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Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies

Tristano Bacchetti De Gregoris12, Marco Borra3, Elio Biffali3, Thomas Bekel4, J Grant Burgess2, Richard R Kirby5 and Anthony S Clare1*

Author Affiliations

1 School of Marine Science and Technology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, England, UK

2 Dove Marine Laboratory, Newcastle University, Cullercoats, Tyne and Wear, NE30 4PZ, England, UK

3 Stazione Zoologica Anton Dohrn, Napoli, Villa Comunale, 80121, Italy

4 Center for Biotechnology (CeBiTec), Bielefeld University, D-33594 Bielefeld, Germany

5 School of Biological Sciences, University of Plymouth, Plymouth, PL4 8AA, England, UK

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BMC Molecular Biology 2009, 10:62  doi:10.1186/1471-2199-10-62

Published: 24 June 2009



Balanus amphitrite is a barnacle commonly used in biofouling research. Although many aspects of its biology have been elucidated, the lack of genetic information is impeding a molecular understanding of its life cycle. As part of a wider multidisciplinary approach to reveal the biogenic cues influencing barnacle settlement and metamorphosis, we have sequenced and annotated the first cDNA library for B. amphitrite. We also present a systematic validation of potential reference genes for normalization of quantitative real-time PCR (qRT-PCR) data obtained from different developmental stages of this animal.


We generated a cDNA library containing expressed sequence tags (ESTs) from adult B. amphitrite. A total of 609 unique sequences (comprising 79 assembled clusters and 530 singlets) were derived from 905 reliable unidirectionally sequenced ESTs. Bioinformatics tools such as BLAST, HMMer and InterPro were employed to allow functional annotation of the ESTs. Based on these analyses, we selected 11 genes to study their ability to normalize qRT-PCR data. Total RNA extracted from 7 developmental stages was reverse transcribed and the expression stability of the selected genes was compared using geNorm, BestKeeper and NormFinder. These software programs produced highly comparable results, with the most stable gene being mt-cyb, while tuba, tubb and cp1 were clearly unsuitable for data normalization.


The collection of B. amphitrite ESTs and their annotation has been made publically available representing an important resource for both basic and applied research on this species. We developed a qRT-PCR assay to determine the most reliable reference genes. Transcripts encoding cytochrome b and NADH dehydrogenase subunit 1 were expressed most stably, although other genes also performed well and could prove useful to normalize gene expression studies.