HUBUNGAN KEKERABATAN SPESIES DALAM GENUS Zanthoxylum MENGGUNAKAN SEKUEN GEN MATURASE K (matK) DNA KLOROPLAS

Manurung, Johannes; Prakasa, Hary; Tanjung, Ulfa Jamily; Harsono, Tri

doi:10.24114/jbio.v4i2.10166

Cited by 3 publications

(4 citation statements)

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“…Chloroplast DNA is DNA with a low genetic recombination frequency that is inherited maternally so that it can be 5 used to analyze relationships between species. However, chloroplast DNA has not been able to separate interspecies relationships [29]. The annotations from the D. rumphii sequence also yielded 142 genes (table 1) with 103 Coding Sequences (CDS).…”

Section: Genome Assembly and Chloroplast Genome Annotationmentioning

confidence: 99%

Understanding Diospyros rumphii Bakh from North Sulawesi through Long-read sequences analysis using MinION Oxford Nanopore Technologies

Salindeho,

Dwiyanti,

Pratama

et al. 2023

IOP Conf. Ser.: Earth Environ. Sci.

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Diospyros rumphii (Ebony) is a high-value timber species native to Indonesia, which is listed as a Data Deficient species by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Therefore, additional data to enrich knowledge on the distribution, ecology, and genetics of this species is urgently needed. Furthermore, this study aimed to generate whole-genome sequencing data, including the low-coverage data for D. rumphii using MinION Oxford Nanopore Technologies (ONT). The sequence data generated from leaf and cambium genomic DNA was assembled to result in a draft of the chloroplast genome and constructed the phylogenetic tree based on partial nucleotide sequences of the rbcL gene. The results showed that DNA sequencing of D. rumphii generated a 3.25 Gb of long-read sequences data and a draft of a partial chloroplast genome with a size of 150,578 bp. Genetic relationship analysis using the rbcL gene showed that D. rumphii was positioned in one clade with Diospyros oblonga, which has a bootstrap value of 87% suggesting that the rbcL gene can be considered as recommended molecular marker for genetic analysis of D. rumphii in the future.

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Section: Genome Assembly and Chloroplast Genome Annotationmentioning

confidence: 99%

Understanding Diospyros rumphii Bakh from North Sulawesi through Long-read sequences analysis using MinION Oxford Nanopore Technologies

Salindeho,

Dwiyanti,

Pratama

et al. 2023

IOP Conf. Ser.: Earth Environ. Sci.

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“…Based on Gunawan's research, (2020) on B. angulata using a marker from the chloroplast genome (trnL-FIGS) showed the appropriate results, namely obtaining the percentage results of G + C (38.4%) and A + T (61.7%). According to Manurung et al, (2018) the nucleotide composition in the non-coding areas of chloroplast DNA contains more adenine and thymine bases. Then for the character of the genetic distance range, the MatK marker has a genetic distance range (0-4%).…”

Section: Sequence Character Analysismentioning

confidence: 99%

“…MatK is one of the genes originating from the chloroplast genome. DNA from the chloroplast genome is inherited maternally or from the female parent, so that in the chloroplast genome the genetic changes that occur are very few and even take a very long time for a change to occur (Manurung et al, 2018). Nevertheless, the data obtained from these few changes can be important information in determining the rate of evolution that occurs in these organisms.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…In recent years, the MatK gene has often been used by experts for molecular phylogenetic analysis in plants in order to understand diversity and answer several phylogenetic problems. Examples of research conducted by Manurung et al, (2018) on the genus Zanthoxylum and Retnaningati (2017) on the species Cucumis melo L. using the MatK marker showed that the MatK marker succeeded in separating the two species at the species level. Therefore, research on the phylogenetic analysis of Baccaurea in West Sumatra using the molecular marker MatK is important to do in order to provide convenience in the process of proving and identifying accurately and quickly.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic Analysis of Baccaurea Spp. in West Sumatra Using MatK Molecular Markers

Saswita,

Syamsuardi,

Nurainas

et al. 2023

J Bio Bio Edu

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Baccaurea is a group of fruit-producing plants found in wild forests. Many of these plant species have not yet explored their potential. The high rate of deforestation in West Sumatra poses a threat of extinction to the genetic resources of the genus Baccaurea before being explored and identified. The research aims to analyze the sequence characters and phylogenetic of Baccaurea found in West Sumatra using the MatK molecular marker. Phylogenetic analysis using the Maximum Likelihood (ML) method in MEGA X application. The results of the analysis of the six species of Baccaurea found that the sequence length ranged from 854-1019bp, the percentage of G+C base composition is 33.4%, the percentage of A+T base composition is 66.6%, the genetic distance range is 0-4% with a conservative character of 484bp and informative characters of 4bp. While the phylogenetic analysis using the ML method grouping the six species of Baccaurea to form a monophyletic clade with a bootstrap value of 100%, all species collected were in the same clade. These results reveal the first time that the MatK sequences from six species Baccaurea native to West Sumatra will be included in NCBI for use by other studies in conducting broader phylogenetic research.

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Barcoding DNA of red rice local varieties in South Sumatra based on matK gene

Hanum,

Fitriana,

Wardana

et al. 2023

Proceedings of the 9th International Symposium on Innovative Bioproduction Indonesia on Biotechnology and Bioengineering 2022:

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HUBUNGAN KEKERABATAN SPESIES DALAM GENUS Zanthoxylum MENGGUNAKAN SEKUEN GEN MATURASE K (matK) DNA KLOROPLAS

Cited by 3 publications

References 0 publications

Understanding Diospyros rumphii Bakh from North Sulawesi through Long-read sequences analysis using MinION Oxford Nanopore Technologies

Understanding Diospyros rumphii Bakh from North Sulawesi through Long-read sequences analysis using MinION Oxford Nanopore Technologies

Phylogenetic Analysis of Baccaurea Spp. in West Sumatra Using MatK Molecular Markers

Barcoding DNA of red rice local varieties in South Sumatra based on matK gene

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