iBeetle-Base: A database for RNAi phenotypes in the red flour beetle Tribolium castaneum

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D720-D725

  Dönitz, Jürgen ^a   Schmitt Engel, Christian ^a,b   Grossmann, Daniela ^a   Gerischer, Lizzy ^c   Tech, Maike ^a   Schoppmeier, Michael ^b   Klingler, Martin ^b   Bucher, Gregor ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^c UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BEETLE; DATA BASE; EMBRYO DEVELOPMENT; EPIDERMIS; GENE SEQUENCE; GENE SILENCING; IBEETLE-BASE; INFORMATION RETRIEVAL; INSECT GENETICS; METABOLISM; METAMORPHOSIS; MUSCLE DEVELOPMENT; NOMENCLATURE; NONHUMAN; ONTOLOGY; OOCYTE DEVELOPMENT; PEST CONTROL; PEST ORGANISM; PHENOTYPE; PRIORITY JOURNAL; RNA INTERFERENCE; TAXON; TRIBOLIUM CASTANEUM; ANATOMY AND HISTOLOGY; ANIMAL; COMPUTER INTERFACE; EMBRYOLOGY; FEMALE; GENE; GENETIC DATABASE; GENETICS; INTERNET; TRIBOLIUM;

ANIMALS; DATABASES, GENETIC; FEMALE; GENES, INSECT; INTERNET; PHENOTYPE; RNA INTERFERENCE; TRIBOLIUM; USER-COMPUTER INTERFACE;

EID: 84941079193     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1054     Document Type: Article

References (30)

