DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples

W. K W Loh, P. Bond, K. J. Ashton, D. T. Roberts, I. R. Tibbetts

Research output: Contribution to journalArticleResearchpeer-review

11 Citations (Scopus)

Abstract

The barcoding of mitochondrial cytochrome c oxidase subunit 1 (coI) gene was amplified and sequenced from 16 species of freshwater fishes found in Lake Wivenhoe (south-eastern Queensland, Australia) to support monitoring of reservoir fish populations, ecosystem function and water health. In this study, 630-650 bp sequences of the coI barcoding gene from 100 specimens representing 15 genera, 13 families and two subclasses of fishes allowed 14 of the 16 species to be identified and differentiated. The mean ± s.e. Kimura 2 parameter divergence within and between species was 0·52 ± 0·10 and 23·8 ± 2·20% respectively, indicating that barcodes can be used to discriminate most of the fish species accurately. The two terapontids, Amniataba percoides and Leiopotherapon unicolor, however, shared coI DNA sequences and could not be differentiated using this gene. A barcoding database was established and a qPCR assay was developed using coI sequences to identify and quantify proportional abundances of fish species in ichthyoplankton samples from Lake Wivenhoe. These methods provide a viable alternative to the time-consuming process of manually enumerating and identifying ichthyoplankton samples.

Original languageEnglish
Pages (from-to)307-328
Number of pages22
JournalJournal of Fish Biology
Volume85
Issue number2
DOIs
Publication statusPublished - 2014

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barcoding
DNA barcoding
fish larvae
freshwater fish
plankton
assay
larva
DNA
ichthyoplankton
assays
fish
gene
sampling
lakes
genes
cytochrome-c oxidase
Queensland
lake
ecosystem function
cytochrome

Cite this

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title = "DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples",
abstract = "The barcoding of mitochondrial cytochrome c oxidase subunit 1 (coI) gene was amplified and sequenced from 16 species of freshwater fishes found in Lake Wivenhoe (south-eastern Queensland, Australia) to support monitoring of reservoir fish populations, ecosystem function and water health. In this study, 630-650 bp sequences of the coI barcoding gene from 100 specimens representing 15 genera, 13 families and two subclasses of fishes allowed 14 of the 16 species to be identified and differentiated. The mean ± s.e. Kimura 2 parameter divergence within and between species was 0·52 ± 0·10 and 23·8 ± 2·20{\%} respectively, indicating that barcodes can be used to discriminate most of the fish species accurately. The two terapontids, Amniataba percoides and Leiopotherapon unicolor, however, shared coI DNA sequences and could not be differentiated using this gene. A barcoding database was established and a qPCR assay was developed using coI sequences to identify and quantify proportional abundances of fish species in ichthyoplankton samples from Lake Wivenhoe. These methods provide a viable alternative to the time-consuming process of manually enumerating and identifying ichthyoplankton samples.",
author = "Loh, {W. K W} and P. Bond and Ashton, {K. J.} and Roberts, {D. T.} and Tibbetts, {I. R.}",
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DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples. / Loh, W. K W; Bond, P.; Ashton, K. J.; Roberts, D. T.; Tibbetts, I. R.

In: Journal of Fish Biology, Vol. 85, No. 2, 2014, p. 307-328.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Tibbetts, I. R.

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