Genetic diversity of commercial sea cucumbers Stichopus (Echinoderm: Stichopodidae) based on DNA Barcoding in Karimunjawa, Indonesia

Sulardiono, Bambang; Hartoko, Agus; Aini, Arifah Nur; Wulandari, Dyah Ari; Budiharjo, Anto

doi:10.13057/biodiv/d230234

Cited by 2 publications

(1 citation statement)

References 12 publications

(12 reference statements)

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“…Coral reef is a coastal ecosystem which contains important and beneficial natural resources. Coral reefs have many good functions in ecology that act as biota habitats for many biotas such as octopus (Kholilah et al 2021), giant clam (DeBoer et al 2012), sea cucumber (Widianingsih et al 2021;Sulardiono et al 2022), and lobsters (Haryono and Ambariyanto 2018). Even the research of Pertiwi et al (2015), states that dead corals can become habitats for decapods.…”

Section: Introductionmentioning

confidence: 99%

DNA barcode of seven species coral from Sepulu, Madura Island, Indonesia

et al. 2023

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Abstract. Insafitri, Nursalim N, Kholilah N, Kurniasih EM, Cahyani NKD, Nugraha WA, Ambariyanto A. 2023. DNA barcode of seven species coral from Sepulu, Madura Island, Indonesia. Biodiversitas 24: 317-323. Diversity of coral species is needed because it affects the disruption of coral reef ecosystems, nutrient recycling, coral reef growth and the habitat of biota that live in these ecosystems. The main constituents of coral reef ecosystems are coral animals that belong to the Anthozoa class. Sepulu waters (Madura Island), Bangkalan District, East Java Province, Indonesia, has a percentage of coral cover that is in the bad category, management of coral reefs in this area has not been the main focus and it is feared that the situation will get worse so efforts are needed to maintain coral reefs to be sustainable and better. This management effort requires an analysis of species identification. DNA barcoding of corals has never been done on corals of Sepulu waters. The purpose of this study is to find out the DNA of barcoding coral species on Sepulu waters. Genetic marker Cytochrome Oxidase I of the mitochondrial genome DNA (mtDNA) was used to analyze genetic diversity. Reconstruction of phylogenetic tree and genetic diversity were done by using software MEGA X. Research results showed that sample DBP011101 closely related to Dipsatraea maxima 99.55%, DBP011102 closely related to Porites rus 99.4%, DBP011103 closely related to Acropora hyacinthus 99.11%, DBP011104 closely related to Porites cf lichen 98.66%, DBP011106 closely related to Dipsastraea rotumana 95.37%, DBP011107 closely related to Porites horrisoni 98.81%, and DBP011108 closely related to Acropora valida 98.38%. The results of the study are the first coral barcode DNA on Sepulu waters that can help in determining coral species that are useful in managing the sustainability of coral resources, especially on Sepulu waters.

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Section: Introductionmentioning

confidence: 99%

DNA barcode of seven species coral from Sepulu, Madura Island, Indonesia

et al. 2023

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New Record of Echinoderms from Gili Ketapang Island by Combining DNA Barcoding and Morphology: A Baseline Report

Nugroho

Ardiansyah

Kurniawan

et al. 2022

Preprint

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Echinoderms are marine water invertebrates that are showing diverse morphologies and grouped in five classes, however the reports on this species from Gili Ketapang Island, East Java is currently limited. DNA barcodes (DNA fragments of the 5' end of the cytochrome c oxidase subunit I gene, COI) have been used to support the morphological examination in identifying evolutionary lineages. This study aims to identify the morphology and supplement of COI sequence and phylogenetic of Echinoderms from Gili Ketapang Island. A total of sixteen samples of Echinoderms were collected from Gili Ketapang, Probolinggo, Indonesia, then identified based on morphological characters, and supports identification was confirmed using molecular data. Subsequently, molecular characterization and identification was conducted based on 503 bp of COI gene similarity, sequence variation, genetic distance, phylogenetic topology, and BOLD System. According to the results, sixteen sample were identified as Diadema setosum; Macrophiothrix longipeda; Archaster typicus; Echinometra mathaei, Holothuria atra; Linckia laevigata, Bohadschia argus, and Ophiactis savignyi. Each species was associated with a specific DNA barcode cluster and the relationship among these species was clearly revealed. Each species based on morphological identification and COI sequence clusters were congruent. The median joining network and Automatic Barcode Gap Discovery (ABGD) analysis showed this Echinoderms population from Probolinggo had relatives of 14 haplotypes and divided into eight haplogroups. Furthermore, the population belonged to the same haplogroup but had different haplotypes. This newly records established sequence reference library for the Gili Ketapang Island.

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Genetic diversity of commercial sea cucumbers Stichopus (Echinoderm: Stichopodidae) based on DNA Barcoding in Karimunjawa, Indonesia

Cited by 2 publications

References 12 publications

DNA barcode of seven species coral from Sepulu, Madura Island, Indonesia

DNA barcode of seven species coral from Sepulu, Madura Island, Indonesia

New Record of Echinoderms from Gili Ketapang Island by Combining DNA Barcoding and Morphology: A Baseline Report

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