IDENTIFIKASI MOLEKULER JERUK NIPIS TEGAL BERDASARKAN FRAGMEN GEN 18S RIBOSOMAL RNA
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Abstract
egal’s lime is a lime that grows in the coastal areas with high salinity, and research on the molecular identification of Tegal’s lime has never been done before. This study aims to determine the molecular identity and its phylogenetic relationship with other oranges in GenBank. DNA isolation was carried out using CTAB. The best DNA purity was 1.883 while the highest DNA concentration was 464.83 ng/?L. DNA amplification was carried out using the PCR method which consisted of denaturation, annealing, and extension steps. DNA was electrophoresed with agarose gel. The DNA band size was 572 bp. The fraqment of 18S rRNA of Tegal’s lime has a greatest similarity of 99,64% with Citrus sinensis, while based on phylogenetic tree it has a closest relationship with C. aurantium (bootstrap value 33%). The alignment of Tegal’s lime against the C. aurantium sample showed that there were 2 gaps and 4 base changes, while the alignment with other oranges and C. medica as an ancestral showed that there were transition and transversion at the 130th and 560th nucleotide respectively.
Jeruk nipis Tegal merupakan jeruk nipis yang tumbuh pada daerah pesisir yang memiliki salinitas cukup tinggi dan penelitian tentang identitas jeruk nipis Tegal masih belum pernah dilakukan sebelumnya. Oleh karena itu, penelitian ini bertujuan untuk mengetahui identitas jeruk nipis Tegal secara molekuler dan mengetahui hubungan kekerabatannya dengan jeruk lainnya pada GenBank. Isolasi DNA dilakukan dengan menggunakan CTAB. Kemurnian DNA terbaik yaitu 1,883 sedangkan konsentrasi DNA tertinggi adalah 464,83 ng/?L. Amplifikasi DNA dilakukan dengan menggunakan metode PCR yang terdiri dari tahap denaturasi, anealing, dan ekstensi. DNA dianalisis menggunakan elektroforesis gel agarosa. Ukuran pita DNA yang didapatkan yaitu 572 pb. Fragmen gen 18S rRNA jeruk nipis Tegal memiliki kesamaan yang paling tinggi dengan Citrus sinensis sebesar 99,64% sedangkan berdasarkan analisis filogenetik, memiliki hubungan kekerabatan yang paling dekat dengan C. aurantium (nilai bootstrap sebesar 33%). Hasil pensejajaran jeruk nipis Tegal terhadap sampel C. aurantium menunjukkan adanya 2 gap dan 4 perubahan basa sedangkan pensejajaran yang dilakukan antara jeruk nipis Tegal dengan jeruk lain dan jeruk nenek moyang C. medica menunjukkan adanya 1 transisi pada basa ke-130 dan 1 transversi pada basa ke-560.
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