scholarly journals Analisis Sekuens DNA Penyandi 18S rRNA pada Tumbuhan Cocor Bebek (Kalanchoe x laetivirens)

2021 ◽  
Vol 11 (2) ◽  
pp. 109
Author(s):  
Felly Andariyusti ◽  
Dewi Indriyani Roslim
Keyword(s):  
Dna Sequence ◽  
Internal Control ◽  
Genomic Dna ◽  
18S Rrna ◽  
Dna Isolation ◽  
Housekeeping Gene ◽  
Validation Process ◽  
Gene Expressions ◽  
Stress Studies ◽  
Total Dna

(Article History: Received January 16, 2021; Revised April 6, 2021; Accepted April 13, 2021) ABSTRAKStudi mengenai stress pada tumbuhan semakin banyak didasarkan pada ekspresi gen. Gen penyandi 18S rRNA merupakan salah satu anggota dari gen housekeeping yang umum digunakan sebagai kontrol internal. Penelitian ini bertujuan untuk menganalisis sekuens DNA penyandi 18S rRNA pada tumbuhan cocor bebek (K. x laetivirens). Metode penelitian meliputi ekstraksi DNA total dari daun segar menggunakan Mini Kit Genomic DNA Mini Kit Plant (Geneaid). Data sekuen DNA diolah menggunakan program BioEdit, BLASTn dan MEGA 6. Sekuen DNA parsial dari gen penyandi 18S rRNA K. x laetivirens telah diperoleh dengan ukuran 419pb. Sekuen tersebut memiliki kemiripan sebesar 99,28% dengan K. daigremontiana. Kalanchoe x laetivirens membentuk satu kelompok dengan sesama anggota dari famili Crassulaceae dan terpisah dari famili lainnya yang diteliti. Primer 18S rRNA spesifik terhadap cocor bebek telah dirancang, yaitu forward 5’- CAA ATT ACC CAA TCC TGA CA -3’ dan reverse 5’- CCA ACG TAA ATA GGA TCG AA -3’. Sekuen yang diperoleh pada penelitian ini berpotensi sebagai gen referensi setelah dilakukan validasi.Kata kunci: 18S rRNA; gen housekeeping; Kalanchoe x laetivirens; kontrol internal; PCR ABSTRACTPlant stress studies are based on gene expressions. This study aims to analyze the DNA sequence of 18S rRNA in cocor bebek (K. x laetivirens). Methods being out are total DNA isolation using Mini Kit Genomic DNA Mini Kit Plant (Geneaid). The DNA sequence was analyzed utilizing BioEdit, BLASTn and Mega 6 programs. Partial DNA sequence of 18S rRNA in K. x laetivirens has been obtained with 419 bp length. The DNA sequence has 99.28% similarity to K. daigremontiana. Kalanchoe x laetivirens formed one group with another species from the same family, Crassulaceae, based on the DNA sequence of 18S rRNA. A primer pair specific to K. x laetivirens for amplifying 18S rRNA has been designed such as forward 5’- CAA ATT ACC CAA TCC TGA CA -3’ and reverse 5’- CCA ACG TAA ATA GGA TCG AA -3’. This DNA sequence is potentially being employed as an internal control once the validation process completed.Keywords: 18S rRNA; housekeeping gene; internal control; Kalanchoe x laetivirens; PCR

scholarly journals Barkoding DNA pada Tumbuhan Durik-Durik (Syzygium sp.) Asal Riau Menggunakan Daerah Gen ndhF

2021 ◽  
Vol 11 (1) ◽  
pp. 41
Author(s):  
Dewi Indriyani Roslim ◽  
Ana Fitriani
Keyword(s):  
Amino Acids ◽  
Data Analysis ◽  
Dna Sequence ◽  
Genomic Dna ◽  
Dna Isolation ◽  
Dna Barcode ◽  
Agarose Gel ◽  
Total Dna ◽  
The One

