Sekwencjonowanie genomów i rozwój biotechnologii

Przybecki, Zbigniew; Pawełkowicz, Magdalena E.; Wóycicki, Rafał

doi:0860-7796

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Title: Sekwencjonowanie genomów i rozwój biotechnologii

Abstract:

As a result of the Human Genome Project and announcement of the project: Archon X Prize for Genomics “genome for 1000$’’, the sequencing technology made huge progress. The purpose was to develop radically new technology that would dramatically reduce the time and cost of sequencing and resequencing eukaryotic genomes (or large region), and transcriptomes. This progress has influenced many areas also widely understood biotechnology. Owing to comparative genomic and sequenced genomes, new opportunities have occurred such as acceleration of genomic polymorphism identification, genes and genome structure prediction. It has also stimulated the development of assignation of functional effect of SNP, CNP or INDEI. polymorphism and enabled functional and structural annotation of genome, establishment of a net of genome interaction (netoms) and netom’s controlling. Genetic and physical mapping of genome elements methods undergo considerable alterations, thus they become critical in association metbodology of genome and their function. The analysis of metabolic network and its elements is basic in planning activities in new biotechnology. Here we present the achievements in cucumber which were possible due to sequencing the genome of this species by our team.

References:

Xiao L. Saldivar J.-S., Zhou C., Chen C., Zhang J., Sirois P., Li K., (2009), Mol. Biotechnol., 41,152-156.
Andersen M. R., Nielsen M. L., Nielsen J., (2008), Molecular Systems Biology, 4, 1-13.
Feist A. M., Palsson B. Ø., (2008) Nature Biotechnology, 26 (6), 659-668.
Feist A. M., Palsson B. O., (2010) Current Opinion in Microbiology, 13, 344-349.
Gomes de Oliveira Dal’Molin C., Quek L.-E., Palfreyman R. W., Brumbley S. M., Nielsen L. K., (2010),Plant Physiology, 152, 579-589.
Cerami E., Demir E., Schultz N., Taylor B. S., Sander C., (2010), PLoS ONE, 5(2), e8918.
Przybecki Z., Wóycicki R., Malepszy S., (2009), Post. Biol. Kom., 36., suppl. 25, 19-31.
Varshney R. K., Nayak S. N., May G. D., Jackson S. A., (2009), Trends in Biotechnol., 27, 522-530.
Varshney R. K., Graner A., Sorrells M. E., (2005), Trends Plant Sci., 10, 621-630.
Masojc P., Lebiecka K., Milczarski P., Wiśniewska M., Łań A., Owsianicki R.. (2009), Euphytica, 170, 123-129.
Barrett j. C., Hansoul S., Nicolae D. L., Cho J. H., Duerr R. H., Rioux J. D.. Brant S. R.. Silverberg M. S„ Taylor K. D., Barmada M. M., Bitton A., Dassopoulos T., Datta L. W., Green T., Griffiths A. M., Kistner E. 0., Murtha M, T., Regueiro M. D., Rotter J. I., Schumm L. P., Steinhart A. H,, Targan S. R., Xavier R. j., (The NIDDK IBD Genetics Consortium), Libioulle C., Sandor C., Lathrop M., BelaicheJ., Dewit 0.. Gut I., Heath S., Laukens D., Mni M., Rutgeerts P.. van Cossum A., Zelenika D., Franchi- mont D., Hugot J.-P., de Vos M., Vermeire S., Louis E., (The Belgian-French IBD Consortium), The Wellcome Trust Case Control Consortium, Cardon L.R., Anderson C. A., Drummond H., Nimmo E., Ahmad T., Prescott N. j., Onnie C. M., Fisher S. A., Marchini J., Ghori J.. Bumpstead S., Gwilliam R., Tremelling M., Deloukas P., Mansfield J., Jewell D., Satsangi J., Mathew C. G., Parkes M., Georges M., Daly M. J., (2008), Nature Genet., 40, 955-962.
Hirschhorn J. N., (2009), N. Engel. J. Med., 360, 1699-1701.
Cookson W., Liang L., Abecasis G., Moffatt M., Lathrop M., (2009), Nature Rev., 10. 184-194.
Emilsson V., Thorleifsson G., Zhang B., Leonardson A. S., Zink F., ZhuJ., Carlson S., Helgason A., Walters G. B., Gunnarsdottir S., Mouy M., Steinthorsdottir V., Eiriksdottir G. H., Bjornsdottir G., Reynisdottir L. Gudbjartsson D., Helgadottir A., Jonasdottir A., Jonasdottir A., Styrkarsdottir U., Gretarsdottir S., Magnusson K. P., Stefansson H., Fossdal R., Kristjansson K., Gislason H. G,, Stefans- son T., I.eifsson B. G., Thorsteinsdottir U., I.ambj. R., CulcherJ. R., Reitman M. 1... Kong A.. Schadt E. E.. Stefansson K., (2008), Nature. 452, 423-428.
