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Pratiwi, Apriliana
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Immunology & microbiology

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In Silico Approach for DNA Barcoding using Phylogenetic Analysis of Coelogyne spp. based on the matK, rpoC1, rbcL and nrDNA Markers Pratiwi, Apriliana; Kinasih, Anggiresti; Meidianing, Maura Indria; Kurniawan, Febri Yuda; Semiarti, Endang
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.73130

Abstract

In silico biology is considered as an effective and applicable approach to initiate various research, such as biodiversity taxonomical conservation. Phylogenetic analysis using in silico taxonomy method for orchid species can provide data on genetic diversity and evolutionary relationships. One particular method that can be used to evaluate specific targets of gene loci in the taxonomic study is DNA barcoding. This research was conducted to determine the specific target locus gene using matK, rbcL, rpoC1, and nrDNA markers for DNA barcoding of the Coelogyne genus with in silico approach using phylogenetic analysis. All marker sequences were collected from the NCBI website and analysed using several softwares and methods, namely Clustal X for sample sequence alignment and MEGA 11 for phylogenetic tree construction and analysis. The results showed that the gene locus in Coelogyne recommended was the nrDNA gene locus. Phylogenetic analysis revealed that the use of the nrDNA gene locus was able to separate 17 Coelogyne species with two outgroup species, namely Cymbidium and Vanilla, then followed with ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) while the other gene loci, namely maturase K (matK) and polymerase beta' subunit (rpoC1) provided a visual phylogenetic tree in which the two outgroup species entered into the same clade as the Coelogyne species. Thus, the results of this study can be used as a reference to support the Coelogyne breeding and conservation program. 
Identifying Single Nucleotide Polymorphisms (SNPs) in OsFER1 and OsFER2 Genes Linked to Iron accumulation in Pigmented Indonesian Rice (Oryza sativa L.) Pratiwi, Apriliana; Bassalamah, Rizka Fahma; Elvani, I Sabila; Sebastian, Alfino; Purwestri, Yekti Asih
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 1 (2024): March
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.78019

Abstract

Iron (Fe) is an essential micronutrient for the well-being of plants, animals, and bacteria. In plants, iron plays a pivotal role in a myriad of metabolic processes, encompassing redox reaction, photosynthesis, respiration, chlorophyll synthesis, and nitrogen fixation. For humans, iron is indespensable for several metabolic functions, particularly in the synthesis of haemoglobin. Iron deficiency can lead to health issues on a global scale, therefore identifying key crops, such as rice for providing sufficient iron in diet intake is very important. In rice, the maintenance of iron homeostasis is orchestrated by various genes, with OsFER1 and OsFER2 acting as iron accumulator genes in leaves, stems, flowers, and grains. The primary objective of this study was to ascertain the single nucleotide polymorphisms (SNP) in the OsFER1 and OsFER2 and to assess the iron content in Indonesian local rice cultivars. To achieve this, we examined partial sequences of OsFER1 and OsFER2 to identify SNPs in the Indonesian rice cultivars used (Cempo Ireng, Pari Ireng, Hitam Kalsel, Merah Pari Eja, and Ciherang). Concurrently, the iron content in the seeds was quantified using Atomic Absorption Spectrophotometry (AAS). The analysis revealed that the OsFER1 gene sequence, specifically exon 5, exhibited a SNP in the form of a transition. In contrast, the OsFER2 gene sequences, specifically in intron 2 displayed SNPs in the form of insertions. Notably, the iron content in the seeds was highest in Cempo Ireng (black rice), while it was lowest in Merah Pari Eja (red rice) and Ciherang (non-pigmented rice). Importantly, the identified SNPs in these partial gene sequences did not exert any discernible influence on iron levels or the formation of ferritin protein. 
Co-Authors Bassalamah, Rizka Fahma Elvani, I Sabila Endang Semiarti Kinasih, Anggiresti Kurniawan, Febri Yuda Meidianing, Maura Indria Sebastian, Alfino Yekti Asih Purwestri