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

De Gregoris TB, Borra M, Biffali E, Bekel T, Burgess JG, Kirby RR, Clare AS (2009)
BMC Molecular Biology 10(1): 62.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA
DOI
URN
urn:nbn:de:0070-pub-15914399
Autor*in
De Gregoris, Tristano Bacchetti; Borra, Marco; Biffali, Elio; Bekel, ThomasUniBi; Burgess, J. Grant; Kirby, Richard R.; Clare, Anthony S.
Einrichtung
Fakultät für Biologie
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Abstract / Bemerkung
BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
Erscheinungsjahr
2009
Zeitschriftentitel
BMC Molecular Biology
Band
10
Ausgabe
1
Seite(n)
62
ISSN
1471-2199
Page URI
https://pub.uni-bielefeld.de/record/1591439

Zitieren

De Gregoris TB, Borra M, Biffali E, et al. Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies. BMC Molecular Biology. 2009;10(1):62.
De Gregoris, T. B., Borra, M., Biffali, E., Bekel, T., Burgess, J. G., Kirby, R. R., & Clare, A. S. (2009). Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies. BMC Molecular Biology, 10(1), 62. https://doi.org/10.1186/1471-2199-10-62
De Gregoris, Tristano Bacchetti, Borra, Marco, Biffali, Elio, Bekel, Thomas, Burgess, J. Grant, Kirby, Richard R., and Clare, Anthony S. 2009. “Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies”. BMC Molecular Biology 10 (1): 62.
De Gregoris, T. B., Borra, M., Biffali, E., Bekel, T., Burgess, J. G., Kirby, R. R., and Clare, A. S. (2009). Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies. BMC Molecular Biology 10, 62.
De Gregoris, T.B., et al., 2009. Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies. BMC Molecular Biology, 10(1), p 62.
T.B. De Gregoris, et al., “Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies”, BMC Molecular Biology, vol. 10, 2009, pp. 62.
De Gregoris, T.B., Borra, M., Biffali, E., Bekel, T., Burgess, J.G., Kirby, R.R., Clare, A.S.: Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies. BMC Molecular Biology. 10, 62 (2009).
De Gregoris, Tristano Bacchetti, Borra, Marco, Biffali, Elio, Bekel, Thomas, Burgess, J. Grant, Kirby, Richard R., and Clare, Anthony S. “Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies”. BMC Molecular Biology 10.1 (2009): 62.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Volltext(e)
Name
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-09-06T08:48:01Z
MD5 Prüfsumme
f1f1338fc3dd8f7c77db7509aa2b9f44