(Article History: Received 11 November 2020; Revised 9 January 2021; Accepted 18 January 2021) ABSTRAKGen ndhF telah digunakan sebagai salah satu barkode DNA pada genus Syzygium karena divergensi urutan asam aminonya lebih besar empat kali dibandingkan rbcL. Penelitian ini bertujuan menganalisis sekuen DNA dari gen ndhF pada durik-durik (Syzygium sp.) asal Riau. Metode penelitian meliputi isolasi DNA total menggunakan kit isolasi DNA (Genomic DNA Mini Kit Plant, Geneaid), PCR, elektroforesis menggunakan 1% gel agarosa, sekuensing dan analisis data menggunakan program BioEdit versi 7, BLASTn dan MEGA 6.0. Sekuen DNA dari gen ndhF durik-durik telah diperoleh dengan ukuran 1370 pb dan memiliki kemiripan paling tinggi dengan yang dimiliki oleh S. malaccense (99,71%) dan paling rendah dengan S. acuminatissimum (98,69%). Terdapat 26 variasi nukleotida di antara aksesi yang diteliti dan dua diantaranya merupakan nukleotida kritis. Durik-durik membentuk satu kelompok dengan S. malaccense dan S. aromaticum. Namun demikian, nama spesies durik-durik belum dapat ditentukan karena tidak ada aksesi yang memiliki kemiripan 100% dengan durik-durik.Kata kunci: Barkode DNA, Danau Kajuik, durik-durik, gen ndhF, Syzygium. ABSTRACTThe ndhF gene has been used as DNA barcode in Syzygium because the divergence of the amino acids sequence is four times greater than rbcL. This study was to analyze the DNA sequence of ndhF gene on durik-durik (Syzygium sp.) origin Riau. Methods included total DNA isolation using Genomic DNA Mini Kit Plant (Geneaid), PCR, electrophoresis using 1% agarose gel, sequencing and data analysis using BioEdit, BLASTn dan MEGA 6.0 programs. The DNA sequence of durik-durik ndhF gene was 1370 bp in size and had the higher similarity to the one of S. malaccense (99.71%) and the lower similarity to the one of S. acuminatissimum (98.69%). There were 26 nucleotide variations and two of them were critical nucleotides. Durik-durik formed one group with S. malaccense dan S. aromaticum. Nevertheless, the species name of durik-durik still unknown because there is no accessions having 100% similarity to durik-durik.Keywords: DNA barcode, durik-durik, Kajuik Lake, ndhF gene, Syzygium.

scholarly journals Sekuen DNA Parsial Dari Gen GAPDH Pada Sirsak (Annona muricata L.)

2020 ◽  
Vol 13 (2) ◽  
pp. 209-217
Author(s):  
Dewi Indriyani Roslim ◽  
Hastini Asih ◽  
Herman Herman
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequence ◽  
Internal Control ◽  
Genomic Dna ◽  
Annona Muricata ◽  
Chain Reaction ◽  
Gapdh Gene ◽  
Gapdh Mrna ◽  
Total Dna ◽  
Polymerase Chain

AbstrakGen glyceraldehyde-3-phosphate dehydrogenase (GAPDH) merupakan salah satu gen referensi yang sering bertindak sebagai kontrol internal pada analisis ekspresi gen di beberapa spesies tumbuhan. Penelitian ini bertujuan menganalisis sekuen gen GAPDH parsial pada sirsak (Annona muricata L.). Metode meliputi persiapan sampel tanaman, isolasi DNA total menggunakan Genomic DNA mini kit Plant (Geneaid), amplifikasi gen GAPDH dengan teknik polymerase chain reaction (PCR), elektroforesis pada 1% gel agarose dan analisis data sekuen DNA. Studi ini telah memperoleh sekuen DNA dari gen GAPDH parsial sirsak sepanjang 961 pb. Sekuen tersebut memiliki kemiripan sekitar 68,93–84,35% dengan sekuen mRNA gen GAPDH pada beberapa spesies tumbuhan. Sekuen ini diprediksi terdiri dari 5 ekson dan 4 intron. Total ekson diprediksi terdiri dari 429 pb. Sekuen ini adalah yang pertama kali dilaporkan dari genus Annona dan juga dari famili Annonaceae. Sekuen ini dapat dimanfaatkan untuk analisis ekspresi gen pada sirsak dan dapat menjadi dasar untuk mengisolasi gen GAPDH spesies lain di dalam genus Annona dan famili Annonaceae. Abstract GAPDH (glyceraldehyde-3-phosphate dehydrogenase) gene is one of reference genes that is frequently became an internal control in any plant species. This study reports a DNA sequence of parsial GAPDH gene on soursop (Annona muricata L.). Methods included sample preparation, total DNA isolation using Genomic DNA mini kit Plant (Geneaid), amplification of GAPDH gene using PCR (polymerase chain reaction) technique, electrophoresis using 1% agarose gel and data analysis. This study had been obtained the DNA sequence of soursop partial GAPDH gene sizing 961 bp. The sequence had 68.93–84.35% similarity to GAPDH mRNA of some plants species. The soursop partial GAPDH gene was predicted consisting of 5 exons and 4 introns. The total exons length was 429 bp. The sequence is the first reported from Annona genus and also Annonaceae family. The sequence can be used for gene expression in soursop and also can be used to isolate GAPDH gene of other species in Annona genus and Annonaceae family.