1. Nüsslein-Volhard, C. and Wieschaus, E. (1980) Mutations affecting segment number and polarity in Drosophila. Nature, 287, 795-801.
2. St Johnston, D. (2002) The art and design of genetic screens: Drosophila melanogaster. Nat. Rev. Genet., 3, 176-188.
3. Brown, S. J., Mahaffey, J. P., Lorenzen, M. D., Denell, R. E. and Mahaffey, J. W. (1999) Using RNAi to investigate orthologous homeotic gene function during development of distantly related insects. Evol. Dev., 1, 11-15.
4. Lynch, J. A. and Desplan, C. (2006) A method for parental RNA interference in the wasp Nasonia vitripennis. Nat. Protoc., 1, 486-494.
5. Hughes, C. L. and Kaufman, T. C. (2000) RNAi analysis of Deformed, proboscipedia and Sex combs reduced in the milkweed bug Oncopeltus fasciatus: novel roles for Hox genes in the hemipteran head. Development, 127, 3683-3694.
6. Miyawaki, K., Mito, T., Sarashina, I., Zhang, H., Shinmyo, Y., Ohuchi, H. and Noji, S. (2004) Involvement of Wingless/Armadillo signaling in the posterior sequential segmentation in the cricket, Gryllus bimaculatus (Orthoptera), as revealed by RNAi analysis. Mech. Dev., 121, 119-130.
7. Marques-Souza, H., Aranda, M. and Tautz, D. (2008) Delimiting the conserved features of hunchback function for the trunk organization of insects. Dev. Camb. Engl., 135, 881-888.
8. Cerny, A. C., Grossmann, D., Bucher, G. and Klingler, M. (2008) The Tribolium ortholog of knirps and knirps-related is crucial for head segmentation but plays a minor role during abdominal patterning. Dev. Biol., 321, 284-294.
9. Bucher, G. and Klingler, M. (2004) Divergent segmentation mechanism in the short germ insect Tribolium revealed by giant expression and function. Dev. Camb. Engl., 131, 1729-1740.
10. Choe, C. P., Miller, S. C. and Brown, S. J. (2006) A pair-rule gene circuit defnes segments sequentially in the short-germ insect Tribolium castaneum. Proc. Natl. Acad. Sci. U. S. A., 103, 6560-6564.
11. Bolognesi, R., Farzana, L., Fischer, T. D. and Brown, S. J. (2008) Multiple Wnt genes are required for segmentation in the short-germ embryo of Tribolium castaneum. Curr. Biol. CB, 18, 1624-1629.
12. Fu, J., Posnien, N., Bolognesi, R., Fischer, T. D., Rayl, P., Oberhofer, G., Kitzmann, P., Brown, S. J. and Bucher, G. (2012) Asymmetrically expressed axin required for anterior development in Tribolium. Proc. Natl. Acad. Sci. U. S. A., 109, 7782-7786.
13. Posnien, N., Koniszewski, N. D. B., Hein, H. J. and Bucher, G. (2011) Candidate gene screen in the red four beetle Tribolium reveals six3 as ancient regulator of anterior median head and central complex development. PLoS Genet., 7, e1002418.
14. Bucher, G., Scholten, J. and Klingler, M. (2002) Parental RNAi in Tribolium (Coleoptera). Curr. Biol., 12, R85-R86.
15. Klingler, M. (2004) Tribolium. Curr. Biol., 14, R639-R640.
16. Schröder, R., Beermann, A., Wittkopp, N. and Lutz, R. (2008) From development to biodiversity-Triboliumcastaneum, an insect model organism for short germband development. Dev. Genes Evol., 218, 119-126.
17. Snodgrass, R. (1954) Insect Metamorphosis: Smithsonian Miscellaneous Collections, V122, No. 9 Literary Licensing, Washington, DC.
18. Chaudhari, S. S., Arakane, Y., Specht, C. A., Moussian, B., Boyle, D. L., Park, Y., Kramer, K. J., Beeman, R. W. and Muthukrishnan, S. (2011) Knickkopf protein protects and organizes chitin in the newly synthesized insect exoskeleton. Proc. Natl. Acad. Sci. U. S. A., 108, 17028-17033.
19. Konopova, B. and Jindra, M. (2007) Juvenile hormone resistance gene Methoprene-tolerant controls entry into metamorphosis in the beetle Triboliumcastaneum. Proc. Natl. Acad. Sci. U. S. A., 104, 10488-10493.
20. Li, J., Lehmann, S., Weißbecker, B., Naharros, I., Schütz, S., Joop, G. and Wimmer, E. A. (2013) Odoriferous Defensive Stink Gland Transcriptome to Identify Novel Genes Necessary for Quinone Synthesis in the Red Flour Beetle, Tribolium castaneum. PLoS Genet, 9, e1003596.
21. Kim, H. S., Murphy, T., Xia, J., Caragea, D., Park, Y., Beeman, R. W., Lorenzen, M. D., Butcher, S., Manak, J. R. and Brown, S. J. (2010) BeetleBase in 2010: revisions to provide comprehensive genomic information for Triboliumcastaneum. Nucleic Acids Res., 38, D437-D442.
22. Mungall, C. J., Gkoutos, G. V., Smith, C. L., Haendel, M. A., Lewis, S. E. and Ashburner, M. (2010) Integrating phenotype ontologies across multiple species. Genome Biol., 11, R2.
23. Washington, N. L., Haendel, M. A., Mungall, C. J., Ashburner, M., Westerfield, M. and Lewis, S. E. (2009) Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol., 7, e1000247.
24. Beck, T., Morgan, H., Blake, A., Wells, S., Hancock, J. M. and Mallon, A.-M. (2009) Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. BMC Bioinformatics, 10, S2.
25. Sprague, J., Bayraktaroglu, L., Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M., Howe, D. G., Knight, J. et al. (2008) The Zebrafsh Information Network: the zebrafsh model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res., 36, D768-D772.
26. Grumbling, G. and Strelets, V. (2006) FlyBase: anatomical data, images and queries. Nucleic Acids Res., 34, D484-D488.
27. Dönitz, J., Grossmann, D., Schild, I., Schmitt-Engel, C., Bradler, S., Prpic, N.-M. and Bucher, G. (2013) TrOn: an anatomical ontology for the beetle Triboliumcastaneum. PLoS One, 8, e70695.
28. Dönitz, J. and Wingender, E. (2012) The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications. Bioinforma. Comput. Biol., 3, 197.
29. Waterhouse, R. M., Tegenfeldt, F., Li, J., Zdobnov, E. M. and Kriventseva, E. V. (2013) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res., 41, D358-D365.
30. McQuilton, P., St Pierre, S. E., Thurmond, J. and FlyBase Consortium (2012) FlyBase 101-the basics of navigating FlyBase. Nucleic Acids Res., 40, D706-D714.