A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis
Gyrinops versteegii and Aquilaria malaccensis are two important species of the Aquilarieae tribe. The main problem of this tribe is the challenge of species identification that is strongly dependent on the presence of flowers and fruit, which are not always available. The availability of whole geno...
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Bogor Agricultural University
2024-12-01
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| Series: | Jurnal Manajemen Hutan Tropika |
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| Online Access: | https://journal.ipb.ac.id/index.php/jmht/article/view/55693 |
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| author | Hartati Hartati Imam Civi Cartealy Supatmi Supatmi Syamsidah Rahmawati N Sri Hartati Ulfah Juniarti Siregar Iskandar Zulkarnaen Siregar |
| author_facet | Hartati Hartati Imam Civi Cartealy Supatmi Supatmi Syamsidah Rahmawati N Sri Hartati Ulfah Juniarti Siregar Iskandar Zulkarnaen Siregar |
| author_sort | Hartati Hartati |
| collection | DOAJ |
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Gyrinops versteegii and Aquilaria malaccensis are two important species of the Aquilarieae tribe. The main problem of this tribe is the challenge of species identification that is strongly dependent on the presence of flowers and fruit, which are not always available. The availability of whole genome information is expected to address the problems of species identification. This research aims to construct and compare the chloroplast and mitochondrial genomes of G. versteegii and A. malaccensis from short-read data using the NOVOplasty and GetOrganelle assembler. The chloroplast genome assembly revealed a full-length quadripartite circular structure with sizes of 174.814 bp (G. versteegii) and 174.821–174.822 bp (A. malaccensis), with highly conserved gene and organization. Meanwhile, the mitochondrial genome is multipartite with a size of 400.012 bp (G. versteegii) and 400.000 bp (A. malaccensis), with highly variable genes and organization due to the presence of gene cluster repeats. The LSC/IR/SCC region borders and phylogenetic analysis in chloroplasts indicate variations between the genomes of these two species. The investigation of nucleotide diversity in the chloroplast genome revealed that the trnL-rpl32 region had the highest nucleotide diversity (Pi = 0.03). This information will be useful in the future for a variety of downstream analyses.
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| format | Article |
| id | doaj-art-4b9c2d7d86934fbda57d280718bef621 |
| institution | OA Journals |
| issn | 2087-0469 2089-2063 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Bogor Agricultural University |
| record_format | Article |
| series | Jurnal Manajemen Hutan Tropika |
| spelling | doaj-art-4b9c2d7d86934fbda57d280718bef6212025-08-20T02:38:10ZengBogor Agricultural UniversityJurnal Manajemen Hutan Tropika2087-04692089-20632024-12-0130310.7226/jtfm.30.3.326A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensisHartati Hartati0Imam Civi Cartealy1 Supatmi Supatmi2Syamsidah Rahmawati3N Sri Hartati4Ulfah Juniarti Siregar5Iskandar Zulkarnaen Siregar6Research Center for Applied Botany, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Bogor, Indonesia 16911Research Center for Computation, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Bogor, Indonesia 16911Research Center for Genetic Engineering, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Bogor, Indonesia 16911Research Center for Genetic Engineering, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Bogor, Indonesia 16911Research Center for Genetic Engineering, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Bogor, Indonesia 16911Department of Silviculture, Faculty of Forestry and Environment, IPB University, Academic Ring Road, Campus IPB Dramaga, Bogor, Indonesia 16680Department of Silviculture, Faculty of Forestry and Environment, IPB University, Academic Ring Road, Campus IPB Dramaga, Bogor, Indonesia 16680 Gyrinops versteegii and Aquilaria malaccensis are two important species of the Aquilarieae tribe. The main problem of this tribe is the challenge of species identification that is strongly dependent on the presence of flowers and fruit, which are not always available. The availability of whole genome information is expected to address the problems of species identification. This research aims to construct and compare the chloroplast and mitochondrial genomes of G. versteegii and A. malaccensis from short-read data using the NOVOplasty and GetOrganelle assembler. The chloroplast genome assembly revealed a full-length quadripartite circular structure with sizes of 174.814 bp (G. versteegii) and 174.821–174.822 bp (A. malaccensis), with highly conserved gene and organization. Meanwhile, the mitochondrial genome is multipartite with a size of 400.012 bp (G. versteegii) and 400.000 bp (A. malaccensis), with highly variable genes and organization due to the presence of gene cluster repeats. The LSC/IR/SCC region borders and phylogenetic analysis in chloroplasts indicate variations between the genomes of these two species. The investigation of nucleotide diversity in the chloroplast genome revealed that the trnL-rpl32 region had the highest nucleotide diversity (Pi = 0.03). This information will be useful in the future for a variety of downstream analyses. https://journal.ipb.ac.id/index.php/jmht/article/view/55693chloroplastGetOrganellemitochondriaNOVOplastyshort-read |
| spellingShingle | Hartati Hartati Imam Civi Cartealy Supatmi Supatmi Syamsidah Rahmawati N Sri Hartati Ulfah Juniarti Siregar Iskandar Zulkarnaen Siregar A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis Jurnal Manajemen Hutan Tropika chloroplast GetOrganelle mitochondria NOVOplasty short-read |
| title | A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis |
| title_full | A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis |
| title_fullStr | A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis |
| title_full_unstemmed | A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis |
| title_short | A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis |
| title_sort | comparative study of the organellar genome of gyrinops versteegii and aquilaria malaccensis |
| topic | chloroplast GetOrganelle mitochondria NOVOplasty short-read |
| url | https://journal.ipb.ac.id/index.php/jmht/article/view/55693 |
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