Deep sequencing of naupliar-, cyprid- and adult-specific normalised expressed sequence tag (EST) libraries of the acorn barnacle Balanus amphitrite

Biofouling

Volumn 27, Issue 4, 2011, Pages 367-374

  de Gregoris, Tristano Bacchetti ^a   Rupp, Oliver ^b   Klages, Sven ^c   Knaust, Florian ^c   Bekel, Thomas ^b   Kube, Michael ^c   Burgess, J Grant ^a   Arnone, Maria Ina ^d   Goesmann, Alexander ^b   Reinhardt, Richard ^c   Clare, Anthony S ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b BIELEFELD UNIVERSITY   (Germany)

^c MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

^d STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

Author keywords

454 sequencing; Barnacles; Development; Lectins; Settlement

Indexed keywords

ADULT; CRUSTACEAN; DATABASE; GENETIC ANALYSIS; LARVAL SETTLEMENT; PROTEIN; SETTLING BEHAVIOR;

ANIMAL; ANIMAL BEHAVIOR; ARTICLE; BIOFOULING; COMPUTER INTERFACE; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE LIBRARY; GENETIC DATABASE; GENETICS; GROWTH, DEVELOPMENT AND AGING; LIFE CYCLE; THORACICA;

ANIMALS; BEHAVIOR, ANIMAL; BIOFOULING; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; LIFE CYCLE STAGES; SEQUENCE ANALYSIS, DNA; THORACICA; USER-COMPUTER INTERFACE;

BALANIDAE; BALANUS AMPHITRITE; CYPRIDIDAE; MEGABALANUS ROSA; THORACICA;

EID: 79956066152     PISSN: 08927014     EISSN: 10292454     Source Type: Journal    
DOI: 10.1080/08927014.2011.577211     Document Type: Article

References (43)