scholarly journals Isolation of Housekeeping Genes on Durik-durik (Syzygium sp)

2018 ◽  
Vol 10 (2) ◽  
pp. 237-244
Author(s):  
Dewi Indriyani Roslim ◽  
Liza Aulia Yusfi ◽  
Desriani Ritawati Hutagalung ◽  
Niswah Faizah ◽  
Lestari Andriani ◽  
...  
Keyword(s):  
Internal Control ◽  
18S Rrna ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Internal Controls ◽  
Expression Data ◽  
Bioinformatic Tools ◽  
Normalize Gene Expression ◽  
Total Dna ◽  
Polymerase Chain

Housekeeping gene is a gene expressed with a fixed level and in abundant amounts under various conditions. After validation, the housekeeping gene can be used as an internal control to normalize gene expression data. This study reports the isolation of several housekeeping genes in Durik-durik plant (Syzygium sp). This plant material in form of fresh leaves from Durik-durik plants are taken from Kajuik Lake, Riau Province. The next stage is total DNA isolation, polymerase chain reaction, electrophoresis, sequencing and data analysis using bioinformatic tools. The isolated housekeeping genes included 18S rRNA, actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Beta-tubulin and Ubiquitin with sizes of 400 bp, 679 bp, 1134 bp, 836 bp, 1167 bp and 2155 bp, respectively. In addition to 18S rRNA, the five housekeeping genes are the first reported from the genus Syzygium and referable to isolate housekeeping genes in other species in this genus. The six housekeeping genes can be used as internal controls on Durik-durik plants after validation.

scholarly journals Disain Primer Aktin Spesifik Tuntun Angin (Elaeocarpus floribundus) (Actin Primer Design Specific of Tuntun Angin (Elaeocarpus floribundus))

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Dewi Indriyani Roslim ◽  
Herman Herman
Keyword(s):  
Internal Control ◽  
Gene Expression Analysis ◽  
Dna Isolation ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Actin Gene ◽  
Chain Reaction ◽  
Reverse Primer ◽  
Dna Fragment ◽  
Polymerase Chain

