Dataset Information

Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters.

ABSTRACT: Anguilliformes, also known as "true eels", are an ecologically diverse group of predominantly marine origin whose members were easily recognized by their extremely elongated bodies with reduced cross-sectional areas and universal lack of pelvic fins. The Marine Eels were collected from landing centres of Parangipettai coastal waters and identified based on their morphometric and meristic characters. The newly recorded species were used for the barcoding analysis. Information on molecular taxonomy of marine eels was very meagre and hence, the present study was aimed to study the barcoding of marine eels which were present along the southeast coast of India. The cube of lateral muscle was exercised for DNA isolation followed by its amplification. Cluster IX 2.06 was used to align the nucleotide sequences (Thomson, 1997). The evolutionary history was inferred using the Neighbor-Joining method (Saitou and Nei, 1987). The evolutionary distances were computed using the Maximum Composite Likelihood method (Tamura et al., 2004). The barcodes sequences were submitted in NCBI (National centre for Biotechnological Information). The species within genera of Muraenidae, Muraenesocidae and Ophichthidae family were clustered in a same clade with high bootstrap value. The evolutionary relationships of six species were analyzed using neighbor joining method. This results of phylogenetic tree showed maximum genetic relatedness with the sequenced results which were submitted in gene bank.

SUBMITTER: Peninal S

PROVIDER: S-EPMC5198627 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters.

Peninal Samuel S Subramanian Janakiraman J Elavarasi Alaganatham A Kalaiselvam Murugaiyan M

Genomics data 20161209

Anguilliformes, also known as "true eels", are an ecologically diverse group of predominantly marine origin whose members were easily recognized by their extremely elongated bodies with reduced cross-sectional areas and universal lack of pelvic fins. The Marine Eels were collected from landing centres of Parangipettai coastal waters and identified based on their morphometric and meristic characters. The newly recorded species were used for the barcoding analysis. Information on molecular taxonom ...[more]

PMID: 28053872

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Project description:The order Tetraodontiformes are one of the most unique groups of teleostean fish, exhibiting highly derived and greatly diversified phenotypes. It is a difficult task for both professionals and nonprofessionals to accurately identify these species only according to morphological characteristics. DNA barcoding can identify species at the molecular level to overcome the limitations of morphological classification. In this study, we collected 616 specimens of pufferfish from the coastal waters of China. According to the morphological characteristics, they were preliminarily identified as 50 species. Further analysis using DNA barcodes identified these specimens as 46 species, belonging to 23 genera, 6 families. According to the species classification results of DNA barcoding, the three species identified by morphology as Takifugu pseudommus, Takifugu chinensis, and Takifugu rubripes should be the same species. Similarly, Lagocephalus wheeleri is the synonym of Lagocephalus spadiceus. Another important discovery of DNA barcoding analysis is that there are closer interspecific genetic distances within the genus Takifugu. If T. rubripes, T. pseudommus, and T. chinensis are taken as one species, the average interspecific to intraspecific genetic distance ratio of Takifugu is only 6.21 times, which does not reach the DNA barcoding threshold of more than 10 times proposed previously. Although the interspecific genetic distance in the genus Takifugu is relatively small, each species can be clustered into independent clades in the NJ tree. In conclusion, this study not only found that there are synonymous phenomena in the order Tetraodontiformes but also provided molecular evidence for the valid species names of Takifugu rubripes and Lagocephalus Spadiceus. The results can provide reliable DNA barcoding information for the identification of pufferfish species, help solve the problem of classification confusion in this order, and provide technical support for the identification of the original components of related commodities on the aquatic product market.

Project description:BACKGROUND: DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region. METHODOLOGY/PRINCIPAL FINDINGS: Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species), and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org). Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125) examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles. CONCLUSIONS/SIGNIFICANCE: This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha taxonomy, barcodes provide robust support for most morphologically based taxon concepts and also highlight key areas of taxonomic uncertainty worthy of reappraisal.

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Dataset Information

Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters.

Publications

Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters.

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