus BI). Biosaintifika: Journal of Biology & Biology Education, 11(2), 194-201.
Singh, S., Gupta, M., Pandher, S., Kaur, G., Rathore, P., & Palli, S. R. (2018). Selection of housekeeping genes and demonstration of RNAi in cotton leafhopper, Amrasca biguttula biguttula (Ishida). PLoS ONE, 13(1), e0191116. doi: 10.1371/journal.pone.0191116.
Sirover, M. A. (2011). On the functional diversity of glyceraldehyde-3-phosphate dehydrogenase: biochemical mechanisms and regulatory control. Biochimica et Biophysica Acta. 1810(8), 741-751.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725-2729.
Tang, F., Chu, L., Shu, W., He, X., Wang, L., & Lu, M. (2019). Selection and validation of reference genes for quantitative expression analysis of miRNAs and mRNAs in Poplar. Plant Methods, 15(1), 35. doi: 10.1186/s13007-019-0420-1.
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3 new capabilities and interfaces. Nucleic Acids Research, 40(15), e115.
Wahab, S. M. A., Jantan, I., Haque, M. A., & Arshad, L. (2018). Exploring the leaves of Annona muricata L. as a source of potential anti-inflammatory and anticancer agents. Frontiers in Pharmacology, 9, 661. doi: 10.3389/fphar.2018.00661.
Zhang, D. Q., Du, Q. Z., Xu, B. H., Zhang, Z. Y., & Li, B. L. (2010). The actin multigene family in Populus: Organization, expression and phylogenetic analysis. Molecular Genetics Genomics, 284(2), 105-119.
Zhao, X., Zhang, X., Guo, X., Li, S., Han, L., Song, Z., … & Li, M. (2016). Identification and validation of reference genes for qRT-PCR studies of gene expression in Dioscorea opposite. Biomed Research International, 2016(3089584), 1-13. doi: 10.1155/2016/3089584.
DOI: https://doi.org/10.15408/kauniyah.v13i2.13964 Abstract - 0 PDF - 0
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