Abstrak Aktin merupakan salah satu dari housekeeping gene yang dapat digunakan sebagai kontrol internal pada analisis ekspresi gen.  Sampai saat ini, sekuen DNA dari gen penyandi aktin pada tanaman tuntun angin (Elaeocarpus floribundus) belum pernah dipublikasikan. Penelitian ini bertujuan merancang primer aktin spesifik untuk tanaman Elaeocarpus floribundus bedasarkan primer aktin degenerate.  Pasangan primer degenerate rancangan yang digunakan adalah PlAc46S sebagai primer forward: 5’- ATGGTNGGNATGGGNCARAA-3’ dan PlAc245N sebagai primer reverse: 3’- GTDATNACYTGNCCRTCNGG-5’.  Metode penelitian meliputi isolasi DNA dari daun segar, amplifikasi dengan teknik polymerase chain reaction (PCR), elektroforesis pada 1,2% gel agarose, perunutan nukleotida, dan analisis data menggunakan program BLASTn dan perangkat lunak MEGA versi 6.06.  Fragmen DNA aktin telah berhasil diamplifikasi menggunakan primer aktin degenerate dan telah dirancang primer aktin spesifik untuk Elaeocarpus floribundus dengan urutan sebagai berikut:5’-CCAAATCATGTTTGAGACCT-3’(forward) dan 5’-GAACACGTTAATTCCTGCTC-3’ (reverse). Primer tersebut selanjutnya dapat digunakan untuk mengamplifikasi gen aktin dari E. floribundus pada analisis ekspresi gen.Kata Kunci: aktin, Elaeocarpus floribundus, PCR, primer degenerate, tuntun angin. Abstract Actin is one of the housekeeping genes which commonly be used as an internal control in gene expression analysis.  Until now, the DNA sequence of actin gene of tuntun angin (Elaeocarpus floribundus) has never been published. This study aimed to design the actin primer specific for E. floribundus based on degenerate actin primer.  The pair of the degenerate actin primers (PlAc46S 5’- ATGGTNGGNATGGGNCARAA-3’ and PlAc245N 3’- GTDATNACYTGNCCRTCNGG-5’) were used in this study.  Methods included DNA isolation from fresh leaf, PCR, electrophoresis, sequencing, and data analysis using BLASTn program and MEGA software version 6.06.  The actin DNA fragment has been successfully amplified using the degenerate actin primer and then the actin primer specific for E. floribundus with the following sequences: 5’-CCAAATCATGTTTGAGACCT-3’ (forward) and 5’- AACACGTTAATTCCTGCTC-3’ (reverse) have been designed.  The primer pairs can be used to amplify the actin gene of E. floribundus.Keywords: actin, degenerate primer, Elaeocarpus floribundus, PCR, tuntun angin.

scholarly journals Characterization of Cornus (Dogwood) Genotypes Using DNA Fingerprinting

1991 ◽  
Vol 116 (6) ◽  
pp. 1103-1107 ◽  
Author(s):  
John H. Culpepper ◽  
Luis A. Sayavedra-Soto ◽  
Brant J. Bassam ◽  
Peter M. Gresshoff
Keyword(s):  
North America ◽  
Dna Sequence ◽  
Genomic Dna ◽  
Geographical Area ◽  
Sequence Divergence ◽  
Species Level ◽  
Length Polymorphisms ◽  
Total Dna ◽  
Restriction Fragment Length

Several horticulturally important members of the genus Cornus were characterized at the DNA level to identify genotypes. Random genomic DNA fragments from Cornus florida L. `Barton' were cloned into pBR322 and λ Gem-11 and used to search for restriction fragment length polymorphisms (RFLPs) among C. sericea L., C. kousa Hance., and four cultivars of C. florida: `Barton', `Cherokee Princess', `Cloud 9', and `Mary Ellen'. Total DNA from these genotypes was restricted with several endonucleases (of which BamHI, EcoRI, and HindIII were used to search for RFLPs), vacuum-blotted onto nylon membranes, and probed with the C. florida `Barton' DNA clones. RFLPs were common among the Cornus species sericea, kousa, and florida, suggesting considerable DNA sequence divergence at the species level. RFLPs were less common among the cultivars of C. florida. These cultivars were selected from a narrow geographical area in North America from nursery-grown trees and exhibit much less DNA sequence divergence.

scholarly journals Isolation of Partial Housekeeping Genes on Tuntun Angin (Elaeocarpus floribundu)

2019 ◽  
Vol 11 (2) ◽  
pp. 194-201
Author(s):  
Dewi Indriyani Roslim ◽  
Ashfira Ashfira ◽  
Dilla Mutiarawati ◽  
Tio Fanny Rosmeilinda ◽  
Nur Aisyah ◽  
...  
Keyword(s):  
Internal Control ◽  
Dna Sequences ◽  
18S Rrna ◽  
Elongation Factor ◽  
Housekeeping Genes ◽  
Bioinformatic Analysis ◽  
Elongation Factor 1 Alpha ◽  
Total Dna ◽  
Polymerase Chain ◽  
26S Rrna

