Molecular Characteristics of Cytochrome B for Mackerel Barcoding

Maulid, Deden Yusman; Nurilmala, Mala; Nurjanah, Nurjanah; Maddupa, Hawis

doi:10.17844/jphpi.v19i1.11686

Cited by 8 publications

(12 citation statements)

References 7 publications

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“…DNA barcoding has advantages in precision and accuracy in the safe identification of species compared with the morphological observations. This method has been successfully proven in different marine organisms (Jefri et al 2015;Prehadi et al 2015;Sembiring et al 2015;Madduppa et al 2016;Maulid et al 2016;Saleky et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Short Communication: DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia

et al. 2017

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DNA Barcoding is a tool in the molecular taxonomy which allows a rapid and precise identification. This tool is needed to mitigate difficulties in identifying species of sea cucumbers in Indonesia. This study was conducted to reveal species diversity in sea cucumbers (Holothuridae and Stichopodidae), commonly harvested in the Kepulauan Seribu reefs, northern Jakarta, Indonesia, by using mitochondrial DNA. Neighbor-joining phylogenetic trees were reconstructed using the Kimura-2 parameter with 1000 of bootstrap values. The genetic distance within and between species was investigated. Conservation and trade status of the species were determined using IUCN and CITES, respectively. DNA barcoding using mitochondrial Cytochrome oxidase 1 (COI) revealed 7 species from 96 samples, of which 4 species belonged to the Stichopodidae (Stichopus herrmanni, Stichopus ocellatus, Stichopus horrens, Stichopus monotuberculatus), and 3 species to the Holothuridae (Bohadschia bivittata, Actinopyga lecanora and Holothuria leucospilota). Phylogenetic analysis showed that the two families were separated with a high bootstrap value. The neighbor-joining tree supported the result of identification of the sea cucumber species. The ingroup haplotypes were clustered into four main clades. Stichopus herrmanni and S. ocellatus were identified as closely related, which matches their morphological characteristics. Bohadschia bivittata is the most distinct species from other species due to the formation of a separate clade in the phylogenetic tree. Stichopus. horrens and S. monotuberculatus were also identified as very closely related, which might explain the frequent morphological misidentification of both types. The conservation status determined one of the investigated species was categorized as vulnerable, one as least concern, one as not evaluated, and four species in data deficient. The population trend of S.s herrmanni was recorded to be decreasing, whereas it remained unknown for the other 6 species. Surprisingly, all identified species in this study were not evaluated yet by CITES. This study suggests that a proper field monitoring and the establishment of a valid list of commercial and scientific names for the sea cucumbers harvested in Kepulauan Seribu is necessary. This would be valuable for keeping trade records and managing and conserving the targeted sea cucumber species in the region.

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Section: Introductionmentioning

confidence: 99%

Short Communication: DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia

et al. 2017

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“…This suorts the taxonomic identification of this specimen and serves as a useful case study demonstrating the utility of molecular methods (Ahmed et al, 2016 andAhmed et al, 2020).There is no information on molecular identification of sea cucumbers from Pakistan, but Kamarul et al (2010) sequenced Holothuriapardalis from Malaysia which aears closely related to sequences from the present study.As compared to morphological observation in isolation, DNA barcoding has advantages in precision and objectivity for the identification of species as it is based purely on systematic analysis of hundreds of observed characters. This method has been successful in different marine organisms including sea cucumbers (Kamarul and Ridzwan, 2005;Kamarul, et al, 2006;Kamarudin, et al 2010;Ismail et al 2012;Jefri et al 2015;Prehadi et al 2015;Sembiring et al, 2015;Kamarudin and Rehan, 2015;Maddua et al 2016;Maulid et al 2016;Saleky et al 2016;Zahra et al 2016;Kamarul et al 2018). Ismail et al (2012 studied the molecular taxonomy of commercially important species of the class Figure 2.…”

Section: Discussionand Conclusionmentioning

confidence: 99%

“…This method has been successful in different marine organisms including sea cucumbers (Kamarul and Ridzwan, 2005;Kamarul, et al, 2006;Kamarudin, et al 2010;Ismail et al 2012;Jefri et al 2015;Prehadi et al 2015;Sembiring et al, 2015;Kamarudin and Rehan, 2015;Maddua et al 2016;Maulid et al 2016;Saleky et al 2016;Zahra et al 2016;Kamarul et al 2018). Ismail et al (2012 studied the molecular taxonomy of commercially important species of the class Figure 3.…”

