Chloroplast Genome of Myristica fragrans: Assembly, Annotation, and Phylogenetic Relationships
Myristica fragrans is a native and economically significant species in Indonesia. However, its complete chloroplast genome, particularly from Indonesia, has not been previously reported. In this study, we successfully sequenced and assembled the complete chloroplast genome of M. fragrans using next-...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2025-04-01
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| Series: | Forest Science and Technology |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/21580103.2025.2482080 |
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| author | Hani Sitti Nuroniah Aditya Nugroho Fitri Indriani Eliya Suita Bakhtiar Basyah Susanna Susanna Ujang Wawan Darmawan Neo Endra Lelana |
| author_facet | Hani Sitti Nuroniah Aditya Nugroho Fitri Indriani Eliya Suita Bakhtiar Basyah Susanna Susanna Ujang Wawan Darmawan Neo Endra Lelana |
| author_sort | Hani Sitti Nuroniah |
| collection | DOAJ |
| description | Myristica fragrans is a native and economically significant species in Indonesia. However, its complete chloroplast genome, particularly from Indonesia, has not been previously reported. In this study, we successfully sequenced and assembled the complete chloroplast genome of M. fragrans using next-generation sequencing technology. The genome has a total length of 155,868 bp and exhibits a typical quadripartite structure, consisting of a large single-copy (LSC) region (87,062 bp), a small single-copy (SSC) region (20,664 bp), and a pair of inverted repeats (IRs) (24,071 bp each). Genome annotation identified 126 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 35 transfer RNA genes. A total of 141 simple sequence repeats (SSRs) were detected, with mononucleotide repeats being the most prevalent (90.07%). Phylogenetic analysis using six Myristica chloroplast genomes and three outgroup species confirmed that M. fragrans is most closely related to M. argentea, providing new insights into the evolutionary relationships within the Myristicaceae family. |
| format | Article |
| id | doaj-art-0b2c2b5cc68a477dac20ee8a0ddc8b1a |
| institution | DOAJ |
| issn | 2158-0103 2158-0715 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Forest Science and Technology |
| spelling | doaj-art-0b2c2b5cc68a477dac20ee8a0ddc8b1a2025-08-20T03:20:51ZengTaylor & Francis GroupForest Science and Technology2158-01032158-07152025-04-0121220721410.1080/21580103.2025.2482080Chloroplast Genome of Myristica fragrans: Assembly, Annotation, and Phylogenetic RelationshipsHani Sitti Nuroniah0Aditya Nugroho1Fitri Indriani2Eliya Suita3Bakhtiar Basyah4Susanna Susanna5Ujang Wawan Darmawan6Neo Endra Lelana7Research Center for Applied Botany, National Research and Innovation Agency, Bogor, IndonesiaResearch Center for Applied Botany, National Research and Innovation Agency, Bogor, IndonesiaResearch Center for Applied Botany, National Research and Innovation Agency, Bogor, IndonesiaResearch Center for Applied Botany, National Research and Innovation Agency, Bogor, IndonesiaFaculty of Agriculture, Syiah Kuala University, Banda Aceh, IndonesiaFaculty of Agriculture, Syiah Kuala University, Banda Aceh, IndonesiaResearch Center for Applied Zoology, National Research and Innovation Agency, Bogor, IndonesiaResearch Center for Applied Microbiology, National Research and Innovation Agency, Bogor, IndonesiaMyristica fragrans is a native and economically significant species in Indonesia. However, its complete chloroplast genome, particularly from Indonesia, has not been previously reported. In this study, we successfully sequenced and assembled the complete chloroplast genome of M. fragrans using next-generation sequencing technology. The genome has a total length of 155,868 bp and exhibits a typical quadripartite structure, consisting of a large single-copy (LSC) region (87,062 bp), a small single-copy (SSC) region (20,664 bp), and a pair of inverted repeats (IRs) (24,071 bp each). Genome annotation identified 126 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 35 transfer RNA genes. A total of 141 simple sequence repeats (SSRs) were detected, with mononucleotide repeats being the most prevalent (90.07%). Phylogenetic analysis using six Myristica chloroplast genomes and three outgroup species confirmed that M. fragrans is most closely related to M. argentea, providing new insights into the evolutionary relationships within the Myristicaceae family.https://www.tandfonline.com/doi/10.1080/21580103.2025.2482080codon usageMyristicaceaenext-generation sequencingnutmegsimple sequence repeat |
| spellingShingle | Hani Sitti Nuroniah Aditya Nugroho Fitri Indriani Eliya Suita Bakhtiar Basyah Susanna Susanna Ujang Wawan Darmawan Neo Endra Lelana Chloroplast Genome of Myristica fragrans: Assembly, Annotation, and Phylogenetic Relationships Forest Science and Technology codon usage Myristicaceae next-generation sequencing nutmeg simple sequence repeat |
| title | Chloroplast Genome of Myristica fragrans: Assembly, Annotation, and Phylogenetic Relationships |
| title_full | Chloroplast Genome of Myristica fragrans: Assembly, Annotation, and Phylogenetic Relationships |
| title_fullStr | Chloroplast Genome of Myristica fragrans: Assembly, Annotation, and Phylogenetic Relationships |
| title_full_unstemmed | Chloroplast Genome of Myristica fragrans: Assembly, Annotation, and Phylogenetic Relationships |
| title_short | Chloroplast Genome of Myristica fragrans: Assembly, Annotation, and Phylogenetic Relationships |
| title_sort | chloroplast genome of myristica fragrans assembly annotation and phylogenetic relationships |
| topic | codon usage Myristicaceae next-generation sequencing nutmeg simple sequence repeat |
| url | https://www.tandfonline.com/doi/10.1080/21580103.2025.2482080 |
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