Molecular Identification and Genetic Diversity ofAcropora hyacinthusfrom Boo and Deer Island, Raja Ampat, West Papua

Wijayanti, Diah Permata; Indrayanti, Elis; Nuryadi, Handung; Dewi, Rose; Sabdono, Agus

doi:10.1088/1755-1315/116/1/012065

Cited by 4 publications

(5 citation statements)

References 18 publications

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“…The use of the whole ITS region is feasible and very sensitive in representing small differences and mutations in E. lamellosa population. The ITS region also provides more robust data than any other genetic markers for coral, such as the mtCOI markers (Wijayanti et al 2018). The Euclidean distance matrix also supports that colonies GPE 33 and GPE 35 are very distinct from other samples in both western and eastern groups (Figure 3).…”

Section: Sequence Identification and Genetic Structurementioning

confidence: 60%

“…This study utilizes the whole ITS region (ITS1-5.8S-ITS2 region) of E. lamellosa rDNA to be amplified as a marker. A previous study conducted by Wijayanti et al (2018) using a mtCOI marker on Acropora hyacinthus populations resulted in accurate genetic identification, but less sensitivity to build a phylogenetic tree. A single copy of ITS (Internal Transcribed Spacer) region has been extensively used for population genetic and phylogenetic studies of corals and symbionts (see Takabayashi et al 2003;Terrana et al 2021).…”

Section: Dna Extractionmentioning

confidence: 99%

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Neither Coral- nor Symbiont- Genetic Diversity may Explain the Resistance of the Coral Echinopora lamellosa to Bleaching

Bachtiar

Ghafari

Rahman

et al. 2021

J.Tropical Biodiversity Biotechnology

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Genetic diversity has an important role in the stability of coral populations in coping with disturbances. In the last three bleaching events, the coral Echinopora lamellosa survived better in the eastern- than the western- Lombok waters that are not related to algal symbiont diversity. The present study aimed to assess the genetic diversity of E. lamellosa from the two locations in the Lombok waters. The ITS1-5.8S-ITS2 (whole ITS region) marker was used to identify and to determine the genetic structure, genetic variation, and demographic pattern of E. lamellosa. The results showed that E. lamellosa of the two locations are two different populations. The haplotype diversity was very high indicating a predominance of sexual reproduction mode for both eastern and western populations. The phylogenetic topology suggests there is possible connectivity between populations, whereas the haplotype network exhibits a restricted gene flow between the two populations. The results suggest that the present E. lamellosa populations were from both surviving colonies and new recruitment of long-distance larvae. Both population likely shares the same larvae supply brought from source-reefs in the Flores Sea or Makassar Strait by the Indonesian Throughflow. The present and previous studies revealed that genetic diversity alone yet to explain the resistance of E. lamellosa in eastern and western Lombok waters.

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Section: Sequence Identification and Genetic Structurementioning

confidence: 60%

Section: Dna Extractionmentioning

confidence: 99%

Neither Coral- nor Symbiont- Genetic Diversity may Explain the Resistance of the Coral Echinopora lamellosa to Bleaching

Bachtiar

Ghafari

Rahman

et al. 2021

J.Tropical Biodiversity Biotechnology

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“…Sample tissue was taken ±2 mm and then inserted into a tube containing 10% Chelex solution. The sample is vortexed for 10-15 seconds (Wijayanti, 2018), then heated using a heating block for 45 mins at a temperature of 95ºC. After being heated, the sample was vortexed again for 10-15 secs.…”

