Perakitan Genom Kloroplas Keruing (Dipterocarpus cinereus Slooten) menggunakan Teknologi Long-Read Sequencing MinION Oxford Nanopore

Abstract

Dipterocarpus cinereus merupakan spesies endemik Pulau Mursala, Sumatera Utara, yang sempat dinyatakan punah di alam liar dan kini berstatus kritis. Ketersediaan data genomik menjadi penting untuk mendukung upaya konservasi dan pemuliaan. Penelitian ini bertujuan menganalisis genom kloroplas D. cinereus berbasis teknologi long-read sequencing MinION Oxford Nanopore serta mengkaji hubungan kekerabatannya melalui analisis filogenetik. Sampel berupa daun muda diekstraksi dengan metode CTAB, dilanjutkan uji kualitas dan kuantitas DNA, sekuensing, perakitan genom, anotasi gen, serta rekonstruksi filogenetik. Hasil penelitian menunjukkan genom kloroplas D. cinereus memiliki panjang 154.987 bp dengan struktur kuadripartit lengkap, berhasil dirakit menjadi 7 contig, serta mengandung 134 gen yang terdiri atas 91 gen protein-coding, 35 gen tRNA, dan 8 gen rRNA. Analisis filogenetik menunjukkan bahwa D. cinereus memiliki kekerabatan terdekat dengan D. alatus sebagai sister group dengan nilai bootstrap 100% dan branch length sebesar 0,0012.

Dipterocarpus cinereus is an endemic species of Mursala Island, North Sumatra, that was once declared extinct in the wild and is currently classified as critically endangered. The availability of genomic data is important to support conservation and breeding efforts. This study aimed to analyze the chloroplast genome of D. cinereus using MinION Oxford Nanopore long-read sequencing technology and to examine its phylogenetic relationship through phylogenetic analysis. Young leaf samples were extracted using the CTAB method, followed by DNA quality and quantity assessment, sequencing, genome assembly, gene annotation, and phylogenetic reconstruction. The results showed that the chloroplast genome of D. cinereus has a length of 154,987 bp with a complete quadripartite structure, was successfully assembled into 7 contigs, and contains 134 genes consisting of 91 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that D. cinereus is most closely related to Dipterocarpus alatus as a sister group, with a bootstrap value of 100% and a branch length of 0.0012.