Section: Discussionand Conclusionmentioning

confidence: 99%

Identification of Sea Cucumber Holothuria (Lessonothuria) Pardalis (Selenka, 1867) and Holothuria (Semperothuria) Cinerascens (Brandt, 1835) (Family-Holothuriidae) based on Morphological and Mitochondrial DNA Evidence and Phylogenetic Analysis from Karachi Coast, Pakistan

Ahmed

Ali

Macdonald

2021

International Journal of Environment and Geoinformatics

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The conventional taxonomy on sea cucumbers is challenging due to their morphological complexity. Molecular investigation of the class Holothuroidea was initiated for further clarity regarding the systematics and taxonomy of this class. A molecular phylogeny of the Holothuroidea was constructed by using maximum likelihood methods, and this unveiled variation in the existing taxonomic classification, which is largely based on the morphology of calcareous parts. H. pardalis and H. cinerascens from Pakistan was identified morphologically but no information was found with regard to molecular identification. This is the first research describing the molecular identification of H. pardalis and H. cinerascens based on 16S rRNAandCOIgenes from the Karachi Coast of Pakistan. Comparisons of mitochondrial 16S rRNAand COI to accessioned sea cucumber sequences on GenBank confirmed H.pardalis'and H. cinerascens identity. This study is the first to report on molecular identification of H.pardalis and H. cinerascens based on the 16S rRNAand COI gene from the Karachi Coast, Pakistan.

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“…Ambiguitas dan kesalahan dalam identifikasi suatu spesies dapat menjadi ancaman bagi kegiatan konservasi maupun perikanan berkelanjutan (Sembiring et al, 2015). Beberapa penelitian telah mampu mengidentifikasi ikan komersil dari perairan Indonesia menggunakan teknik genetika molekuler diantaranya pada ikan kakap (Lutjanus), kerapu (Epinephelus), makarel (Scomberomorus), tuna (Thunnus) (Abdullah dan Rehbein 2016; Jefri et al, 2015;Maulid et al, 2016Nurimala et al, 2016: Akbar dan Labenua, 2018. Manfaat studi morfometrik sendiri yaitu dapat mengetahui dan mendeskripsikan pola pola keragaman morfologis dan pola pertumbuhan baik itu antar populasi ataupun spesies (Strauss & Bond, 1990 CA-3' (Ward et al, 2005).…”

Section: Pendahuluanunclassified

IDENTIFIKASI IKAN SARDIN KOMERSIAL (Dussumieria elopsoides) YANG DIDARATKAN DI PASAR MUARA ANGKE, JAKARTA MENGGUNAKAN PENGAMATAN MORFOLOGI, MORFOMETRIK DAN DNA BARCODING

Rahim

Madduppa

2020

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Sardines are an important commodity in import activities. Excessive imports and lack of catch data are feared to reduce fish stocks. To complete the fish catch data required knowledge of body type and size. This study aims to identify and confirm commercial sardines species landed at Muara Angke Market, Jakarta using morphological, morphometric, and DNA barcoding methods targeting the Mitochondrial Cytochrome c oxidase-I (COI) gene. The results of morphological and morphometric analysis showed that the samples are the genus Dussumieria originating from the Dussumieriidae family, the Order Clupeidae, having silver-colored body characteristics with reflections resembling rainbows, slender bodies and rounded stomachs with a maximum length of up to 14.4 cm, then less abdominal fins advance from the midsection. Based on the relationship of body weight length, this fish is negative allometric. Molecular DNA barcoding analysis using COI, obtained by type of Dussumieria elopsoides fish with local name of rainbow sardines, similarity level with Query Cover percentage was 94% and Per percentage. Ident of 91.64%. DNA barcoding analysis has corroborated morphological and morphometric observations by obtaining fish samples identified as Dussumieria elopsoides.

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Molecular Characteristics of Cytochrome B for Mackerel Barcoding

Cited by 8 publications

References 7 publications

Short Communication: DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia

Short Communication: DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia

Identification of Sea Cucumber Holothuria (Lessonothuria) Pardalis (Selenka, 1867) and Holothuria (Semperothuria) Cinerascens (Brandt, 1835) (Family-Holothuriidae) based on Morphological and Mitochondrial DNA Evidence and Phylogenetic Analysis from Karachi Coast, Pakistan

IDENTIFIKASI IKAN SARDIN KOMERSIAL (Dussumieria elopsoides) YANG DIDARATKAN DI PASAR MUARA ANGKE, JAKARTA MENGGUNAKAN PENGAMATAN MORFOLOGI, MORFOMETRIK DAN DNA BARCODING

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