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matK Sequence Analysis and Phylogenetic of Pakoba and Its Relationship with Its Allied Species

Tallei, Trina Ekawati (2016) matK Sequence Analysis and Phylogenetic of Pakoba and Its Relationship with Its Allied Species. In: International Conference on Biodiversity, May 28, 2016, UNPAD Bandung .

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      Abstract

      Background and Objective: Pakoba, an endemic plant in North Sulawesi, has a great nutraceutical and medicinal properties. Its scientific name is often debated, because there is no clear placement for this plant in the classification. Currently, there are three scientific names for this plant: Tricalysia minahassae, Syzygium sp., and Euginia cumini. This research aimed at determining relationship of this plant with its relatives based on matK gene. Materials and Methods: The total DNA was extracted from young Pakoba leave. matK DNA was amplified using PCR with primer sets of matK-1RKIM-f/r. A single clear cut band fragment was purified and sequenced bidirectionally. The resulting sequences were processed using Geneious V6.1.6. A BLAST search was performed to identify the closest allied of Pakoba. All closest matK sequences were subjected to final alignment using Multalin V.5.4.1. Phylogenetic tree was constructed using MEGA 6.06. Results: BLAST search showed that Pakobe has an E-value 0,0 with other Syzygium, indicating that this plant is very closely related to Syzygium genera. The highest scores are for S. sandwicense, S. samarangense, S. macilwraithianum, S. australe, and S. aqueum. Nucleotide sequence analysis shows that Pakoba has only few nucleotides difference with those Syzygium. The nucleotide divergence between Pakoba and S. sandwicense is 0.004, the lowest compared to Pakoba and its other allied Syzygium genera. Conclusion: We conclude that Pakoba is one of Syzygium genera.

      Item Type: Conference or Workshop Item (Speech)
      Subjects: Q Science > QH Natural history > QH301 Biology
      Divisions: Fakultas Matematika dan IPA > Biologi
      Depositing User: Mr. Benhard W. Tampangela, ST
      Date Deposited: 19 Oct 2016 14:49
      Last Modified: 01 Dec 2016 10:17
      URI: http://repo.unsrat.ac.id/id/eprint/1256

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