Identification of Channa species using the partial cytochrome c oxidase subunit I (COI) gene as a DNA barcoding marker

Zhu, Shu-Ren; Fu, Jianjun; Wang, Qun; Li, Jiale

doi:10.1016/j.bse.2013.08.011

Cited by 31 publications

(14 citation statements)

References 29 publications

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“…For example, BIN ABW0048 consisted of 17 individuals; nine C. sp ., one C. maculata , six C. argus , one C. argus (male) x C. maculata (female) ( Figure 1 ), and therefore result in multiple species sharing the same BIN. The presumptive reference DNA barcodes for C. argus were obtained from sequences deposited on GenBank for individuals sourced from China (Zhou et al unpublished, [36] , [37] ), while the C. maculata reference specimens were sourced Vietnam (NRSC042-11; [38] ) and China ( [36] , [37] , [39] ; Zhu et al 2013, Wang et al 2013) (see C. maculata ; Table 3 ). The C. argus specimen whole mitochondrial genome sequence [40] clustered in the same BIN (ABW0048) as the C. maculata and C. maculata (F) x C. argus (M) hybrid mitochondrial genome sequences of specimens [36] , [39] , [40] , and therefore highlights the difficulties with identification of this species.…”

Section: Resultsmentioning

confidence: 99%

Calibrating Snakehead Diversity with DNA Barcodes: Expanding Taxonomic Coverage to Enable Identification of Potential and Established Invasive Species

2014

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Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species) and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius) are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway analysis.

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Section: Resultsmentioning

confidence: 99%

Calibrating Snakehead Diversity with DNA Barcodes: Expanding Taxonomic Coverage to Enable Identification of Potential and Established Invasive Species

2014

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“…Both factors may explain the observed polyphyly (sensu Funk & Omland, 2003) among the geographically isolated groups. For C. striata, mtDNA markers had been demonstrated to be informative for higher level phylogenies (Adamson et al, 2010;Lakra et al, 2010;Song, Munian, Rashid, & Bhassu, 2013;Zhu et al, 2013), but a multi-locus approach is necessary for intra-population studies. In this regard, neutral microsatellite markers are better suited for population-level analyses of C. striata as they are more polymorphic due to absence of selective constraints and because they are usually comprised of randomly segregated, non-linked nuclear DNA loci.…”

Section: Introductionmentioning

confidence: 99%

Population genetic structure of Asian snakehead fish (Channa striata) in North Borneo: Implications for conservation of local freshwater biodiversity

Robert

Amit

Sukarno

et al. 2018

Ecological Research

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This study quantified the intra‐specific diversity and characterized the population structure of the Asian snakehead fish, Channa striata in Sabah, North Borneo by determining the variability at six microsatellite loci. Range of genetic diversity across all sampled populations was comparatively moderate in relation to levels reported for C. striata populations occurring elsewhere and the overall Sabah population is highly structured, reflecting isolations across geological and ecological time scales. Two reciprocally monophyletic genodemes were identified along the west and east coast that may have been separated by mountain upthrusts throughout the central region of Sabah. Despite kinship among populations within each genodeme, individual demes were discrete as indicated by significant genotypic differentiation (all P < 0.0014) and low estimates of gene flow between them that likely reflect natural fragmentation of freshwater habitats they occupy. Our findings underline the potential of molecular markers in delimiting and delineating geospatial units of conservation in Sabah. Lowland freshwater ecosystems in the area may comprise two geographically isolated ecoregions, in which each hypothetically harbours biota that have evolved allopatrically. Additionally, identification of biodiversity hotspots within these putative ecoregions can be greatly facilitated with genetic‐level investigations as the rate by which freshwater communities are inventoried has been extremely slow in most habitats.

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“…For example, among the more recent tools is the DNA barcoding of eukaryotes by targeting the conserved region of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial DNA (mtDNA), a concept that was introduced about 15 years ago (Hebert et al 2003a). Thereafter, copious amounts of related data have been accumulating rapidly in DNA databases, and many studies have been published using this technology (Hebert et al 2003b;Ward et al 2008;Steinke et al 2009Steinke et al , 2016Ma et al 2012;Zhu et al 2013;Khedkar et al 2014;Chen et al 2015;Dhar and Ghosh 2015). Taxonomic resolution and accuracy of species identification have improved greatly with the accumulation of barcode-associated sequence data (Zhang and Hanner 2012).…”

Section: Introductionmentioning

confidence: 99%

Genetic difference between African and Japanese scombropid populations based on cytochrome c oxidase subunit I gene sequences

Oyama

Itoi

Ueda

et al. 2019

Mitochondrial DNA Part B

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The fish family Scombropidae consists of a single genus, Scombrops, and is distributed in the waters of the northwestern Pacific Ocean, southwestern Indian Ocean and western Atlantic Ocean, including the Caribbean Sea. Among these, the population of South Africa has been renamed from Scombrops dubius to Scombrops boops, which is known to be distributed in waters around Japanese Archipelago. We are skeptical of this revision as the two populations are geographically isolated between the waters of the Far East and the southern end of the Africa coast. Recently, our lab determined the sequences of the complete mitochondrial genome of three Japanese gnomefish, S. boops, Scombrops gilberti and an undescribed scombropid species (Scombrops sp.). Here, we compared the partial sequence of cytochrome c oxidase subunit I (COI) from the three Japanese gnomefish with that of the African population. The African sequences showed 95.5-96.6% identity with the Japanese sequences, while the corresponding sequences from the Japanese species showed 98.2-100% identity with each other. A maximum likelihood tree based on the partial sequence of COI also demonstrated that the clade of African gnomefish is distinct from those of Japanese species including S. boops. These results suggest that the scombropid fish in the African waters is a different species from S. boops and that it is appropriate to resurrect the name Scombrops dubius for the African population.

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Identification of Channa species using the partial cytochrome c oxidase subunit I (COI) gene as a DNA barcoding marker

Cited by 31 publications

References 29 publications

Calibrating Snakehead Diversity with DNA Barcodes: Expanding Taxonomic Coverage to Enable Identification of Potential and Established Invasive Species

Calibrating Snakehead Diversity with DNA Barcodes: Expanding Taxonomic Coverage to Enable Identification of Potential and Established Invasive Species

Population genetic structure of Asian snakehead fish (Channa striata) in North Borneo: Implications for conservation of local freshwater biodiversity

Genetic difference between African and Japanese scombropid populations based on cytochrome c oxidase subunit I gene sequences

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