DNA Barcoding of Medicinal Orchid Dendrobium discolor Lindl. Tanimbar Using rbcL and ITS genes

Perwitasari, Dian; Rohimah, Siti; Ratnasari, Tri; Sugiharto, Bambang; Su’udi, Mukhamad

doi:10.21082/bullittro.v31n1.2020.8-20

Cited by 7 publications

(8 citation statements)

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“…This suggests that ITS2 has a faster mutation rate than the CO1 sequences (Batovska et al, 2017). The ITS2 sequence is a nuclear locus that undergoes frequent cross-overs, resulting in recombinants with significant genetic variation (Perwitasari et al, 2020). Based on this, the abundant genetic variation in the ITS2 sequences has the potential to detect the emergence of new taxa (Fang et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

In silico exploration of the potential barcode DNA in Anopheles sp., a malarian vector from Indonesia

Wathon¹,

Astikaningrum²,

Ardyah³

et al. 2023

Biolokus

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Malaria is an infectious disease caused by Plasmodium and transmitted to humans through the Anopheles mosquito vector. The large diversity of Anopheles in Indonesia, which consists of similar complex species, makes it difficult to identify species based on morphological characteristics. Therefore, it is necessary to have another approach to identifying species based on molecular characteristics using DNA molecular markers. This approach becomes important as a basis for vector-based malaria control efforts. This research aims to explore potential DNA barcodes based on in silico studies as a reference for DNA barcoding analysis of Anopheles species in Indonesia. The data sequences of CO1 and ITS2 from Anopheles sp. were collected on the NCBI database. The sequence alignment was performed using CLUSTALX2. The construction of a phylogenetic tree was carried out using MEGA XI. Data analysis was performed by observing the construction of phylogenetic trees, bootstrap scores, and genetic distance. The data sequence in NCBI shows that 10 species of the genus Anopheles as malaria vectors have been studied in Indonesia. Sequence alignment of the 10 species based on CO1 and ITS2 markers showed that ITS2 markers had higher genetic variation than CO1. Therefore, the ITS2 sequence has the potential to be a DNA barcode for the molecular identification of Anopheles.

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Section: Resultsmentioning

confidence: 99%

In silico exploration of the potential barcode DNA in Anopheles sp., a malarian vector from Indonesia

Wathon¹,

Astikaningrum²,

Ardyah³

et al. 2023

Biolokus

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“…Ident 99% menunjukkan kemungkinan adanya kemiripan dengan spesies B. lobii sampel penelitian. Nilai E-value sampel anggrek B. lobbii sekuen ITS2 sebesar 0.0 menunjukkan pensejajaran seluruh sekuen signifikan antara B. lobii dengan 5 sekuen homolognya (Perwitasari et al, 2020).…”

Section: Analisis Molekuler Dna Barcoding Anggrek Bulbophyllum Lobbii...unclassified

Evaluasi Lokus Potensial matK dan ITS2 Untuk DNA Barcoding Anggrek Bulbophyllum lobbii Lindl.

Su'udi,

Ulum,

Ardiyansah

et al. 2024

Al-Kauniyah J. Biol.

