Amplification and Analysis of Rbcl Gene (Ribulose-1,5-Bisphosphate Carboxylase) of Clove in Ternate Island

Abstract

DNA Barcoding is recommended as a tool for identifying and confirming species within the taxonomy framework. The rbcL gene is the barcode DNA for plant species. Ternate Island is one of clove plantation center in North Maluku. The diversity and productivity of cloves on the Ternate island known since in earlier times. This study has a purpose to amplify the rbcL gene in clove plants collected from clove plantations of communities in Ternate island. Isolation of total DNA carried out with using ZymoBiomic (Zymo Research DNA Extraction) Kit from leaves tissue, then DNA specimen is amplified based on rbcL gene with forwarding sequence rbcLaF 5′-ATG TCA CCA CAA ACA GAG ACT AAA GC-3′ and reverse sequence is rbcLaR 5′-GTA AAA TCA AGT CCA CCR CG-3′. The results showed that the specimen was successfully amplified with an amplicon size of 600 bp. Furthermore, BLASTN analysis results note that the sequence has a similarity of 99% with Syzygium cumini vc. J.R. Abbott 23676 (FLAS) ribulose-1,5-bisphosphate carboxylase large subunit (rbcL) gene, but phylogenetically the precise position of sample could not found because the limitation of rbcL gene.

Evaluation of Genetic Diversity and Identification of <i>Huperzia</i> Species Collected in Some Different Areas in Vietnam by Molecular Markers

“…PCR reaction was performed with the primers rbcL. The results showed that 35 samples of Huperzia were a single-form band with the size of 650 bp (Figure 1), which was a resemblance to the report of Sundary and Papuangan [22] who applied the rbcL gene for analysing of Syzygium aromaticum.…”

“…Among them, there was only one sample (BK3) belonging to H.phlegmarioides group, and the others of the 34 samples were clustered in H.squarrosa group, respectively (Figure 3 and Figure 4). In the fact that the available databases on the rbcL gene are very useful and facilitated to identify phylogenetic relationships of many plant species at interfamilial levels [25,22]. Dubisson [26] successfully applied rbcL sequences of 18 species of the fern genus Trichomanes for assessing their systematic relationships which showed a more accurate reflection of the generic concept applied to other fern and angiosperms.…”

“…To the best our knowledge, over 251 plant species have been successfully applied and reached 100% by use of two primary types [27,22], and acquired a greater length (around 1.428 to 2500 bp) by applying full-length rbcL [28]. Additionally, Kesanakuthi et al [29] used rbcL sequence alone to investigate 85% plant species groups of all root samples, and spelling out the ecological factors that contributed to the subterranean spatial organization of plant diversity in nature.…”

“…A: Habit; B: upward turned stem [4] International Letters of Natural Sciences Submitted: 2019-10-31 ISSN: 2300-9675, Vol. 80, pp [13][14][15][16][17][18][19][20][21][22][23] Revised: 2020-05-27 doi:10.18052/www.scipress.com/ILNS.80. 13 Accepted: 2020-05 -29 2020SciPress Ltd, Switzerland Online: 2020 H. squarrosa is known as a highly valuable medicinal plant, which contains alkaloids, flavones, triterpenes, phenolic acids, especially including Huperzine A (Hup A), Huperzine B (Hup B), N-methyl-huperzine B, Huperzinine, Lycoporine A, Carina-tumine A, etc [5].…”

Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India

“…Maturase K ( matK (XF/5R)) and Kim matK (3F_KIM/1R_KIM), the plant plastidial gene in the chloroplast region that splices group II introns in the conserved domain X of the reverse transcriptase domain can be used as a universal DNA barcode primer for plants [ 16 ]. The chloroplast DNA sequence, ribulose–bisphosphate carboxylase ( rbcL ), is one of the universal barcode genes used in species discrimination studies due to high amplification and low mutation rate [ 17 ]. Ycf1 is the second largest gene in the plastid genome, encodes about 1800 amino acids, and is a reliable candidate for DNA barcoding [ 18 ].…”