DNA barcoding Australia's fish species

Abstract

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.

Host species as a strong determinant of the intestinal microbiota of fish larvae

“…A 652 bp COI gene was amplified by the following primers: FishF1 (5 -TCAACCAACCACAAA GACATTGGCAC-3 ) and FishR1 (5 -TAGACTTCTGGG TGGCCAAAGAATCA-3 ) (Ward et al, 2005). All PCR amplifications of eukaryotic genes were performed in the same reaction mixture as described for prokaryotic gene amplification.…”

Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

“…The CO1 gene (%666 bp) was amplified with the primers FishF1 and FishR1 as described by Ward et al (2005). One cyt b gene sequence in Coreoperca herzi was amplified with the primers L14724 and H15915 as reported by Xiao et al (2001), and other cyt b genes were reported in a previous paper (Chen et al, 2007).…”

Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic

“…DNA barcoding is the third approach, and rather than defining taxa a priori, it uses sequence similarity at a single 'barcode' locus (in Metazoa, usually the mitochondrial locus cytochrome c oxidase subunit I, coxI) to allocate unknown specimens to morphologically 115 determined voucher taxa (Floyd et al 2002;Blaxter 2004;Powers, 2004;Blaxter et al, 2005;Hajibabaei et al, 2005;Lambert et al, 2005;Ward et al, 2005). The underlying rationale for DNA barcoding is that sequence variation among species is greater than (and discrete from) variation within species: in other words, that sequence variation at the selected locus shows a 'barcoding gap' (Fig.1).…”