Please use this identifier to cite or link to this item:
http://repository.ipb.ac.id/handle/123456789/106947
Title: | Analisis Long-Read Sequences dengan Teknologi MinION Oxford Nanopore pada Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) |
Other Titles: | Long-Read Sequences Analysis with MinION Oxford Nanopore Technology of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) |
Authors: | Siregar, Iskandar Zulkarnaen Pratama, Rahadian Nurfajri, Siska |
Issue Date: | 2021 |
Publisher: | IPB University |
Abstract: | Balsa (O. pyramidale) merupakan salah satu spesies tanaman hutan cepat
tumbuh bernilai ekonomi yang diintroduksi ke Indonesia dengan informasi genetik
yang masih terbatas. Penelitian ini bertujuan untuk menghasilkan data genomik dan
menganalisis hubungan kekerabatan balsa (O. pyramidale) berbasis long-read
sequences dengan teknologi Oxford Nanopore (ONT). Penelitian terdiri dari
beberapa tahapan yaitu ekstraksi DNA, uji kualitas dan kuantitas DNA, proses
sekuensing DNA menggunakan mesin MinION ONT, dan analisis bioinformatik.
Hasil penelitian menunjukkan bahwa proses sekuensing pada balsa (O. pyramidale)
menghasilkan sekuen partial whole genome kloroplas sebesar 155.430 bp yang
dapat digunakan untuk analisis hubungan kekerabatan berbasis DNA barcode pada
genom kloroplas. Analisis filogeni menunjukkan bahwa jenis balsa (O. pyramidale)
secara genetik (multi-genotipe) berada satu clade dengan sesama jenis O.
pyramidale pada setiap penggunaan gen atau marka baik rbcL, matK, maupun
kombinasi gen rbcL dan matK. Jenis gen atau marka yang cocok digunakan dalam
analisis hubungan kekerabatan pada balsa (O. pyramidale) dapat menggunakan
matK dan kombinasi rbcL dan matK. Balsa (O. pyramidale) is one of the fast-growing forest plant species with high economic value and was introduced to Indonesia, but there is not much genetic information available. The main objective of this research was to generate genomic data and analyze the phylogeny of balsa (O. pyramidale) based on long-read sequences with Oxford Nanopore Technology (ONT). The research consisted of several steps: i) DNA extraction, ii) testing the quality and quantity of DNA, iii) the DNA sequencing process using a machine MinION ONT, and vi) bioinformatic analysis. Research results showed that the sequencing process in balsa (O. pyramidale) produced partial whole-genome chloroplast of 155,430 bp which can be used for relationship analysis based on DNA barcodes on the genome. Phylogeny analysis showed that balsa (O. pyramidale) genetically (multi-genotype) is positioned in the same clade with other O. pyramidale deposited samples in every use of genes or markers rbcL, matK, or a combination of genes rbcL and matK. MatK or a combination of both rbcL and matK can be recommended to be used for analysis phylogeny of balsa (O. pyramidale). |
URI: | http://repository.ipb.ac.id/handle/123456789/106947 |
Appears in Collections: | UT - Silviculture |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
Cover, Lembar Pernyataan, Abstrak, Lembar Pengesahan Prakata, dan Daftar isi.pdf Restricted Access | Cover | 1.67 MB | Adobe PDF | View/Open |
E44170035_Nurfajri Siska.pdf Restricted Access | Fullteks | 6.83 MB | Adobe PDF | View/Open |
Lampiran.pdf Restricted Access | Lampiran | 1.12 MB | Adobe PDF | View/Open |
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.