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Afifatul Achyar
State University of Padang
Education Languange, Linguistic, Communication & Media Other

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ANALISIS FILOGENETIK GEN atpA PADA GENUS Oryza MENGGUNAKAN PERANGKAT LUNAK MEGA DENGAN PENDEKATAN NEIGHBOR-JOINING Zacki Rafila; Violita; Afifatul Achyar
Jurnal Biogenerasi Vol. 11 No. 2 (2026): April - Juni 2026
Publisher : Universitas Cokroaminoto Palopo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30605/1ptac474

Abstract

This study aims to analyze the phylogenetic relationship of the atpA gene in the genus Oryza using Molecular Evolutionary Genetics Analysis (MEGA) software. The atpA gene, which plays a role in ATP synthesis in chloroplasts, was selected because of its relatively conserved nature and relevance in plant molecular evolution studies. The atpA gene sequences from 13 Oryza species were obtained from the NCBI GenBank database and analyzed using the Neighbor-Joining (NJ) method with the Kimura 2-Parameter model to reconstruct the phylogenetic tree. The reliability of the tree branches was tested through a bootstrap analysis of 10,000 repetitions. The results showed a pattern of kinship consistent with existing taxonomic classifications, in which Oryza sativa tended to form a single clade with Oryza rufipogon as its closest ancestor, while wild species such as Oryza punctata and Oryza officinalis formed a separate and more divergent clade. The relatively high bootstrap values at several branches indicate the reliability of the phylogenetic inferences generated. These findings reinforce the hypothesis that rice domestication involved wild species genetically close to cultivated species and suggest that the atpA gene has the potential to be used as an effective molecular marker in phylogenetic studies of the genus Oryza.
Analisis Pohon Filogenetik Genus Oryza Berdasarkan Gen matK Yoana Marizky Siregar; Violita Violita; Afifatul Achyar
Jurnal Biogenerasi Vol. 11 No. 2 (2026): April - Juni 2026
Publisher : Universitas Cokroaminoto Palopo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30605/6myncp72

Abstract

The genus Oryza includes both cultivated and wild rice species that play an important role in global food systems and crop improvement. These species also exhibit complex evolutionary patterns, making the study of their phylogenetic relationships essential for understanding domestication and genetic diversity. In this study, phylogenetic relationships within the genus Oryza were analyzed using chloroplast matK gene sequences through a bioinformatics approach. A total of twelve species, representing both cultivated and wild taxa, were selected from the GenBank database. Sequence alignment and tree reconstruction were carried out using MEGA version 11. The phylogenetic tree was generated using the Neighbor-Joining method with the Maximum Composite Likelihood model, and its reliability was assessed through 10,000 bootstrap replications. The results show a clear distinction between cultivated and wild Oryza species. Oryza sativa (Japonica and Indica) is closely associated with O. nivara, supported by high bootstrap values, indicating a strong evolutionary link. Meanwhile, several wild species form separate clades, suggesting earlier divergence within the genus. Overall, the matK gene proves useful for describing phylogenetic relationships at the genus level, although its ability to resolve relationships among closely related species remains limited. These findings contribute to a better understanding of the evolutionary structure of Oryza and highlight the potential importance of wild rice species in future conservation and breeding efforts.
Co-Authors Violita Violita Violita Yoana Marizky Siregar Zacki Rafila