Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study
Balsa (Ochroma pyramidale) is fast-growing forest plant species introduced to Indonesia with limited genetic information. Genetic information can be obtained through molecular assessment which is now feasible due to sequencing technology development. This is supported by the third-generation sequenc...
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| Format: | Article |
| Language: | English |
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Universitas Brawijaya
2023-08-01
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| Series: | AGRIVITA Journal of Agricultural Science |
| Subjects: | |
| Online Access: | https://agrivita.ub.ac.id/index.php/agrivita/article/view/3930 |
| _version_ | 1827755071656427520 |
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| author | Siska Nurfajri Fifi Gus Dwiyanti Rahadian Pratama Muhammad Majiidu Iskandar Z. Siregar |
| author_facet | Siska Nurfajri Fifi Gus Dwiyanti Rahadian Pratama Muhammad Majiidu Iskandar Z. Siregar |
| author_sort | Siska Nurfajri |
| collection | DOAJ |
| description | Balsa (Ochroma pyramidale) is fast-growing forest plant species introduced to Indonesia with limited genetic information. Genetic information can be obtained through molecular assessment which is now feasible due to sequencing technology development. This is supported by the third-generation sequencer technology, which has been developed using long-read sequencing technology. MinION Oxford Nanopore Technology is one of the long-read sequence-based sequencers with a real-time process and portable. This study aims to generate genomic data and analyze the phylogenetic relationship of balsa (O. pyramidale) based on long-read sequences with MinION Oxford Nanopore Technologies. Balsa long-read sequencing generated a partial chloroplast genome (cpDNA) sequence of 155,430 bp, which can be used for further DNA barcode-based phylogenetic analysis from the chloroplast genome. Phylogenetic analysis showed that the balsa species (O. pyramidale) was genetically grouped in one clade with other O. pyramidale species in phylogeny analysis based on rbcL, matK, and a combination of rbcL and matK genes indicated that those genes were a suitable marker for phylogenetic analysis in balsa species (O. pyramidale). |
| first_indexed | 2024-03-11T07:59:07Z |
| format | Article |
| id | doaj.art-c45db98572a54dba9bdd2808e24cac3f |
| institution | Directory Open Access Journal |
| issn | 0126-0537 2477-8516 |
| language | English |
| last_indexed | 2024-03-11T07:59:07Z |
| publishDate | 2023-08-01 |
| publisher | Universitas Brawijaya |
| record_format | Article |
| series | AGRIVITA Journal of Agricultural Science |
| spelling | doaj.art-c45db98572a54dba9bdd2808e24cac3f2023-11-17T04:19:00ZengUniversitas BrawijayaAGRIVITA Journal of Agricultural Science0126-05372477-85162023-08-0145343044210.17503/agrivita.v41i0.3930758Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic StudySiska Nurfajri0Fifi Gus Dwiyanti1Rahadian Pratama2Muhammad Majiidu3Iskandar Z. Siregar4Department of Silviculture, Faculty of Forestry and Environment, IPB University Bogor IndonesiaDepartment of Silviculture, Faculty of Forestry and Environment, IPB University Bogor IndonesiaDepartment of Biochemistry, Faculty of Mathematic and Natural Science, IPB UniversityAdvanced Research Laboratory (ARLab), IPB University, Bogor, IndonesiaDepartment of Silviculture, Faculty of Forestry and Environment, IPB University Bogor, IndonesiaBalsa (Ochroma pyramidale) is fast-growing forest plant species introduced to Indonesia with limited genetic information. Genetic information can be obtained through molecular assessment which is now feasible due to sequencing technology development. This is supported by the third-generation sequencer technology, which has been developed using long-read sequencing technology. MinION Oxford Nanopore Technology is one of the long-read sequence-based sequencers with a real-time process and portable. This study aims to generate genomic data and analyze the phylogenetic relationship of balsa (O. pyramidale) based on long-read sequences with MinION Oxford Nanopore Technologies. Balsa long-read sequencing generated a partial chloroplast genome (cpDNA) sequence of 155,430 bp, which can be used for further DNA barcode-based phylogenetic analysis from the chloroplast genome. Phylogenetic analysis showed that the balsa species (O. pyramidale) was genetically grouped in one clade with other O. pyramidale species in phylogeny analysis based on rbcL, matK, and a combination of rbcL and matK genes indicated that those genes were a suitable marker for phylogenetic analysis in balsa species (O. pyramidale).https://agrivita.ub.ac.id/index.php/agrivita/article/view/3930matkminionochroma pyramidalephylogenyrbcl |
| spellingShingle | Siska Nurfajri Fifi Gus Dwiyanti Rahadian Pratama Muhammad Majiidu Iskandar Z. Siregar Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study AGRIVITA Journal of Agricultural Science matk minion ochroma pyramidale phylogeny rbcl |
| title | Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study |
| title_full | Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study |
| title_fullStr | Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study |
| title_full_unstemmed | Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study |
| title_short | Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study |
| title_sort | generating long read sequences of balsa ochroma pyramidale cav ex lam urb using minion oxford nanopore technology and utilization for phylogenetic study |
| topic | matk minion ochroma pyramidale phylogeny rbcl |
| url | https://agrivita.ub.ac.id/index.php/agrivita/article/view/3930 |
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