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Molecular Identification and Genetic Characteristics of Genus Mystacoleucus Based on Gene Cytochrome Oxidase C Subunit I (COI) in Sengguruh Dam
Abstract and Figures
In general, the process of naming several species of fish including species from the genus Mystacoleucus is still carried out based on morphological characters, which are often found in almost the same morphological characters in different fish species. Therefore, it is necessary to apply a more accurate identification method, which is a DNA-based identification method called DNA barcoding. The purpose of this study was to identify the species of the genus Mystacoleucus on the Sengguruh Dam molecularly based on the Cytochrome Oxidase C Subunit I (COI) gene. A caudal fin was taken on the test fish and preserved in 95% ethanol solution for molecular identification. The results of the identification showed that the sample belonged to the Mystacoleucus marginatus species with Identity values between 99-100% and E-value 0.0. The data obtained showed that from the calculation of genetic distance presented in the form of data matrix and phylogenetic tree reconstruction, there were 2 species that had a far genetic distance from the M. marginatus sample from the Sengguruh Dam namely M. atridorsalis with the furthest genetic distance of 0.1932-0.2595 and M. lepturus with genetic distance between 0.1117-0.1193. However, there is one species that has the closest distance, M. padangensis with genetic distance between 0.0019-0.0038 and identity values up to 99%.
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... Based on geographical distribution (Fig. 1), M. marginatus is found in Brantas River, East Java and has been recorded in West java (Dahruddin et al. 2017;Valen et al. 2020;Valen et al. 2019aValen et al. , b, 2021 with high average amounts of adenine and thymine, so that the COI gene of this genus is categorized as an A-T rich group (A-T rich). The A-T hydrogen bond consists of 2 hydrogen bonds which are weaker than the G-C hydrogen bond which has 3 hydrogen bonds, so the possibility of species mutation is higher. ...
sss Abstract Mystacoleucus marginatus and M. padangenesis are freshwater fish species that found in Indonesia. Mystacoleucus marginatus is native to Indonesia and M. padangensis is an endemic species to West Sumatra, Indonesia. This study aimed to investigate the relationship between M. marginatus from the Berantas River, East Java, and M. padangensis from Singkarak Lake, West Sumatra based on the Cytochrome Oxidase subunit I (COI) gene. Based on the results, M. marginatus and M. padangenesis have a close genetic distance, with similarity of 99.81%, having difference of 3 nucleotide bases; then they can be identical or synonym. The nucleotide composition in M. marginatus and M. padangensis are almost similar where the percentage of nucleotide composition in M. marginatus is T (28.1%), C (29.2%), A (27.0%) and G (15.8%) and that of M. padangensis is T (28.3%), C (28.8%), A (26.8%) and G (16.2%). Based on phylogenetic tree, both species are closely related in the same cluster. Therefore, it is suggested they are a same species based on the COI gene, but suggesting further research using mitochondrial DNA complex and in-depth morphological analysis.
... In this work, we also provide morphological and molecular data of the collected specimens to identify them. For molecular identification, we used DNA barcoding based on Cytochrome C Oxidase subunit I (COI), a standard method for species identification with a high level of accuracy (Hubert et al., 2008;Luo et al., 2011;Valen et al. 2019a;Lutfiatunnisa et al., 2021). ...
A new distributional record of flying barb, Esomus metallicus (Actinopterygii: Cyprinidae), from Kapalo Abstract: A new locality was reported for Esomus metallicus in Kapalo Banda River, 50 Kota Regency, West Sumatra Province, Indonesia, about 74 km from Maninjau Lake. Identification of species was made by morphological and molecular methods using the COI gene. We also applied the Neighbor-Joining method to construct the phylogenetic tree. Based on morphological analysis, the specimens from Kapalo Banda River were E. metalicus with the unique feature of having long maxillary barbels. Based on the DNA sequence, specimens of West Sumatra were identical to E. metallicus sequence of Thailand specimens with a similarity of 99-100%, suggesting the probable origination of the Kapalo Banda River from Thailand.
