The IMBB Genome Laboratory

The IMBB Genome laboratory (IGL) was established in 1997. The decision was based on the successful participation of several IMBB groups in research programms in the field of genomics. These included the Louis and Savakis groups in the European Union-funded European Drosophila Genome Project (EDGP), the Alexandraki and Thireos groups in the European Union-funded Yeast Sequencing Project, and the participation of the Moschonas group in the Human Genome Project.

The first project to be managed by the IGL was the participation in the last phase of the EDGP (sequencing of the three distalmost chromosomal divisions of chromosome X). Of the total of about 2.6 Mb of finished sequences produced by the EDGP consortium, the IGL produced ~592 Kb of high quality sequence, in addition to about 680 Kb of scaffold (low coverage) sequences. Furthermore, the IGL also determined (and already published) the sequence of the mtDNA of the Mediterranean fruitfly Ceratitis capitata and,so far, about 250 kb of genomic sequences for the malaria mosquito Anopheles gambiae. Finally, in collaboration with F.C. Kafatos, the IGL has finished the first comparative genomic study of Anopheles gambiae and Drosophila melanogaster.

In addition to its participation in genome analysis projects, the IGL provides the groups of the IMBB and the other biological research institutions in Heraklion with high quality service sequencing at a cost basis (currently about 120 sequencing reactions/month).

The plans for the immediate future include the participation of the IGL in the Anopheles gambiae genome project, and an increased involvement in RNA profiling projects. For that latter activity the IGL has already purchased an Array Reader, while an Arrayer has already been ordered.

Available technology and equipment:

* Semiautomatic preparation of double-stranded sequencing templates in 96-well format using Biomek 2000° robotic workstation (96 templates in 2 hours).
* Semiautomatic preparation of cycle sequencing reactions with dye-terminator chemistry in 96-well format using Biomek 2000° robotic workstation (192 templates in 30 minutes).
* Running two ABI399 Prism° sequencers with total daily sequence output of up to ~120 kb.
* Sequence assembly and analysis with Phred/Phrap/Consed software on a UNIX computer (DEC personal workstation 500au).
* GSI Lumonics Scannarray 5000 array reader (incl. necessary software and peripheral equipment).
* Packard Bioscience SpotArray 24 spotter (incl. necessary software and peripheral equipment).
* Other equipment available: bench top centrifuge, PCR machines, PCs and MacIntoshes, common bench equipment.

Personel:

* Prof. Christos Louis (Acting head)
* Lefteris Spanos, Research Assistant
* George Papagiannakis, Research Assistant

Publications:

1. Louis, C. (1999). Malaria entomology: can genomics help?. Parassitologia, 41, 489-492. (PMID: 10697907)

2. Benos, P. V., Gatt, M. K., Ashburner, M., Murphy, L., Harris, D., Barrell, B., Ferraz, C., Vidal, S., Brun, C., Demailles, J., Cadieu, E., Dreano, S., Gloux, S., Lelaure, V., Mottier, S., Galibert, F., Borkova, D., Minana, B., Kafatos, F.C., Louis, C., Sidιn-Kiamos, I., Bolshakov, S., Papagiannakis, G., Spanos, L., Cox, S., Madueno, E., de Pablos, B., Modolell, J., Peter, A., Schoettler, P., Werner, M., Mourkioti, F., Beinert, N., Dowe, G., Schaefer, U., Jaeckle, H., Bucheton, A., Callister, D.M., Campbell, L.A., Darlamitsou, A., Henderson, N. S., McMillian, P.J., Salles, C., Tait, E.A., Valenti, P., Saunders, R. D. C. and Glover, D. M. (2000). From Sequence to Chromosome: the tip of the X chromosome of D. melanogaster. Science. 287, 2220-2222. (PMID: 10731137)

3. Adams, M., (...), Bolshakov, S., (...),Sidιn-Kiamos, I., (...) and Venter, J.C. (2000) The Genome Sequence of Drosophila melanogaster. Science. 287, 2185-2195. (PMID: 10731132)

4. Spanos, L., Koutroubas, G., Kotsyfakis, M. and Louis, C. (2000). The complete sequence of the mitochondrial genome of the Medfly, Ceratitis capitata. Ins. Mol. Biol. 9, 139-144. (PMID: 10762421)

5. Benos, P.V., Gatt, M.K., Murphy, L., Harris, D., Barrell, B., Ferraz, C., Vidal, S., Brun, C., Demaille, J., Cadieu, E., Dreano, S., Gloux, S., Lelaure, V., Mottier, S., Galibert, F., Borkova, D., Minana, B., Kafatos, F.C., SidŽn-Kiamos, I., Bolshakov, S., Papagiannakis, G., Spanos, L., Louis, C., Madueno, E., de Pablos, B., Modolell, J., Peter, A., Schšttler, P., Werner, M., Mourkioti, F., Beinert, N., Dowe, G., SchŠfer, U., JŠckle, H., Bucheton, A., Callister, D., Campbell, L., Henderson, N.S., McMillan, P.J., Salles, C., Tait, E., Valenti, P., Pachter, L., Saunders, R.D.C., Glover, D.M. and Ashburner, M. (2001) From First Base: The sequence of the tip of the X chromosome of D. melanogaster. Genome Res., 11, 710-730. (PMID: 11337470)

6. Favia, G., Lanfrancotti, A., Spanos, L., Caruso M., SidŽn-Kiamos, I., Coluzzi, M. and Louis, C. (2001). Molecular characterization of ribosomal DNA (rDNA) polymorphisms discriminating among chromosomal forms of Anopheles gambiae s.s.. Insect Mol. Biol. 10, 19-23. (PMID: 11240633)

7. Peter, A., Schottler, P., Werner, M., Beinert, N., Dowe, G., Burkert, P., Mourkioti, F., Dentzer, L., He, Y., Deak, P., Benos, P.V., Gatt, M.K., Murphy, L., Harris, D., Barrell, B., Ferraz, C., Vidal, S., Brun, C., Demaille, J., Cadieu, E., Dreano, S., Gloux, S., Lelaure, V., Mottier, S., Galibert, F., Borkova, D, Minana, B., Kafatos, F.C., Bolshakov, S., Siden-Kiamos, I., Papagiannakis, G., Spanos, L., Louis. C, Madueno, E., de Pablos, B., Modolell, J., Bucheton, A., Callister, D., Campbell, L., Henderson, N.S., McMillan, P.J., Salles, C., Tait E., Valenti, P., Saunders, R.D., Billaud, A., Pachter, L., Klapper, R., Janning, W., Glover, D.M., Ashburner, M., Bellen, H.J., Jackle, H., and Schafer, U. (2002) Identification and mapping of vital gene functions of the Drosophila X-chromosome. EMBO Rep. 3, 34-38. (PMID: 11779831)

8. Bolshakov, V., Topalis, P., Blass, della Torre, A. C., Kafatos, F.C. and Louis, C. (2002). A comparison of the genomes of the fruitfly Drosophila melanogaster and the malaria mosquito Anopheles gambiae based on long-range genomic sequences and EST analysis. Genome Res. 12, 57-66. (PMID: 11337470)