Section: Dna Extraction and Isolationmentioning

confidence: 99%

DNA Barcoding and Morphological Characters of Two Trevally Fish species (Caranx Spp.) Collected from Youtefa Bay, Papua, Indonesia

et al. 2023

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Trevally fish (Caranx spp,) or Kuwe fish (local name) are small pelagic fish that are mostly caught in the waters of Youtefa Bay. There are two types of Kuwe fish that are difficult to distinguish due to morphological similarities. These Kuwe fish have no scientific species identification so they have several different local names. Accordingly, it is necessary to identify and find out the proper naming of the two Kuwe fish. DNA barcoding is a technique used to speed up and simplify the process of identifying organisms. Hence, the purpose of this research was to identify the proper scientific name of the two Kuwe species in Youtefa Bay waters, as well as the kinship between these two types by applying a DNA barcoding technique. Nineteen Kuwe fish were sampled at Youtefa Bay, Jayapura, Papua in July 2022. Samples were studied morphologically, then carried directly to the Integrated Laboratory of Diponegoro University for molecular studies. DNA extraction, amplification, and DNA sequencing were carried out to further validate the species’ identification. The results showed that in the initial assessment of the specimens using taxonomic keys, 10 specimens were identified as Caranx sexfasciatus and 9 specimens were identified as Caranx tille. The relationship between length and weight of C. sexfasciatus and C. tille have resulted in b = 2.5754 with R2 = 0.8564 and = 1.7119 with R2 = 0.6705, respectively. All identifications were confirmed as correct based on BLASTn results. The BLAST analysis demonstrated that 10 samples were closely related to C. sexfasciatus (99%-100% in similarity) and 9 samples were similar to C. tille (97%- 99%). The genetic distance between individuals in C. sexfasciatus and C. tille has a value ranging from 0% - 0.2%, and the phylogenetic tree exposed that the two species are included in different clades. This study revealed that there are two species of Kuwe fish (C. sexfasciatus and C. tille) in Youtefa Bay, Papua, Indonesia.

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“…In order to comprehend the status of the existing stock, baseline data must be established. The previous research on DNA Barcode and phylogenetic tree has been carried out on marine organism like fish [6][7] [8], shellfish [9][10] [11], crustacean [12][13] and coral reef [14] [15]. The ability to identify species at any stage of an organism's development (such as larval, juvenile, or adult stages), as well as at early stages that cannot be done using descriptions, is the most promising advantage of DNA barcoding and phylogenetic trees for species authentication, morphology and interspecies connections.…”

Section: Introductionmentioning

confidence: 99%

Molecular analysis of the blood cockle, Tegillarca granosa (Linnaeus 1758) from Indonesia

Castaneda,

Hardianto,

Setyobudi

et al. 2023

IOP Conf. Ser.: Earth Environ. Sci.

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The blood cockle, Tegillarca granosa, is one of the key member of shellfish communities that are ecologically and economically important specially in Indonesia. We collected samples from four sites in Indonesia: Banyuwangi, Bali Island, Maros and Buru Island. Nucleotide sequence analysis was performed on PCR-amplified mitochondrial DNA COI gene. In total, 556-558 base pair nucleotide sequences were obtained from 12 individuals. Molecular analyses revealed samples belonging to the T. granosa species. Phylogenetic analyses were carried out by comparing the gene sequences of T. granosa haplotypes in Indonesia with gene sequences of the same base pair length and with the of Anadara tuberculosa which was used as an outgroup. The phylogenetic trees were consistent and indicated in the two sub-clades. The presence of T. granosa and the phylogenetic status of the T. granosa Indonesian haplotype were reported. Clarifying the phylogenetic status of ecologically important species provides basic information studies for possible future conservation and control programs.

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Molecular Identification and Genetic Diversity ofAcropora hyacinthusfrom Boo and Deer Island, Raja Ampat, West Papua

Cited by 4 publications

References 18 publications

Neither Coral- nor Symbiont- Genetic Diversity may Explain the Resistance of the Coral <i>Echinopora lamellosa</i> to Bleaching

Neither Coral- nor Symbiont- Genetic Diversity may Explain the Resistance of the Coral <i>Echinopora lamellosa</i> to Bleaching

DNA Barcoding and Morphological Characters of Two Trevally Fish species (Caranx Spp.) Collected from Youtefa Bay, Papua, Indonesia

Molecular analysis of the blood cockle, Tegillarca granosa (Linnaeus 1758) from Indonesia

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