Some genes like 18S rRNA, 26S rRNA, elongation factor 1-alpha (EF1a), and beta-tubulin (TUB) are members of housekeeping genes group that are commonly used as internal control in gene expression study. This study aimed to isolate those four housekeeping genes of tuntun angin (Elaeocarpus floribundus). The research material included fresh leaves of E. floribundus that were picked up from Kajuik Lake in Riau Province and four primer pairs. The procedures consisted of total DNA isolation using Genomic DNA Mini Kit Plant (Geneaid), polymerase chain reaction (PCR), electrophoresis on 1% agarose gel, sequencing, and bioinformatic analysis. This study has been isolated 18S rRNA, 26S rRNA, EF1a, and TUB genes with the size of 422 bp, 922 bp, 856 bp, and 877 bp, respectively. The EF1a and TUB genes has never been reported in Elaeocarpaceae family. Thus, those partial DNA sequences are the first sequences reported from this species and can be used as reference genes in this plant after validation.

scholarly journals Sekuen Penyandi 18S Ribosomal RNA dan Ubiquitin pada Pandanus sp. Asal Riau (Sequences Encoding 18S Ribosomal RNA and Ubiquitin on Pandanus sp. from Riau)

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Dewi Indriyani Roslim ◽  
Nurin Nuryani ◽  
Herman Herman
Keyword(s):  
Ribosomal Rna ◽  
Internal Control ◽  
18S Rrna ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
18S Ribosomal Rna ◽  
Expression Studies ◽  
Genes Encoding ◽  
Blastn Analysis ◽  
Gene Expression Studies

Abstrak Gen penyandi 18S ribosomal RNA (18S rRNA) dan ubiquitin merupakan anggota dari housekeeping genes yang sering digunakan sebagai kontrol internal pada analisis ekspresi.  Penelitian bertujuan mengisolasi kedua gen tersebut pada tanaman Pandanus sp asal Riau.  Metode penelitian meliputi isolasi DNA total, elektroforesis, PCR, purifikasi gel, sekuensing, dan analisis data sekuen DNA menggunakan program BioEdit version 7.0.0, BLASTn, dan MEGA6.  Sekuen DNA penyandi 18S rRNA (420 bp) dan ubiquitin (493 bp) telah diperoleh.  Sekuen 18S rRNA Pandanus sp memiliki kemiripan sebesar 99% dengan beberapa spesies Pandanus. Sekuen ubiquitin Pandanus sp memiliki kemiripan sebesar 87%-89% dengan sekuen ubiquitin dari beberapa tanaman dan alga hijau.  Dendrogram yang diturunkan dari kedua sekuen juga mendukung hasil tersebut bahwa sekuen 18S rRNA dari Pandanus sp. membentuk satu kelompok dengan sesama sekuen 18S rRNA, begitu pula dengan sekuen ubiquitin Pandanus sp. membentuk satu kelompok dengan sesama sekuen ubiquitin. Kedua gen berpotensi dijadikan kontrol internal setelah dilakukan validasi.Kata kunci: RNA ribosom 18S, housekeeping gene, Pandanus sp., Riau, ubiquitin. Abstrak This research aimed to isolate genes encoding 18S rRNA and ubiquitin in Pandanus sp. from Riau. The research method included total DNA extraction, polymerase chain reaction, electrophoresis, gel purification, sequencing, and DNA sequence analysis using BioEdit version 7.0.0, BLASTn, and MEGA6 programs. Sequences encoding 18S rRNA (420 bp) and ubiquitin (493 bp) had been obtained. The BLASTn analysis showed that 18S rRNA of Pandanus sp. had 99% similarity to some species of Pandanus. Ubiquitin sequence in Pandanus sp. had 87%-89% similarity to ubiquitin sequences of some plants and green algae.  Dendrograms generated from both sequences also supported the results that 18S rRNA sequence of Pandanus sp. was the same group as 18S rRNA on Pandanus genus. Similarly, ubiquitin sequence of Pandanus sp was the same cluster as other plants. Both genes were potentially used as internal control in gene expression studies after their validation.Keywords: 18S ribosomal RNA, housekeeping gene, Pandanus sp., Riau, ubiquitin.

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