DNA barcoding for identification of fish species in the Taiwan Strait

Abstract

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

“…For what nucleotide composition concerns, results are very similar to those found in Australian (Ward et al, 2005), Canadian (Hubert et al, 2008), Cuban (Lara et al, 2010) and Taiwanese (Bingpeng et al, 2018) fish species, with the AT content (53.1%) higher than GC content (46.9%), with the predominance of the T (29.6%).…”

“…The size of the coI fragment analysed in the present study (678 bp without stop codons) prevented bias in the molecular species identification or attribution, probably due to the occurrence of nuclear mitochondrial pseudogenes (NUMT). Indeed, NUMTs, in vertebrates, are usually represented by segments smaller than 600 bp (Zhang & Hewitt, ); and it is recommended to work on longer fragments (BingPeng et al ., ) in order to avoid both misidentification of species and misestimation of the biodiversity. The coI sequences belonging to some of these species were almost identical to those reported for the same species from the Indo‐West Pacific Ocean, suggesting that these species have a wide distribution range with high potential for dispersal.…”

“…Within this context, it is worth noting that many marine fish species recorded in the Mediterranean Sea have been determined to be alien species of Red Sea origin (Bariche et al ., ), suggesting the possibility of high similarity between The Gulf and Red Sea, even though there is not much fish DNA barcoding data from the Red Sea (Isari et al ., ; Trivedi et al ., ). For what nucleotide composition concerns, results are very similar to those found in Australian (Ward et al ., ), Canadian (Hubert et al ., ), Cuban (Lara et al ., ) and Taiwanese (Bingpeng et al ., ) fish species, with the AT content (53.1%) higher than GC content (46.9%), with the predominance of the T (29.6%).…”

“…The 90% boundaries of the K2P distributions showed that the genetic variability ranges from 0.20 to 0.28 (Figure 4). Among the 55 families tested, only the following 10 showed the occurrence of molecular diag- usually represented by segments smaller than 600 bp (Zhang & Hewitt, 1996); and it is recommended to work on longer fragments (BingPeng et al, 2018) in order to avoid both misidentification of species and misestimation of the biodiversity. The coI sequences belonging to some of these species were almost identical to those reported for the same species from the Indo-West Pacific Ocean, suggesting that these species have a wide distribution range with high potential for dispersal.…”

Encephalomyocarditis virus is potentially derived from eastern bent-wing bats living in East Asian countries

“…To determine the species that contributed most to the guano formation collected, animal species identification was done through NGS using the 1545-bp, at the 5'-end of the mitochondrial gene COI as the DNA barcode region. This COI gene locus, being easily amplified using universal primers, shows low intraspecific and high interspecific divergence (Dentinger et al, 2011), and possesses a higher range of phylogenetic signal than any other mitochondrial genes (Hebert et al, 2003a), and has been proven to be highly effective in identifying the species of various organisms (Andujar et al, 2018;Bingpeng et al, 2018;Changbunjong et al, 2018;Yassin et al, 2010;Hubert et al, 2008;Ward et al, 2005;Hebert et al, 2004Hebert et al, , 2003b.…”