Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene

Riani, Sri; Prabowo, Romanus Edy; Nuryanto, Agus

doi:10.13057/biodiv/d220349

Cited by 4 publications

(4 citation statements)

References 48 publications

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“…This result is consistent with previous decisions on the taxonomic status of the samples, where they showed similar traits as the reference conspecific in the databases. Previous studies reported that a 3% genetic divergence is widely used in animal barcoding as a species border (Hubert et al 2012;Ko et al 2013;Mohammed et al 2021;Riani et al 2021). Several studies have also explored various thresholds as species border during molecular identification from less than 1% to 5% (Cote et al 2013;Aguilar et al 2017: Ha et al 2019Abdalwahhab et al 2020).…”

Section: Taxonomic Status Of Crustacean Larvaementioning

confidence: 99%

DNA barcoding of crustacean larvae with two new records of Caridina gracilipes and Ptychognathus altimanus in the Western Region of Segara Anakan lagoon in Indonesia

2023

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Abstract. Winarni ET, Simanjuntak SBI, Nuryanto A. 2023. DNA barcoding of crustacean larvae with two new records of Caridina gracilipes and Ptychognathus altimanus in the Western Region of Segara Anakan lagoon in Indonesia. Biodiversitas 24: 341-348. Several studies have been carried out on crustacean larvae diversity, but they focused on the eastern and central regions of the Segara Anakan lagoon/estuary, Cilacap District, Central Java Province, Indonesia. Furthermore, one study has explored crustaceans in the western region but focused on adult individuals and used morphological characteristics. Currently, there is no internet data on the crustacean larvae diversity from the estuary's western region, and there is a high possibility that some species are unidentified. This study aims to describe crustacean larvae diversity in the western region of the Segara Anakan lagoon in Indonesia by using DNA barcoding. Sequence divergence of 3% to databases in GenBank and BOLDsystems was used as a genetic threshold for species border. A total of 14 morphotypes were barcoded, but only nine were successful, of which three were identified as bacteria and six as crustaceans. Based on the predetermined genetic threshold, all crustacean morphotypes can be identified at the species level, and six species were obtained. Meanwhile, a previous study on the adult individual only identified specimens at the genus level, and only one genus was similar to these obtained results. A total of 5 out of 6 species were new records to the western region Cilacap, while 2, namely Caridina gracilipes and Ptychognathus altimanus, are newly recorded in the Segara Anakan lagoon. These results contribute significantly to the information on crustacea larvae diversity, which is essential for sustainable management.

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Section: Taxonomic Status Of Crustacean Larvaementioning

confidence: 99%

DNA barcoding of crustacean larvae with two new records of Caridina gracilipes and Ptychognathus altimanus in the Western Region of Segara Anakan lagoon in Indonesia

2023

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“…Species identification and population genetic studies were conducted using various molecular markers (Nuryanto et al 2017;Butet et al 2019;Nuryanto et al 2019;Elvyra et al 2020;Riani et al 2021;Setyaningrum et al 2022). The cytochrome c oxidase 1 (COI) gene is a common marker used in species determination (Ko et al 2013;Muchlisin et al 2013;Dahruddin et al 2016;Irmawati et al 2017;Syaifudin et al 2020) and population genetic studies (Song et al 2013;Zhang et al 2014;Fahmi 2015;Nuryanto et al 2019).…”

Section: Classicalmentioning

confidence: 99%

“…A genetic threshold between 4% and 5% is permissible for genetic species determination, although additional considerations should be accounted for (Higashi et al 2011;Jeffrey et al 2011). Previous studies also utilized a genetic threshold of 5% during species determination (Candek and Kuntner 2015;Kusbiyanto et al 2020;Riani et al 2021).…”

Section: Amino Acid Compositionmentioning

confidence: 99%

Morphological and molecular characterization of mole crab (Genus: Emerita) in the Cilacap coastlines of Indonesia, with particular focus on genetic diversity of Emerita sp. nov.

et al. 2022

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Abstract.Bhagawati D, Nuryanto A, Winarni ET, Pulungsari AE. 2022. Morphological and molecular characterization of mole crab (Genus: Emerita) in the Cilacap coastlines of Indonesia, with particular focus on genetic diversity of Emerita sp. nov. Biodiversitas 23: 2395-2404. Previous studies reported Emerita emeritus is the only species of the Genus Emerita inhabiting the coastal ecosystem of the Cilacap District. A recent study reported the presence of suspected new Emerita species living on the Cilacap sandy beach but used a small number of specimens and no reports about genetic diversity. This study used more Emerita samples than the previous study. This study aimed to identify Emerita specimens based on the morphology and the cytochrome c oxidase 1 gene and analyzed the genetic diversity of Emerita sp. nov. Emerita samples were collected from three different beaches in Cilacap District, Central Java, Indonesia. Morphological identification placed the samples into two different morphotypes. Morphotype A was identified as Emerita emeritus. Morphotype B was determined as Emerita sp. nov. Molecular data support the placement of Emerita samples into Emerita emeritus, and Emeritasp. nov. Emeritasp. nov. has haplotype diversity of 0.857±0.057, indicating a high genetic diversity. Haplotype H2 was suggested as the most primitive one because other haplotypes radiated from it. This study concluded that two sympatric Emerita species inhabit Cilacap coastlines, and Emeritasp. nov. has high genetic diversity.

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“…Molecular biology is the science of organization, activity, and gene regulation on the molecular level [32]. Molecular biology can be used for species identification on the molecular level, which cannot be done at the level of morphological characteristics [33], [34]. At the molecular level, genetic diversity was becoming a challenge for determining the genetic structure and its relationship between environment, human activity, and impact on urbanization [35], also conservation success [36].…”

Section: Molecular Biology As the Key To Bioinformaticsmentioning

confidence: 99%

Current Evidence on Bioinformatics Role and Digital Forensics That Contribute to Forensic Science: Upcoming Threat

Hakim¹,

Putri

Hidayah

et al. 2022

JURRIMIPA

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Forensics has become an essential part of the disclosure of criminal evidence. A bioinformatics approach in the form of DNA forensics and digital forensics can be a good combination in disclosing digital-based criminal evidence. This study explains how the role of bioinformatics through the digital approach can be a means of forming new approaches in integration with digital forensics, called cyber-bioinformatics. Despite many hopes and challenges ahead, it does not rule out the possibility of criminal cases related to the privacy of human genomic data, so it proposes a new hypothesis, “cyber-bioinformatics.” The role of cyber-bioinformatics is very central in this regard.

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Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene

Cited by 4 publications

References 48 publications

DNA barcoding of crustacean larvae with two new records of Caridina gracilipes and Ptychognathus altimanus in the Western Region of Segara Anakan lagoon in Indonesia

DNA barcoding of crustacean larvae with two new records of Caridina gracilipes and Ptychognathus altimanus in the Western Region of Segara Anakan lagoon in Indonesia

Morphological and molecular characterization of mole crab (Genus: Emerita) in the Cilacap coastlines of Indonesia, with particular focus on genetic diversity of Emerita sp. nov.

Current Evidence on Bioinformatics Role and Digital Forensics That Contribute to Forensic Science: Upcoming Threat

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