KEANEKARAGAMAN DAN KEKERABATAN GENETIK ARTOCARPUS BERDASARKAN PENANDA DNA KLOROPLAS matK &amp; rbcL: KAJIAN IN SILICO

Mursyidin, Dindin Hidayatul; Makruf, Muhammad Irfan

doi:10.32556/floribunda.v6i5.2020.322

Cited by 5 publications

(4 citation statements)

References 22 publications

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“…According to Mascher et al (2019), this institution provides a comprehensive database of nucleotide sequences or gene descriptions that are freely accessed. Hence, such a study does not require high costs and is applicable to support germplasm conservation, breeding, and cultivation programs (Mursyidin & Makruf, 2020). In other words, our findings may be usable as a reference in supporting the conservation and breeding programs of Phalaenopsis, both locally and globally.…”

Section: Introductionmentioning

confidence: 66%

Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

et al. 2021

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In silico is the more comprehensive and applicable approach in supporting, both conservation and breeding programs of germplasm. The study aimed to analyze and determine the genetic diversity and relationships of 24 species of Phalaenopsis using two DNA barcoding markers, namely the rbcL and trnL-F, by in silico approach. All sequences of these markers were collected randomly from the NCBI website and analyzed using several softwares and methods, such as ClustalW and MultAlin for multiple sequence alignments and MEGA-X to determine its genetic diversity and relationships. Specifically, the genetic diversity was determined using a nucleotide diversity index and their relationships by the Maximum Likelihood method. The results showed that Phalaenopsis has a low genetic diversity of 0.24, 0.32, and 0.19, respectively. The phylogenetic analysis revealed that this orchid separated into five (for the rbcL), six (trnL-F), and seven clades (a combined one), where the closest relationship is shown by P. amboinensis vs. P. venosa, whereas the farthest by P. gibbosa vs. P. doweryensis, P. stuartiana vs. P. micholitzii, and P. celebensis vs. P. pulchra. The results have novel information on the diversity and relationships of Phalaenopsis on the in silico approach. Thus, our findings might be used in supporting the conservation and breeding program of Phalaenopsis, both locally and globally.

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Section: Introductionmentioning

confidence: 66%

Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

et al. 2021

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“…Two molecular markers namely rbcL and accD genes were selected for constructing phylogenetic tree of C. inophyllum. The Consortium for the Barcode of Life recommends the use of the rbcL gene as a reliable and efficient method for evaluating the genetic condition of a species with thoroughness, precision, and promptness [28]. The rbcL gene in cpDNA encodes RuBisCo and exhibits a high degree of species similarity due to its low mutation rate [29].…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Characterization of the chloroplast genome sequence of Calophyllum inophyllum, a bioenergy tree species, using Oxford Nanopore Technologies

Kristianti,

Dwiyanti,

Pratama

et al. 2024

IOP Conf. Ser.: Earth Environ. Sci.

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Calophyllum inophyllum is a forest tree species that offers significant renewable energy benefits. However, the genetic information of these bioenergy tree species for the study of tree improvement is still limited. This study aimed to assemble the draft chloroplast genome using MinION Oxford Nanopore Technologies (ONT) and analyze the genetic relationship based on molecular markers for C. inophyllum. The study involved several steps: DNA extraction and isolation using the CTAB method, DNA library preparation, DNA sequencing using MinION Oxford Nanopore Technologies (ONT), and phylogenetic analysis based on selected DNA markers. The results showed that 115.1 Mb of high-quality DNA was successfully generated using ONT long-read sequencing, and 114.708 bp was annotated into partial genome chloroplast. The genetic relationship analysis using two selected DNA barcodes, namely rbcL and accD showed that the accD gene is more recommended for constructing a phylogenetic tree for the genus Calophyllum than the rbcL gene as it has a high bootstrap value (93%). Furthermore, the accD gene can also be considered a potential marker for further genetic analysis of C. inophyllum.

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“…In general, matK DNA sequences have better ability to distinguish genera and species than rbcL (Ismail et al, 2020). The matK gene could evolve faster than the rbcL gene and consistently showed a high level of discrimination, especially in Angiosperms (Mursyidin & Makruf, 2020). The matK gene played a role in the expression of the K subunit maturase in the plant chloroplast genome (Lian et al, 2022).…”

Section: Phylogenetic Tree Of Matk Markersmentioning

confidence: 99%

“…In plants, this information is obtained from the chloroplast genome which contains genes that can be used as a study material for evolution at a high taxonomic level (Taberlet et al, 1991). Several genes located on cpDNA are known as universal markers and has been widely used to study genetic kinship relationships at high taxonomic levels including the large subunit of the rbcL (ribulosebisphosphate carboxylase) (Mursyidin et al, 2021) and matK (Maturase K), which is a coding region with a high level of amino acid gene substitution and nucleotide level compared to rbcL (Mursyidin & Makruf, 2020). This genetic resource information is obtained by DNA sequencing, which is a technique used to sequence nucleotides in a DNA molecule (Roslim et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study

2023

Agrivita.J.Agr.Sci

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Balsa (Ochroma pyramidale) is fast-growing forest plant species introduced to Indonesia with limited genetic information. Genetic information can be obtained through molecular assessment which is now feasible due to sequencing technology development. This is supported by the third-generation sequencer technology, which has been developed using long-read sequencing technology. MinION Oxford Nanopore Technology is one of the long-read sequence-based sequencers with a real-time process and portable. This study aims to generate genomic data and analyze the phylogenetic relationship of balsa (O. pyramidale) based on long-read sequences with MinION Oxford Nanopore Technologies. Balsa long-read sequencing generated a partial chloroplast genome (cpDNA) sequence of 155,430 bp, which can be used for further DNA barcode-based phylogenetic analysis from the chloroplast genome. Phylogenetic analysis showed that the balsa species (O. pyramidale) was genetically grouped in one clade with other O. pyramidale species in phylogeny analysis based on rbcL, matK, and a combination of rbcL and matK genes indicated that those genes were a suitable marker for phylogenetic analysis in balsa species (O. pyramidale).

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KEANEKARAGAMAN DAN KEKERABATAN GENETIK ARTOCARPUS BERDASARKAN PENANDA DNA KLOROPLAS matK & rbcL: KAJIAN IN SILICO

Cited by 5 publications

References 22 publications

Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

Characterization of the chloroplast genome sequence of Calophyllum inophyllum, a bioenergy tree species, using Oxford Nanopore Technologies

Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study

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