Analisis Empat Sekuen Barkode DNA Pada Pandan (Benstonea sp.) Asal Danau Kajuik, Riau
Abstract
Barkode DNA merupakan sekuen DNA berukuran pendek yang digunakan untuk identifikasi organisme secara molekuler. Penelitian bertujuan menganalisis empat barkode DNA pada tumbuhan pandan (Benstonea sp.) asal Danau Kajuik, Riau. Metode meliputi isolasi DNA, PCR, elektroforesis, purifikasi, sekuesing, serta analisis bioinformatika. Pada penelitian ini telah diperoleh sekuen DNA untuk atpB-rbcL IGS, trnV-ndhC IGS, ndhF-rpl32 IGS, dan trnQ-5’rps16 IGS sepanjang 812 pb, 924 pb, 952 pb, dan 886 pb, secara berturut-turut. Aksesi yang muncul paling atas pada analisis BLASTn pada keempat sekuen tersebut tidak ada yang memiliki kemiripan 100% dengan Benstonea sp. asal Danau Kajuik, Riau. Walaupun nilai query cover tinggi (93–100%) dan E-value sebesar 0,00. Pada keempat barkode DNA yang diteliti, terdapat beberapa perbedaan nukleotida yang disebabkan oleh mutasi insersi-delesi (indel) (6,99%) maupun subtitusi (4,96%). Mutasi indel paling banyak dijumpai pada sekuen trnV-ndhC IGS dan mutasi subtitusi paling banyak terjadi pada sekuen ndhF-rpl32 IGS. Nukleotida kritis yang menjadi penciri bagi Benstonea sp. asal Danau Kajuik, Riau, dijumpai pada sekuen ndhF-rpl32 IGS dan trnQ-5’rps16 IGS. Simpulan, dua sekuen DNA yaitu ndhF-rpl32 IGS dan trnQ-5’rps16 IGS berpotensi menjadi barkode DNA untuk identifikasi tumbuhan ini secara molekuler. Ketersediaan barkode DNA pada database publik sangat diperlukan untuk menunjang identifikasi organisme secara molekuler.
Abstract
DNA barcode is a piece of short DNA that is developed for molecular identification of organisms. This study aims to analyze four DNA barcodes in pandan plant (Benstonea sp.) from Kajuik Lake, Riau. Methods included DNA extraction, PCR, electrophoresis, purification, sequencing, and bioinformatics analysis. The DNA sequences of atpB-rbcL IGS, trnV-ndhC IGS, ndhF-rpl32 IGS, and trnQ-5’rps16 IGS have been obtained with the length of 812 pb, 924 pb, 952 pb, and 886 pb, respectively. The top accession in BLASTn analysis results showed that there was no accession that had 100% similarity to Benstonea sp. from Kajuik Lake, Riau even though the query cover high (93–100%) and E-value of 0,00. There were some nucleotide variations caused by insertion-deletion (indel) mutation (6,99%) and subtitution (4,96%). Indel was most occur in trnV-ndhC IGS and subtitution in ndhF-rpl32 IGS. Critical nucleotides that were be a characteristic for Benstonea sp. from Kajuik Lake, Riau were seen in ndhF-rpl32 IGS and trnQ-5’rps16 IGS. Conclusion, both of ndhF-rpl32 IGS and trnQ-5’rps16 IGS are potentially as DNA barcodes for molecular identification of this plant. The avaibility of the DNA barcodes is very important to support of organisms molecular identifications.
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DOI: https://doi.org/10.15408/kauniyah.v16i1.21697 Abstract - 0 PDF - 0
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