DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh

This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.

Pragmatic applications of DNA barcoding markers in identification of fish species – a review

DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.

An Extensive Survey of Ciguatoxins on Grouper Variola louti from the Ryukyu Islands, Japan, Using Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS)

Ingesting fish contaminated with ciguatoxins (CTXs) originating from epibenthic dinoflagellates causes ciguatera fish poisoning (CFP). CFP occurs mainly in the tropical and subtropical Indo–Pacific region and the Caribbean Sea. Furthermore, it occurs sporadically in Japan, especially in the Ryukyu Islands between Taiwan and Kyushu, Japan. Variola louti is the most frequently implicated fish with a suggested toxin profile, consisting of ciguatoxin-1B and two deoxy congeners. Therefore, using the liquid chromatography–tandem mass spectrometry (LC-MS/MS), we analyzed CTXs in the flesh of 154 individuals from various locations and detected CTXs in 99 specimens (64%). In 65 fish (43%), CTX levels exceeded the Food and Drug Administration (FDA) guidance level (0.01 µg/kg). Furthermore, in four specimens (3%), the guideline level in Japan (>0.18 µg/kg) was met. Additionally, although the highest total CTX level was 0.376 µg/kg, the consumption of 180 g of this specimen was assumed to cause CFP. Moreover, only CTX1B, 52-epi-54-deoxyCTX1B, and 54-deoxyCTX1B were detected, with the relative contribution of the three CTX1B analogs to the total toxin content (35 ± 7.7 (SD)%, 27 ± 8.1%, and 38 ± 5.6%, respectively) being similar to those reported in this region in a decade ago. Subsequently, the consistency of the toxin profile in V. louti was confirmed using many specimens from a wide area. As observed, total CTX levels were correlated with fish sizes, including standard length (r = 0.503, p = 3.08 × 10−11), body weight (r = 0.503, p = 3.01 × 10−11), and estimated age (r = 0.439, p = 3.81 × 10−7) of the specimens. Besides, although no correlation was observed between condition factor (CF) and total CTX levels, a significance difference was observed (p = 0.039) between the groups of skinnier and fattier fish, separated by the median CF (3.04). Results also showed that the CF of four specimens with the highest CTX level (>0.18 µg/kg) ranged between 2.49 and 2.87, and they were skinnier than the average (3.03) and median of all specimens.

Triplophysa ferganaensis, a new loach species from Fergana Valley in Central Asia (Teleostei: Nemacheilidae)

Triplophysa ferganaensis sp. nov. is described from the Shakhimardan stream, a small tributary of the Syr Darya, which does not reach the river in Fergana Valley. It can be distinguished from other valid Triplophysa loaches based on the following combination of characters: body smooth and scaleless, lateral line complete, posterior chamber of air bladder degenerated, inner gill rakers 10-11 on the first-gill arch, outer gill rakers absent, vertebrae 4 + 35-36, 8 + 8 branched caudal-fin rays, caudal peduncle depth 2.1-2.7 times its length, two supratemporal pores, dorsal-fin origin closer to the caudal-fin base than to the snout tip, caudal fin emarginated and pelvic-fin tip reaching the anus. The new species can also be distinguished from its congeners based on the molecular analyses of mitochondrial cytochrome oxidase subunit I (coI) gene sequences. The phylogenetic position of this new species indicates that it is a sister taxon of Triplophysa tenuis.

Determining the Authenticity of Shark Meat Products by DNA Sequencing

Given that the global shark meat market is poised to grow in future years, the aim of this study was to use DNA sequencing of the cytochrome c oxidase I (COI) and NADH dehydrogenase subunit 2 (NADH2) mitochondrial genes to examine the market of shark meat products in Italy. This made it possible to analyze patterns of species utilization and commercialization of threatened, endangered and/or prohibited species, focusing on fraudulent activities in the shark food chain in order to propose seafood safety and environmental sustainability solutions. The study shows that the labeling of shark meat products generally lacks comprehensive information, thus making it difficult for consumers to make informed purchasing decisions and fails to comply with European Union (EU) legislation regarding seafood labelling. Molecular investigation reveals a high mislabeling rate (45.4%), highlighting widespread use of cheaper species either in order to replace species that are better known and more popular, or else in order to sell various threatened species. Considering that seafood mislabeling can circumvent the management of sustainable fisheries and facilitate Illegal, Unreported and Unregulated (IUU) fishing, the routine use of genetic analysis should be encouraged among control and enforcement agencies in order to implement effective management measures. This would help to build a species-specific reporting system for all catches, and enhance control measures, in order to prevent illegal activities connected with shark catches and trade around the world.