15 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

The Barnacle Balanus improvisus as a Marine Model - Culturing and Gene Expression.
Jonsson PR, Wrange AL, Lind U, Abramova A, Ogemark M, Blomberg A., J Vis Exp (138), 2018
PMID: 30148484
Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics.
Rodrigues M, Ostermann T, Kremeser L, Lindner H, Beisel C, Berezikov E, Hobmayer B, Ladurner P., Biofouling 32(9), 2016
PMID: 27661452
Sequence basis of Barnacle Cement Nanostructure is Defined by Proteins with Silk Homology.
So CR, Fears KP, Leary DH, Scancella JM, Wang Z, Liu JL, Orihuela B, Rittschof D, Spillmann CM, Wahl KJ., Sci Rep 6(), 2016
PMID: 27824121
Differential utility of the Bacteroidales DNA and RNA markers in the tiered approach for microbial source tracking in subtropical seawater.
Liu R, Cheng KH, Wong K, Cheng SC, Lau SC., Appl Microbiol Biotechnol 99(13), 2015
PMID: 25652655
Quantitative proteomics study of larval settlement in the Barnacle Balanus amphitrite.
Chen ZF, Zhang H, Wang H, Matsumura K, Wong YH, Ravasi T, Qian PY., PLoS One 9(2), 2014
PMID: 24551147
Identification of reference genes for qRT-PCR analysis in Yesso scallop Patinopecten yessoensis.
Feng L, Yu Q, Li X, Ning X, Wang J, Zou J, Zhang L, Wang S, Hu J, Hu X, Bao Z., PLoS One 8(9), 2013
PMID: 24069432
Expression of calmodulin and myosin light chain kinase during larval settlement of the Barnacle Balanus amphitrite.
Chen ZF, Wang H, Matsumura K, Qian PY., PLoS One 7(2), 2012
PMID: 22348072
Metamorphosis in the cirripede crustacean Balanus amphitrite.
Maruzzo D, Aldred N, Clare AS, Høeg JT., PLoS One 7(5), 2012
PMID: 22666355
Avoiding pitfalls of internal controls: validation of reference genes for analysis by qRT-PCR and Western blot throughout rat retinal development.
Rocha-Martins M, Njaine B, Silveira MS., PLoS One 7(8), 2012
PMID: 22916200
Transcriptomic analysis of neuropeptides and peptide hormones in the barnacle Balanus amphitrite: evidence of roles in larval settlement.
Yan XC, Chen ZF, Sun J, Matsumura K, Wu RS, Qian PY., PLoS One 7(10), 2012
PMID: 23056329
Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacle Balanus amphitrite.
De Gregoris TB, Rupp O, Klages S, Knaust F, Bekel T, Kube M, Burgess JG, Arnone MI, Goesmann A, Reinhardt R, Clare AS., Biofouling 27(4), 2011
PMID: 21526438
Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance.
Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M., BMC Genomics 12(), 2011
PMID: 21679424
Toward an understanding of the molecular mechanisms of barnacle larval settlement: a comparative transcriptomic approach.
Chen ZF, Matsumura K, Wang H, Arellano SM, Yan X, Alam I, Archer JA, Bajic VB, Qian PY., PLoS One 6(7), 2011
PMID: 21829555
The GABAergic-like system in the cyprid of Balanus amphitrite (=Amphibalanus amphitrite) (Cirripedia, Crustacea).
Gallus L, Ferrando S, Gambardella C, Diaspro A, Bianchini P, Piazza V, Bonanno G, Milanese M, Ramoino P, Tagliafierro G., Biofouling 26(2), 2010
PMID: 19882419
Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina.
Wang H, Zhang H, Wong YH, Voolstra C, Ravasi T, B Bajic V, Qian PY., Proteomics 10(16), 2010
PMID: 20540116

38 References

Daten bereitgestellt von Europe PubMed Central.