... Tidak hanya teridentifikasi dan tervalidasi secara morfologi, beberapa spesies dari genus Channa di Indonesia telah teridentifikasi secara molekuler dengan metode DNA Barcoding, yang mana DNA Barcoding tersebut telah disubmit pada database NCBI Genbank. Keberadaan DNA Barcoding pada NCBI genbank dapat dimanfaatkan untuk penelitian lebih lanjut seperti analisis spesies (Valen et al., 2019a) filogenetik (Valen et al., 2022;Valen et al., 2019b) pada suatu genus dan keragaman genetik (Valen et al., 2021). Analisis filogenetik untuk Genus Channa sendiri di Indonesia belum dilakuakn sehingga pada penelitian ini kami akan melakukan analisis filogenetik untuk melihaat kekerabatan antar spesies pada genus Channa yang tersebar di Indonesia dengan memanfaatkan DNA Barcoding yang ada pada Genbank NCBI. ...
Artikel ini bertujuan untuk menjelaskan dan mengambarkan filogenetik genus Channa di Indonesia menggunakan gen COI (Chytocrome C Oxydase Sub unit I). Sebanyak sembilan (9) spesies Channa yang tersebar di Indonesia dan terdata di NCBI Genbank terdiri dari Channa limbata,Channa bankanensis,Channa lucius,Channa marulioides,Channa melasoma, Channa micropeltes,Channa pleurophthalma, Channa gachua dan Channa striata telah dianalisis filogenetik dan jarak genetik antar spesiesnya. Jarak genetik terdekat yaitu pada Channa pleurophthalma dengan Channa striata yaitu 0.000. dengan komposisi nukleutida pada keduanya adalah timin sebanyak 26,98%, sitosin sebanyak 29,80%, adenin sebanyak 25,16% dan guanin sebanyak 18,04%.
... Especially in Java, M. marginatus was spread in the Brantas basin, East Java (Dahruddin et al., 2017;Valen et al., 2019). The genetic diversity of M. marginatus in Brantas upstream has not been recorded. ...
Mystacoleucus marginatus, a native freshwater fish in the family Cyprinidae, is known from parts of Southeast Asia and Western Indonesia Archipelago (Borneo, Sumatra, and Java). This study aims to identify the genetic diversity of M. marginatus in the Brantas basin upstream, Java, Indonesia based on the Cytochrome C Oxidase Subunit I (COI) gene. The results showed that M. marginatus in the Brantas basin upstream had 2 Haplotypes with Haplotype diversity (Hd) = 0.222 and nucleotides diversity (Pi) = 0.00041.
The Spanner barb, Barbodes lateristriga, a Cyprinid, lives as a benthopelagic in the clear mountain streams with rocks and boulders beds, frequently found below waterfalls. This species was previously recorded from Southern Thailand; Malay Peninsula, Singapore and Borneo. In this study, we report from Bangka Island, Indonesia. The Bangka Islands are located on the Sundaland, which has a quite high biodiversity. The specimens of B. lateristriga were taken from the Menumbing Hill River, Bangka Island, Indonesia and then identified morphologically and molecularly. The molecular identification was carried out using the DNA barcoding method and the standardized cytochrome c oxidase subunit I (COI) gene. The results of molecular analysis revealed that specimens of the Bangka Islands are B. lateristriga with a similarity level of up to 100%. This is also confirmed by the results of phylogenetic tree analysis where samples from the Bangka Islands clustered in the same group as B. lateristriga found in the Genbank.
Barbonymus gonionotus is a species of cyprinid native to river drainages in southeastern Asia, which occurs in the Cambodia, Vietnam, Thailand, Laos and Indonesia. This study aims to identify the molecular phylogenetic of Barbonymus gonionotus in Java, Indonesia based on the Cytochrome C Oxidase Subunit I (COI) gene. Specimen from the Opak river had 656 base pairs with the Identity values 100% to Barbonymus gonionotus. The genetic distance of Barbonymus gonionotus in the Java was 0.000-0.005. Phylogenetic tree of Barbonymus gonionotus in the Java is provided.
