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All Journal The Journal of Experimental Life Sciences (JELS) Jurnal Biosilampari: Jurnal Biologi
Estri Laras Arumingtyas
Universitas Brawijaya
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Immunology & microbiology Medicine & Pharmacology Neuroscience

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USING SHORT SEQUENCE matK GENE AS BARCODE DNA FOR IDENTIFICATION OF DURIO Sp IN TERNATE ISLAND S. Sundari; Abdu Mas’ud; Estri Laras Arumingtyas; Didik Wahyudi
Jurnal Biosilampari : Jurnal Biologi Vol 5 No 1 (2022): Biosilampari
Publisher : LP4MK STKIP PGRI Lubuklinggau

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31540/biosilampari.v5i1.1528

Abstract

The Barcode of Life Consortium (CBOL) recommended a standard method for the identification of plant species using matK and rbcL barcoding gene. This study was aimed to evaluate the efficiency of matK DNA barcoding for identification of local durian (Durio sp.) from Ternate Island. Total 15 local durian has been used in this study. Whole genom DNA was isolated by Geneid plant DNA kit and then successfully amplified by the Polymerase Chain Reaction (PCR) technique using specific primer. MatK successfully amplified with 245 bp in length. MatK has sequencing success (71.3%) and relative high of Quality value 20+ (86%). BLAST analysis of the sequence showed that local durian in Ternate are identifies as Durio zibethinus and Neesia malayana with query cover 97%-99%. It could be concluded that matK with short sequence is not efficience for durian identification. The recommended in this studies for using of molecular markers with sequence lengths above 500 bp would be more effective for the identification of cryptic species Durio sp. and other.
Genetic Variation Analysis of Four Local Varieties of Indonesian Black Rice (Oryza sativa L.) Based on Partially rbcL cpDNA Gene Sequence Abdul Basith; Estri Laras Arumingtyas; Widodo Widodo
The Journal of Experimental Life Science Vol. 11 No. 1 (2021)
Publisher : Postgraduate School, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jels.2021.011.01.01

Abstract

Black rice (Oryza sativa L.) varieties i.e. Toraja (South Sulawesi), Cempo Ireng (Yogyakarta), Wojalaka (East Nusa Tenggara), and Manggarai (East Nusa Tenggara) are four local black rice varieties in Indonesia whose character has not been widely studied, especially the character of genetic variation. Research aimed to determine the variation of the rbcL gene in the four local black rice varieties. The sample for testing the variation of the rbcL gene sequence in the form of black rice leaves six weeks after planting. Dendogram was carried out using the UPGMA method with the Kimura 2-parameter algorithmic calculation model using the MEGA5 version 5.2.2 program. The results showed that partially the rbcL gene sequence was successfully amplified on four black rice varieties with a sequence length of 487 bp. The partial rbcL sequence of black rice consisted of 26.58% tyrosine, 21.38% cytosine, 28.86% adenine, and 23.18% guanine. The value of G + C content was 0.446, with the frequency of invariable sites of 97.13%. The frequency of informative parsimony sites was 1.43% with a nucleotide diversity (Pi) value of 42-10, the number of haplotypes was 5, and the total number of mutations and polymorphic sites was 14. The ratio between transition and transversion (ts/tv ratio k) for purine bases was 1.741 and pyrimidine was 3.571, with the estimated overall ratio between transition and transversion (R) of 1.31. Based on the dendogram, the farthest genetic distance was found in Wojalaka and Manggarai varieties, which were 0.019 respectively.Keywords: black rice, genetic variation, local varieties, rbcL gen
Co-Authors Abdul Basith Didik Wahyudi Masud, Abdu S. Sundari Widodo Widodo