1. Aldred N, Clare AS. 2008. The adhesive strategies of cyprids and development of barnacle resistant marine coatings. Biofouling 24:351-363.
2. Aldred N, Scardino A, Cavaco A, de Nys R, Clare AS. 2010. Attachment strength is a key factor in the selection of surfaces by barnacle cyprids (Balanus amphitrite) during settlement. Biofouling 26:287-299.
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
4. Anderson DT. 1994. Barnacles. Structure, function, development and evolution. London: Chapman & Hall. p. 179-190.
5. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, et al. 2000. InterPro-an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16:1145-1150.
6. Bacchetti De Gregoris T, Borra M, Biffali E, Bekel T, Burgess JG, Kirby RR, Clare AS. 2009. Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies. BMC Mol Biol 10:62.
7. Bachmann K, Rheinsmith EL. 1973. Nuclear DNA amounts in Pacific Crustacea. Chromosoma 43:225-236.
8. Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, et al. 2009. 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. J Biotechnol 140:3-12.
9. Bettencourt R, Pinheiro M, Egas C, Gomes P, Afonso M, Shank T, Santos R. 2010. High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus. BMC Genomics 11:559.
10. Cambi A, Figdor CG. 2003. Dual function of C-type lectinlike receptors in the immune system. Curr Opin Cell Biol 15:539-546.
11. Clare AS, Høeg JT. 2008. Balanus amphitrite or Amphibalanus amphitrite? A note on barnacle nomenclature. Biofouling 24:55-57.
12. Crisp DJ, Meadows PS. 1962. The chemical basis of gregariousness in Cirripedes. Proc R Soc Lond B 156: 500-520.
13. Dreanno C, Kirby RR, Clare AS. 2006a. Locating the barnacle settlement pheromone: spatial and ontogenetic expression of the settlement-inducing protein complex of Balanus amphitrite. Proc R Soc Lond B 273:2721-2728.
14. Dreanno C, Matsumura K, Dohmae N, Takio K, Hirota H, Kirby RR, Clare AS. 2006b. An alpha2-macroglobulinlike protein is the cue to gregarious settlement of the barnacle Balanus amphitrite. Proc Natl Acad Sci USA 103:14396-14401.
15. Evans LV. 2009. Editor's note. Biofouling 25:81. Fleury E, Huvet A, Lelong C, de Lorgeril J, Boulo V, Gueguen Y. 2009. Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase. BMC Genomics 10:341.
16. Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F. 2005. BRIGEP-the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Res 33:710-716.
17. Hofmann K, Stoffel W. 1993. TMbase-a database of membrane spanning proteins segments. Biol Chem 374:166-168.
18. Holmström C, Rittschof D, Kjelleberg S. 1992. Inhibition of settlement by larvae of Balanus amphitrite and Ciona intestinalis by a surface-colonizing marine bacterium. Appl Environ 3 Microbiol 58:2111-2115.
19. Hou Y, Lin S. 2009. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes. PLoS ONE 4:e6978.
20. Kato-Yoshinaga Y, Nagano M, Mori S, Clare AS, Fusetani N, Matsumura K. 2000. Species specificity of barnacle settlement-inducing proteins. Comp Biochem Physiol A 125:511-516.
21. Khandeparker L, Anil AC, Raghukumar S. 2003. Barnacle larval destination: piloting possibilities by bacteria and lectin interaction. J Exp Mar Biol Ecol 289:1-13.
22. Khandeparker L, Anil AC, Raghukumar S. 2006. Relevance of biofilm bacteria in modulating the larval metamorphosis of Balanus amphitrite. FEMSMicrobiol Ecol 58:425-438.
23. Kilpatrick DC. 2002. Animal lectins: a historical introduction and overview. Biochim Biophys Acta 1572:187-197.
24. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567-580.
25. Li H, Thiyagarajan V, Qian P-Y. 2010. Response of cyprid specific genes to natural settlement cues in the barnacle-Balanus (1/4 Amphibalanus) amphitrite. J Exp Mar Biol Ecol 389:45-52.
26. Maki JS, Mitchell R. 1985. Involvement of lectins in the settlement and metamorphosis of marine invertebrate larvae. Bull Mar Sci 37:675-683.
27. Matsumura K, Mori S, Nagano M, Fusetani N. 1998a. Lentil lectin inhibits adult extract-induced settlement of the barnacle, Balanus amphitrite. J Exp Biol 280:213-219.
28. Matsumura K, Nagano M, Kato-Yoshinaga Y, Yamazaki M, Clare AS, Fusetani N. 1998b. Immunological studies on the settlement-inducing protein complex (SIPC) of the barnacle Balanus amphitrite and its possible involvement in larva-larva interactions. Proc R Soc Lond B 265:1825-1830.
29. O'Connor NJ, Richardson DL. 1998. Attachment of barnacle (Balanus amphitrite Darwin) larvae: responses to bacterial films and extracellular materials. J Exp Mar Biol Ecol 226:115-129.
30. Okazaki Y, Shizuri Y. 2000. Structures of six cDNAs expressed specifically at cypris larvae of barnacles, Balanus amphitrite. Gene 250:127-135.
31. Okazaki Y, Shizuri Y. 2001. Identification of the aromatic Lamino acid decarboxylase (AADC) gene and its expression in the attachment and metamorphosis of the barnacle, Balanus amphitrite. Dev Growth Diff 43:33-41.
32. Olivier F, Tremblay R, Bourget E, Rittschof D. 2000. Barnacle settlement: field experiments on the influence of larval supply, tidal level, biofilm quality and age on Balanus amphitrite cyprids. Mar Ecol Prog Ser 199:185-204.
33. Pop M. 2009. Genome assembly reborn: recent computational challenges. Brief Bioinform 10:354-366.
34. Prendergast GS, Zurn CM, Bers V, Head RM, Hansson LJ, Thomason JC. 2009. The relative magnitude of the effects of biological and physical settlement cues for cypris larvae of the acorn barnacle, Semibalanus balanoides L. Biofouling 25:35-44.
35. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463:1079-1083.
36. Rittschof D, Sandford Branscomb E, Costlow JD. 1984. Settlement and behavior in relation to flow and surface in larval barnacles, Balanus amphitrite Darwin. J Exp Mar Biol Ecol 82:131-146.
37. Robson MA, Thomason JC, Wolff K. 2009. Eight polymorphic microsatellite loci markers for the barnacle Balanus amphitrite (syn. Amphibalanus amphitrite) Darwin 1854. Mol Ecol Res 9:368-369.
38. Shcheglov A, Zhulidov P, Bogdanova E, Shagin D. 2007. Normalization of cDNA libraries. Nucleic acids hybridization: modern applications. In: Buzdin A, Lukyanov S, editors. Nucleic acids hybridization: modern applications. Dordrecht, The Netherlands: Springer. p. 97-124.
39. Takamatsu N, Heishi M, Muramoto K, Kamiya H, Shiba T. 1994. Cloning and analysis of the gene encoding lectin from the acorn barnacle Megabalanus rosa. Gene 150:407-408.
40. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.
41. Thiyagarajan V, Qian P-Y. 2008. Proteomic analysis of larvae during development, attachment, and metamorphosis in the fouling barnacle, Balanus amphitrite. Proteomics 8:3164-3172.
42. Townsin RL. 2003. The ship hull fouling penalty. Biofouling 19:9-15.
43. Walker G, Yule AB, Nott JA. 1987. Structure and function in balanomorph larvae. In: Southward AJ, editor. Barnacle biology. Rotterdam: A.A. Balkema. p. 307-328.