An annotated checklist of the fishes of the Endau River drainage in southeastern Peninsular Malaysia is provided. A total of 108 species in 26 families is reported from the Endau basin, of which 36 are new records and 2 are new species of catfish described here. Akysis microps, new species (Akysidae) resembles A, heterurus, but differs from it and other congeners by the following unique combination of characters: depth of caudal peduncle 8.3%-9.6% SL length of anal-fin base 16.2%-18.6% SL, length of adipose-fin base 15.2%-23.0% SL, eye diameter 9%-13% HL, length of nasal barbel 95%-106% HL, length of maxillary barbel 139%-170% HL, length of inner mandibular barbel 94-102% HL, length of outer mandibular barber 110%-154% HL, 10-11 anal-fin rays, and 5-7 serrations on the posterior edge of the pectoral spine. Nanobagrus nebulosus, new species (Bagridae), is characterized by large eyes (eye diameter 14.1%-15.1% HL), pectoral spine with 16 serrations on the posterior edge, 35-36 vertebrae, and a dark grayish-brown body with a series of cream-colored spots mostly on the dorsal surface of the body. It is also the Ist record of the genus from Peninsular Malaysia.
Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
Mystacoleucus padangensis or bilih fish is an endemic species of Singkarak Lake. It has accidentally introduced to Anai River through water canal from Singkarak's hydroelectric system. Changes in habitat type from lentic to lotic have been suppossed to force this species to make morphological adaptation. This study aimed to compare morphological variation of bilih fish living at the two habitat types. We measured 29 morphological characters of 400 individuals from each habitat. We also measured 19 environmental parameters. To clarify differentiation between the two population and environmental parameters we used mann-whitney U-test. The results showed differentiation between 13 characters of Anai bilih fish, i.e. preorbital distance, eye diameter, postorbital distance, head length, prepelvic distance, predorsal distance, head depth, body depth, caudal fork length, caudal peduncle length (ventral), anal fin base length, pelvic and pectoral fin length. The differences between some environmental parameters could take responsible to the differentiation of bilih. This study supports that adaptation to the water velocity has caused anterior differences between the two populations.
The fish diversity of the Nam Theun and Xe Bangfai drainages was surveyed between 1996 and 2012. 74 species are now recorded from the Nam Theun and 178 from the Xe Bangfai drainages. Twenty-one (28%) of the Nam Theun species are endemic and 9 (5%) of the Xe Bangfai species. At the time of the respective surveys, 54 species were new records for Laos, and 25 species were new to science. While the fish fauna of Xe Bangfai is similar to that of the other main tributaries of the Mekong in Laos, the fish fauna of the Nam Theun is characterised by a great proportion of endemics, several of which have affinities with species known from the opposite slope of the Annamite Range, in Vietnam. Besides, work conducted in relation with aquatic biodiversity surveys for the Nam Theun 2 project resulted in an increase of the fish fauna of Laos from 210 to 481 in 3 years between March 1996 and June 1999 and the discovery of 128 species new to science and lead to the publication of an identification guide. Specific studies have been conducted to assess the status of some of the endemic species that were potentially threatened by the Nam Theun 2 scheme: Scaphognathops theunensis (still observed in 2012 downstream of Nakai Dam), Tor ater (mainly restricted to streams upstream of the reservoir), and Oryzias sp. 'swamp' (along the fringe of the reservoir). The status of the bitterling Rhodeus laoensis and its associated mussel is still not clear. Most of the species endemic to the Nam Theun drainage are known upstream of the reservoir, which is a protected area. The endemic species known on Nakai Plateau and downstream of the dam are more at risk and require closer monitoring.
Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous and the taxonomic knowledge is scattered in the literature. The present study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of the present study, a checklist was compiled based on online catalogs. A total of 95 sites were visited and a library including 1,046 DNA barcodes for 159 species was assembled. Nearest neighbor distance was 28-fold higher than maximum intra-specific distance on average and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e.24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies. This article is protected by copyright. All rights reserved.
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