A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers
We present a useful refinement of the molecular karyotype of clone CL Brener, the reference clone of the Trypanosoma cruzi Genome Project. The assignment of 210 genetic markers (142 expressed sequence tags (ESTs), seven cDNAs, 32 protein-coding genes, eight sequence tagged sites (STSs), 21 repetitiv...
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todo:paper_03781119_v308_n1-2_p53_Porcile2023-10-03T15:31:48Z A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers Porcile, P.E. Santos, M.R.M. Souza, R.T. Verbisck, N.V. Brandão, A. Urmenyi, T. Silva, R. Rondinelli, E. Lorenzi, H. Levin, M.J. Degrave, W. Da Silveira, J.F. Chromosome specific marker Expressed sequence tag Linkage group Repetitive sequence Yeast artificial chromosome contig complementary DNA contig article chromosomal localization chromosome band chromosome marker expressed sequence tag gene mapping gene sequence genetic code genetic linkage genetic marker genome karyotype molecular cloning molecular phylogeny nonhuman nucleotide repeat nucleotide sequence priority journal pulsed field gel electrophoresis sequence tagged site Trypanosoma cruzi unindexed sequence yeast artificial chromosome Trypanosoma Trypanosoma cruzi Trypanosoma cruzi We present a useful refinement of the molecular karyotype of clone CL Brener, the reference clone of the Trypanosoma cruzi Genome Project. The assignment of 210 genetic markers (142 expressed sequence tags (ESTs), seven cDNAs, 32 protein-coding genes, eight sequence tagged sites (STSs), 21 repetitive sequences) to the chromosomal bands separated by pulsed field gel electrophoresis (PFGE) identified 61 chromosome-specific markers, two size-polymorphic chromosomes and seven linkage groups. Fourteen new repetitive elements were isolated in this work and mapped to the chromosomal bands. We found that at least ten repetitive elements can be mapped to each chromosomal band, which may render the whole genome sequence assembly a difficult task. To construct the integrated map of chromosomal band XX, we used yeast artificial chromosome (YAC) overlapping clones and a variety of probes (i.e. known gene sequences, ESTs, STSs generated from the YAC ends). The total length covered by the YAC contig was approximately 1.3 Mb, covering 37% of the entire chromosome. We found some degree of polymorphism among YACs derived from band XX. These results are in agreement with data from phylogenetic analysis of T. cruzi which suggest that clone CL Brener is a hybrid genotype [Mol. Biochem. Parasitol. 92 (1998) 253; Proc. Natl. Acad. Sci. USA 98 (2001) 7396]. The physical map of the chromosomal bands, together with the isolation of specific chromosomal markers, will contribute in the global effort to sequence the nuclear genome of this parasite. © 2003 Elsevier Science B.V. All rights reserved. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_03781119_v308_n1-2_p53_Porcile |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Chromosome specific marker Expressed sequence tag Linkage group Repetitive sequence Yeast artificial chromosome contig complementary DNA contig article chromosomal localization chromosome band chromosome marker expressed sequence tag gene mapping gene sequence genetic code genetic linkage genetic marker genome karyotype molecular cloning molecular phylogeny nonhuman nucleotide repeat nucleotide sequence priority journal pulsed field gel electrophoresis sequence tagged site Trypanosoma cruzi unindexed sequence yeast artificial chromosome Trypanosoma Trypanosoma cruzi Trypanosoma cruzi |
| spellingShingle |
Chromosome specific marker Expressed sequence tag Linkage group Repetitive sequence Yeast artificial chromosome contig complementary DNA contig article chromosomal localization chromosome band chromosome marker expressed sequence tag gene mapping gene sequence genetic code genetic linkage genetic marker genome karyotype molecular cloning molecular phylogeny nonhuman nucleotide repeat nucleotide sequence priority journal pulsed field gel electrophoresis sequence tagged site Trypanosoma cruzi unindexed sequence yeast artificial chromosome Trypanosoma Trypanosoma cruzi Trypanosoma cruzi Porcile, P.E. Santos, M.R.M. Souza, R.T. Verbisck, N.V. Brandão, A. Urmenyi, T. Silva, R. Rondinelli, E. Lorenzi, H. Levin, M.J. Degrave, W. Da Silveira, J.F. A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers |
| topic_facet |
Chromosome specific marker Expressed sequence tag Linkage group Repetitive sequence Yeast artificial chromosome contig complementary DNA contig article chromosomal localization chromosome band chromosome marker expressed sequence tag gene mapping gene sequence genetic code genetic linkage genetic marker genome karyotype molecular cloning molecular phylogeny nonhuman nucleotide repeat nucleotide sequence priority journal pulsed field gel electrophoresis sequence tagged site Trypanosoma cruzi unindexed sequence yeast artificial chromosome Trypanosoma Trypanosoma cruzi Trypanosoma cruzi |
| description |
We present a useful refinement of the molecular karyotype of clone CL Brener, the reference clone of the Trypanosoma cruzi Genome Project. The assignment of 210 genetic markers (142 expressed sequence tags (ESTs), seven cDNAs, 32 protein-coding genes, eight sequence tagged sites (STSs), 21 repetitive sequences) to the chromosomal bands separated by pulsed field gel electrophoresis (PFGE) identified 61 chromosome-specific markers, two size-polymorphic chromosomes and seven linkage groups. Fourteen new repetitive elements were isolated in this work and mapped to the chromosomal bands. We found that at least ten repetitive elements can be mapped to each chromosomal band, which may render the whole genome sequence assembly a difficult task. To construct the integrated map of chromosomal band XX, we used yeast artificial chromosome (YAC) overlapping clones and a variety of probes (i.e. known gene sequences, ESTs, STSs generated from the YAC ends). The total length covered by the YAC contig was approximately 1.3 Mb, covering 37% of the entire chromosome. We found some degree of polymorphism among YACs derived from band XX. These results are in agreement with data from phylogenetic analysis of T. cruzi which suggest that clone CL Brener is a hybrid genotype [Mol. Biochem. Parasitol. 92 (1998) 253; Proc. Natl. Acad. Sci. USA 98 (2001) 7396]. The physical map of the chromosomal bands, together with the isolation of specific chromosomal markers, will contribute in the global effort to sequence the nuclear genome of this parasite. © 2003 Elsevier Science B.V. All rights reserved. |
| format |
JOUR |
| author |
Porcile, P.E. Santos, M.R.M. Souza, R.T. Verbisck, N.V. Brandão, A. Urmenyi, T. Silva, R. Rondinelli, E. Lorenzi, H. Levin, M.J. Degrave, W. Da Silveira, J.F. |
| author_facet |
Porcile, P.E. Santos, M.R.M. Souza, R.T. Verbisck, N.V. Brandão, A. Urmenyi, T. Silva, R. Rondinelli, E. Lorenzi, H. Levin, M.J. Degrave, W. Da Silveira, J.F. |
| author_sort |
Porcile, P.E. |
| title |
A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers |
| title_short |
A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers |
| title_full |
A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers |
| title_fullStr |
A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers |
| title_full_unstemmed |
A refined molecular karyotype for the reference strain of the Trypanosoma cruzi genome project (clone CL Brener) by assignment of chromosome markers |
| title_sort |
refined molecular karyotype for the reference strain of the trypanosoma cruzi genome project (clone cl brener) by assignment of chromosome markers |
| url |
http://hdl.handle.net/20.500.12110/paper_03781119_v308_n1-2_p53_Porcile |
| work_keys_str_mv |
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1807315402225614848 |