Sekwencjonowanie największego chromosomu Paramecium tetraurelia - przykład opracowania metody

Nowak, Jacek K.

doi:IChB B-86

Przejdź do menu głównego
Przejdź do wyszukiwarki
Przejdź do treści
Przejdź do stopki

Pobierz

Tytuł: Sekwencjonowanie największego chromosomu Paramecium tetraurelia - przykład opracowania metody

Abstrakt:

The largest, megabase, somatic chromosome of P. tetraurelia was isolated and sequenced in order to explore its organization and gene content. The AT-rich chromosome is compact with very small introns, short intergenic regions and a coding density of at least 74%, higher than that reported for budding yeast or any other free-living eukaryote. Homology to known proteins could be detected only for 57% of the 464 potential protein coding genes. Subsequently, the megabase chromosome sequence was used during the whole genome sequencing project as a reference to evaluate sequence assembly and gene annotation accuracy. In a pilot project of the global analysis of P. tetraurelia gene expression during autogamy, DNA microarrays were used. Statistical data analysis allowed the identification of four clusters of co-ex- pressed genes. Screening for silencing phenotypes of 15 autogamy specific genes revealed that 4 genes were essential during vegetative growth and 3 others were essential for successful sexual process.

Bibliografia:

BeissonJ., Betermier M., Bre M.-H., Cohen J., Duharcourt S., Duret L., Kiing C., Malinsky S., Meyer E., Preer J. R. jr, Sperling L., (2010), Cold Spring Harb Protoc, 2010doi:I0.1101/pdb.emol40
Caron F., Meyer E., (1985), Nature, 314(6007), 185-188.
Preer J. R. jr., Preer L. B., Rudman B. M., Barnett A. J., (1985), Nature, 314(6007), 188-190.
Greider C. W., Blackburn E. H., (1985), Celi, 43(2 Pt 1), 405-413.
Jaillon O., Bouhouche K., Gout J.. Aury J., Noel B., Saudemont B., Nowacki M., Serrano V., Porcel B., Segurens B., Le Mouel A., Lepere G., Schachter V., Betermier M., Cohen J., Wincker P., Sperling L., Duret L., Meyer E., (2008), Nature, 451 (7176), 359-362.
Duharcourt S., Lepere G., Meyer E., (2009), Trends Genet., 25(8), 344-350.
Gratias A., Betermier M., (2001), Biochimie, 83, 1009-1022.
Yao M. C., Duharcourt S., Chalker D. L., (2002), Mobile DNA II, Eds. Craig N. L., Craigie R., Gellert M., Lambowitz A. M., ASM Press, Washington DC.
Dessen P., Zagulski M., Gromadka R., Plattner H., Kissmehl R., Meyer E., Betermier M., Schultz J. E., Linder J. U., Pearlman R. E., Kung C., Forney J., Satir B. H., van Houten j. L., Keller A. M., Froissard M., Sperling L., Cohen J., (2001), Trends Genet., 17(6), 306-308.
Sperling L., Dessen P., Zagulski M., Pearlman R. E., Migdalski A., Gromadka R., Froissard M., Keller A. M., Cohen J., (2002), Eukaryot. Celi., 3, 341-352.
Staden R., (1996), Mol. Biotechnol., 5, 233-241.
Tettelin H., Radune D., Kasif S., Khouri H., Salzberg S., (1999), Genomics, 62, 500-507.
Forney J., Rodkey K., (1992), Nucleic Acids Res., 20, 5397-5402.
Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D.J., (1990), J. Mol. Biol., 215, 403-410.
Salzberg S., Pertea M., Delcher A., Gardner M., Tettelin FI., (1999), Genomics, 59, 24-31.
Rutherford K., ParkhillJ., CrookJ., Florsnell T., Rice P., Rajandream M. A., Barrell B., Bioinformatics, (2000), 16, 944-945.
Zagulski M., Nowak J. K., Le Mouel A., Nowacki M., Migdalski A., Gromadka R., Noel B., Blanc 1., De- ssen P., Wincker P., Keller A. M., Cohen j., Meyer E., Sperling L., (2004), Curr. Biol., 15, 1397-1404.
AuryJ. M., Jaillon O., Duret L., Noel B., jubin C., Porcel B. M., Segurens B., Daubin V., Anthouard V., Aiach N., Arnaiz 0., Billaut A., Beisson j., Blanc 1., Bouhouche K., Camara F., Duharcourt S., Guigo R., Gogendeau D., Katinka M., Keller A.-M., Kissmehl R., Klotz C., Koll F., Le Mouel A., Lepere G., Malinsky S., Nowacki M., Nowak j. K., Plattner FI., Poulain J., Ruiz F., Serrano V., Zagulski M., De- ssen P., Betermier M., Weissenbach j., Scarpelli C., Schachter V., Sperling L., Meyer E., Cohen J., Wincker P., (2006), Nature, 444 (7116), 171-178.
Arnaiz O., Cain S., Cohen J., Sperling L., (2007), Nucleic Acids Res., 35 (Database issue), D439-444.
Ohno S., (1970), Evolution by Gene Duplication, Ed. Allen 8; Unwin, London.
Carver T.J., Rutherford K. M., Berriman M., Rajandream M. A., Barrell B. G., ParkhillJ., (2005), 21, 3422-3423.
Lepere G., Nowacki M., Serrano V., Gout J.-F., Guglielmi G., Duharcourt S., Meyer E., (2009), Nucleic Acids Res., 37(3), 903-915.
Lepere G., Betermier M., Meyer E., Duharcourt S., (2008), Genes Dev., 22(11), 1501-1512.
Ponting C. P., Oliver P. L, Reik W., (2009), Cell, 136, 629-641.
Dudley D. D., Chaudhuri J., Bassing C. FI., Alt F. W., (2005), Adv. Immunol., 86, 43-112.
Galvani A., Sperling L., (2001), Nucleic Acids Res., 29, 4387-4394.
Baudry C., Malinsky S., Restituito M., Kapusta A., Rosa S., Meyer E., Betermier M., (2009), Genes Dev., 23, 2478-2483.