Schadt E. E.. Monks S. A., Drake T. A., Lusisk A. J., Chek N., Colinayok V., RuffT. G., Milligan S. B., Lamb J. R., Cavet G., Linsley P. S., Mao M.. Stoughton R. B., Friend S. H., (2003), Nature. 422, 297-302.
HANS NABsys. http://nabsys.com/
Wang Z., Gerstein M., Snyder M., (2009), Nature Rev. Genet., 10, 57-63.
Yassoura M., Kapłana T., Fraser H. B., LevinJ. Z., Pflffner J., Adiconis X., Schroth G.. Luo S., Khrebtu- kova L, Gnirke A., Nusbaum C.. Thompson D.-A., Friedman N.. Regev A., (2009), PNAS, 106, 3264-3269.
Yin Z., Meng F., Song H., Wang X., Xu X., Yu D., (2010), Plant Physiology, 152, 1625-1637.
Chen X.. Hackett C. A., Niks R. E., Hedley P. E., Booth C., et al., (2010), PLoS ONE, 5( 1). e8598.
Carr P. A., Church G. M., (2009), Nature Biotechnol., 27, 12, 1151-1163.
Dietz S., Panke S., (2010), BioEssays, 32, 356-362.
Gibson D. G., Benders G. A., Andrews-Pfannkoch C., Denisova E. A., Baden-Tillson H., Zaveri J., Stoc- kwell T. B., Brownley A.. Thomas D. W., Algire M. A., Merryman C., Young 1.., Noskov V. N., Glass J. I., Venter J. C., Hutchison III C. A., Smith H. O., (2008), Science, 319, 1215-1220.
Itaya M., Tsuge K., Koizumi M., Fujita K., (2005), Proc. Natl. Acad. Sci. USA, 102, I597I-I5976.
Wang H. H., Isaacs F.J., Carr P. A., Sun Z. Z., Xu G., Forest C. R., Church G. M.. (2009), Nature, 460, 894-898.
Posfai G., Plunkett III G.. Feher T., Frisch D., Keil G. M., UmenhofFer K., Kolisnychenko V., Stahl B., Sharma S. S., de Arruda M.. Burland V., Harcum S. W., Blattner F. R., (2006), Science, 312, 1044-1046.
Shimizu Y., Kanamori T., Ueda T., (2005), Methods, 36, 299-304.
Chan L. Y., Kosuri S., Endy D., (2005). Mol. Syst. Biol., I, 2005.0018.
Purnick P. E. M., Weiss R., (2009), Nature Rev. Mol. Cell Biol.. 10, 410-422.
Khalil A. S., Collins J. J., (2010), Nature Rev. Genet., II, 367-379.
Tyo K. E. J., Kocharin K., Nielsen J., (2010), Curr. Opinion in Microbiol., 13, 1-8.
McArthur IV G. H., Fong S. S., (2010), J. of Biomed. and Biotech., Article ID 459760.
Friedland A. E., Lu T. K., Wang X., Shi D., Church G., Collins J. J., (2009), Science, (May 29), 324(5931); 1199-1202.doi: 10.1126/science. 1172005.
Huang S., Li R., Zhang Z., Li L., Gu X.. Fan W., Lucas W. J., Wang X., Xie B., Ni P., Ren Y., Zhu H., Li J., Lin K.,Jin W., Fei Z., Li G., StaubJ.. Kilian A., van der Vossen E. A G.. Wu Y., GuoJ., HeJ., Jia Z., Ren Y., Tian G., Lu Y., Ruan J., Qian W., Wang M., Huang Q., Li B., Xuan Z., CaoJ., Asan. Wu Z., Zhang J., Cai Q., Bai Y., Zhao B., Han Y., Li Y., Li X., Wang S., Shi Q., Liu S., Cho W. K., Kim J. Y., Xu Y., Heller-Uszynska K., Miao H.. Cheng Z., Zhang S., Wu J., Yang Y., Kang H., Li M., Liang H., Ren X., Shi Z., Wen M.,Jian M., Yang H., Zhang G., Yang Z., Chen R.. Liu S., LiJ., Ma L., Liu H., Zhou Y., ZhaoJ., Fang X., Li G., Fang L., Li Y., Liu D., Zheng H., Zhang Y., Qin N., Li Z., Yang G., Yang S., Bolund L., Kristiansen K., Zheng H., Li S., Zhang X., Yang H., WangJ., Sun R., Zhang B., Jiang S., Wang J., Du Y., Li S., (2009), Nat. Genet., published online, I November 2009; doi;IO.I038/ng.475.
Wóycicki R., WitkowiczJ., Pawelkowicz M., Siedlecka E., Gutman W., Pląder W., Seroczyńska A., Śmiech M., Niemirowicz-Szczytt K., Bartoszewski G., Gawroński P., Dąbrowska]., Karpiński S., Bo- rodovsky M., Lomsadze A., Malepszy S., Przybecki Z. (w przygotowaniu).
Miller J.. Koren S., Walenz B., Sutton G., Knight J., Jarvie T., Kodira C., AfFourtit J., Harkins T., (2009), Poster Santa Fe.
Gawroński P., Dąbrowską J., Wóycicki R., Bartoszewski G., Przybecki Z., Malepszy S., Karpiński S., (2010), SEB Annual Main Meeting 2010 Clarion Congress Hotel, Prague, Czech Republic 30''’June - 3"i July 2010.