The ship hull fouling penalty.
Townsin RL., Biofouling 19 Suppl(), 2003
PMID: 14618699
Balanus amphitrite or Amphibalanus amphitrite? A note on barnacle nomenclature.
Clare AS, Hoeg JT., Biofouling 24(1), 2008
PMID: 18092215
An alpha2-macroglobulin-like protein is the cue to gregarious settlement of the barnacle Balanus amphitrite.
Dreanno C, Matsumura K, Dohmae N, Takio K, Hirota H, Kirby RR, Clare AS., Proc. Natl. Acad. Sci. U.S.A. 103(39), 2006
PMID: 16983086
Relationship between bacterial community profile in biofilm and attachment of the acorn barnacle
Qian P-Y, Thiyagarajan V, Lau SCK, Cheung SCK., 2003
Attachment of barnacle (Darwin) larvae: responses to bacterial films and extracellular materials
O'Connor NJ, Richardson DL., 1998
Complementary DNA sequencing: expressed sequence tags and human genome project.
Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF., Science 252(5013), 1991
PMID: 2047873
Expressed sequence tags--ESTablishing bridges between genomes.
Marra MA, Hillier L, Waterston RH., Trends Genet. 14(1), 1998
PMID: 9448457
Developmental and morphogenetic gene regulation in larvae at metamorphosis
Degnan BM, Morse DE., 1995
Gene expression during early ascidian metamorphosis requires signalling by Hemps, an EGF-like protein.
Woods RG, Roper KE, Gauthier M, Bebell LM, Sung K, Degnan BM, Lavin MF., Development 131(12), 2004
PMID: 15169757
Metamorphic competence, a major adaptive convergence in marine invertebrate larvae
Hadfield MG, Carpizo-Ituarte EJ, del K, Nedved BT., 2001
Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays.
Bustin SA., J. Mol. Endocrinol. 25(2), 2000
PMID: 11013345
Quantification of mRNA using real-time RT-PCR.
Nolan T, Hands RE, Bustin SA., Nat Protoc 1(3), 2006
PMID: 17406449
Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction.
Bustin SA, Nolan T., J Biomol Tech 15(3), 2004
PMID: 15331581
Real-time RT-PCR normalisation; strategies and considerations.
Huggett J, Dheda K, Bustin S, Zumla A., Genes Immun. 6(4), 2005
PMID: 15815687
The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization.
Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GA, Zumla A., Anal. Biochem. 344(1), 2005
PMID: 16054107
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F., Genome Biol. 3(7), 2002
PMID: 12184808
Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations.
Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP., Biotechnol. Lett. 26(6), 2004
PMID: 15127793
Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets.
Andersen CL, Jensen JL, Orntoft TF., Cancer Res. 64(15), 2004
PMID: 15289330
The D.P. Wilson Lecture: Research on settlement and metamorphosis of marine invertebrate larvae: past, present and future
Hadfield MG., 1998
Proteomic analysis of larvae during development, attachment, and metamorphosis in the fouling barnacle, Balanus amphitrite.
Thiyagarajan V, Qian PY., Proteomics 8(15), 2008
PMID: 18654988
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
Increasing genomic information in bivalves through new EST collections in four species: development of new genetic markers for environmental studies and genome evolution.
Tanguy A, Bierne N, Saavedra C, Pina B, Bachere E, Kube M, Bazin E, Bonhomme F, Boudry P, Boulo V, Boutet I, Cancela L, Dossat C, Favrel P, Huvet A, Jarque S, Jollivet D, Klages S, Lapegue S, Leite R, Moal J, Moraga D, Reinhardt R, Samain JF, Zouros E, Canario A., Gene 408(1-2), 2007
PMID: 18054177
Towards a catalogue of genes transcribed in multiple tissues of Mytilus galloprovincialis.
Venier P, Pallavicini A, De Nardi B, Lanfranchi G., Gene 314(), 2003
PMID: 14527715
Exogenous reference RNA for normalization of real-time quantitative PCR.
Smith RD, Brown B, Ikonomi P, Schechter AN., BioTechniques 34(1), 2003
PMID: 12545545
SPUD: a quantitative PCR assay for the detection of inhibitors in nucleic acid preparations.
Nolan T, Hands RE, Ogunkolade W, Bustin SA., Anal. Biochem. 351(2), 2006
PMID: 16524557
Evidence for the involvement of cyclic AMP in the pheromonal modulation of barnacle settlement
Clare A, Thomas R, Rittschof D., J. Exp. Biol. 198(Pt 3), 1995
PMID: 9318389

Sambrook J, Russell WD., 2001
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Ewing B, Hillier L, Wendl MC, Green P., Genome Res. 8(3), 1998
PMID: 9521921
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Kuster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Puhler A, Stoye J, Goesmann A., J. Biotechnol. 140(1-2), 2009
PMID: 19297685
The TIGR gene indices: reconstruction and representation of expressed gene sequences.
Quackenbush J, Liang F, Holt I, Pertea G, Upton J., Nucleic Acids Res. 28(1), 2000
PMID: 10592205
CAP3: A DNA sequence assembly program.
Huang X, Madan A., Genome Res. 9(9), 1999
PMID: 10508846
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
Profile hidden Markov models.
Eddy SR., Bioinformatics 14(9), 1998
PMID: 9918945
InterPro--an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM; InterPro Consortium., Bioinformatics 16(12), 2000
PMID: 11159333
BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.
Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980569
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Primer3 on the WWW for general users and for biologist programmers
Rozen S, Skaletsky HJ., 2000
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 19552808
PubMed | Europe PMC

Suchen in

Google Scholar