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AbstrakBulbophyllum lobbii Lindl. merupakan anggrek dari famili Orchidaceae yang berpotensi sebagai bahan baku obat herbal. Identikasi morfologi anggrek B. lobii memiliki keterbatasan karena kemiripan spesies dengan anggrek lain. Alternatif identifikasi secara molekuler menggunakan sekuen matK dan ITS2 sebagai barcode dalam DNA barcoding diharapkan menjadi salah satu lokus pembeda spesies anggrek B. lobbii secara akurat dan efisien. Penelitian ini bertujuan untuk mengidentifikasi sekuen matK dan ITS2 sebagai penanda molekuler yang efektif untuk anggrek B. lobbii. DNA genom B. lobbii diisolasi dengan metode Cethyl Trimethyl Ammonium Bromide (CTAB) dan amplifikasi DNA dengan PCR. Hasil penelitian menunjukkan sekuen matK dari B. lobbii memiliki tingkat homologi tinggi dengan dua spesies B. lobbii (KY966747.1 dan KY966691.1) dari China dengan nilai Per. Ident sebesar 99,20%, sedangkan sekuen ITS2 memiliki homologi tertinggi dengan nilai Per. Ident sebesar 99,76% pada spesies B. lobbii (MG253848.1) dari Polandia. Hasil analisis menunjukkan sekuen ITS2 dapat mengidentifikasi spesies dari tingkatan subspesies atau diatasnya (ordo atau genus) dan juga meningkatkan resolusi filogenetik yang baik pada hasil BLAST, sedangkan sekuen matK memberikan sedikit kontribusi dalam pengelompokkan hubungan kekerabatan antara spesies B. lobbii dengan spesies pembanding lainnya. Sekuen ITS2 dapat direkomendasikan sebagai penanda molekuler yang paling baik untuk identifikasi sampel anggrek Bulbophyllum, khususnya Bulbophyllum lobbii.AbstractBulbophyllum lobbii Lindl. is an orchid from the Orchidaceae family which has potential as a raw material for herbal medicine. Morphological identification of the B. lobii orchid has limitations due to the species' similarity to other orchids. The alternative molecular identification using matK and ITS2 sequences as barcodes in DNA barcoding is expected to be one of the loci for distinguishing the B. lobbii orchid species accurately and efficiently. This study aims to identify matK and ITS2 sequences as effective molecular markers for the orchid B. lobbii. Bulbophyllum lobbii genomic DNA was isolated using the Cethyl Trimethyl Ammonium Bromide (CTAB) method and DNA amplification by PCR. The results showed that the matK sequence from B. lobbii has a high level of homology with two B. lobbii species (KY966747.1 and KY966691.1) from China with a value of Per. Ident is 99.20%, while the ITS2 sequence has the highest homology with a Per. Ident value of 99.76% with the species B. lobbii (MG253848.1) from Poland. The results of the analysis show that the ITS2 sequence can identify species from the subspecies level or above (ordo or genus) and also improves good phylogenetic resolution in BLAST results, while the matK sequence makes little contribution in grouping the relationship between the B. lobbii species and other comparison species. The ITS2 sequence can be recommended as the best molecular marker for identifying Bulbophyllum orchid samples, especially Bulbophyllum lobbii.

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“…The PCR process goes well if thick and clear bands are obtained as a sign that PCR has reached optimum conditions so that it can proceed to the sequencing process [15].…”

Section: A C C E P T E D Mmentioning

confidence: 99%

“…The higher the percentage of similarity obtained, the higher the level of homology of the two sequences being analyzed [15]. The high homology value of a sequence causes low genetic variation between two individuals.…”

Section: A C C E P T E D Mmentioning

confidence: 99%

Identification of DNA Barcodes from rbcL Chloroplast DNA in Katokkon Chili (Capsicum annuum var. chinense) Origin of Tana Toraja, South Sulawesi

Muthiadin,

Arma,

Aziz

et al. 2024

J. Multidiscip. Appl. Nat. Sci.

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Katokkon chili (Capsicum annuum var. chinense) is a type of chili which are commonly found in Tana Toraja. It has a distinctive aroma, high spiciness, and a potential economic value but has not been widely identified and explored, thus, it is necessary to carry out molecular identification using DNA barcodes from chloroplast DNA. The aim of this study was to determine genetic variation and the results of constructing a phylogenetic tree from DNA sequences katokkon chili (C. annuum var. chinense) using the rbcL marker. This study used 6 samples of katokkon chilies (C. annuum var. chinense) and 3 outgroup samples (C. frutescens, C. chinense and C. baccatum). The stages of the research included total DNA isolation, qualitative and quantitative tests, PCR amplification using rbcL primers, and sequencing. Data analysis used is sequence alignment, phylogenetic, genetic distance matrix, haplotypes and phylogeography. The results showed genetic variation with 7 polymorphisms consisting of 4 singleton sites at the nucleotide base sequences of 6th, 525, 715 and 737, and 3 parsimony informative sites at the nucleotide base sequences 370, 616 and 902 and the haplotype distribution is divided into 4 haplotypes namely Hap_1 (A1, A2, A3, B1, B2 and B3), Hap_2 (C1), Hap_3 (C2), and Hap_3 (C3). The phylogenetic tree construction formed two clades, namely clade I consist of six samples of katokkon chilies (C. annuum var. chinense) and clade II consisting of three outgroup samples. Mark the highest bootstrap is 96 and the lowest bootstrap value is 29. Genetic distance matrix values are in the range of 0.000–0.005.

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DNA Barcoding of Medicinal Orchid Dendrobium discolor Lindl. Tanimbar Using rbcL and ITS genes

Cited by 7 publications

References 0 publications

In silico exploration of the potential barcode DNA in Anopheles sp., a malarian vector from Indonesia

In silico exploration of the potential barcode DNA in Anopheles sp., a malarian vector from Indonesia

Evaluasi Lokus Potensial matK dan ITS2 Untuk DNA Barcoding Anggrek Bulbophyllum lobbii Lindl.

Identification of DNA Barcodes from rbcL Chloroplast DNA in Katokkon Chili (Capsicum annuum var. chinense) Origin of Tana Toraja, South Sulawesi

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