Hybridization mapping of <i>Trypanosoma cruzi</i> chromosomes III and IV

Hanke, Jens; Frohme, Marcus; Laurent, Jean‐Pierre; Swindle, John; Hoheisel, Jörg D.

doi:10.1002/elps.1150190405

Cited by 14 publications

(10 citation statements)

References 11 publications

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“…This hybridization pattern corroborates the hypothesis that bands XVI and XVII carry size-polymorphic homologous chromosomes (Table 1). The existence of two homologs of a diploid chromosome that differ in size had been reported previously in T. cruzi and Trypanosoma brucei (Turner et al 1997;Frohme et al 1998;Hanke et al 1998;Melville et al 1998).…”

Section: Identification Of Markers For Chromosomal Bands XVI and Xviisupporting

confidence: 61%

Physical Mapping of a 670-kb Region of Chromosomes XVI and XVII from the Human Protozoan Parasite Trypanosoma cruzi Encompassing the Genes for Two Immunodominant Antigens

Santos

Lorenzi²,

Porcile³

et al. 1999

Genome Res.

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As part of the Trypanosoma cruzi Genome Initiative, we have mapped a large portion of the chromosomal bands XVI (2.3 Mb) and XVII (2.6 Mb) containing the highly repetitive and immunodominant antigenic gene families h49 and jl8. Restriction mapping of the isolated chromosomal bands and hybridization with chromosome specific gene probes showed that genes h49 and jl8 are located in a pair of size-polymorphic homologous chromosomes. To construct the integrated map of the chromosomes harboring the h49 and jl8 loci, we used YAC, cosmid, and phage overlapping clones, and long range restriction analysis using a variety of probes (i.e., known gene sequences, ESTs, polymorphic repetitive sequences, anonymous sequences, STSs generated from the YAC ends). The total length covered by the YAC contig was approximately 670 kb, and its map agreed and was complementary to the one obtained by long-range restriction fragment analysis. Average genetic marker spacing in a 105 kb region around h49 and jl8 genes was estimated to be 6.2 kb/marker. We have detected some polymorphism in the H49/JL8 antigens-encoding chromosomes, affecting also the coding regions. The physical map of this region, together with the isolation of specific chromosome markers, will contribute in the global effort to sequence the nuclear genome of this parasite.

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Section: Identification Of Markers For Chromosomal Bands XVI and Xviisupporting

confidence: 61%

Physical Mapping of a 670-kb Region of Chromosomes XVI and XVII from the Human Protozoan Parasite Trypanosoma cruzi Encompassing the Genes for Two Immunodominant Antigens

Santos

Lorenzi²,

Porcile³

et al. 1999

Genome Res.

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“…Certain DNA features -centromeric and telomeric sequences for example -are common between different chromosomes, however, and could cause the approximately 10% overlap between libraries. Only the higher degree of similarity between chromosomes I11 and IV suggests additional sequence homologies between the two chromo- somes, a result that could be validated by the appearance of some cosmid clones in the physical clone maps of both chromosomes 111 and IV [8], partly caused by the presence of repeats, for instance. Several dispersed repetitive DNA sequences are known to be present in T cruzi, from the approximately 200 copies of the DGF element to the 10000 copies of the El3 sequence [14], and could account for part of the overlaps.…”

Section: Discussionmentioning

confidence: 94%

“…DNA corresponding to about 5-10 million epimastigotes was used in each well. The DNA was transferred to nylon membranes by standard techniques [9]; cosmid DNA was labeled and hybridized as described in detail elsewhere [8]. Preparative PFGE was done in 1% SeaPlaque GTG LMP agarose using a pulse time of 55 s at 6 V/cm for 40 h. On these gels, DNA equivalent to about 15-30 million epimastigotes was used per well.…”

Section: Pfgementioning

confidence: 99%

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Selective generation of chromosomal cosmid libraries within the Trypanosoma cruzi genome project

et al. 1998

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From a total genomic cosmid library of the pathogen Trypanosoma cruzi, specific sublibraries of the smallest four chromosomes were isolated by hybridization of the respective chromosomal bands obtained from pulsed-field gels. These libraries form the basis for initial mapping analyses that should provide information useful for both the ongoing physical mapping of the entire genome and eventual sequence analyses. Selectivity of the procedure was high with 75% to 92%, although cross-hybridization had to be expected from ubiquitous DNA features, such as centromeric and telomeric sequences, and other regions homologous between individual chromosomes. Overall, the number of identified clones was slightly higher than expected but well within the intrinsic experimental variation considering the uncertainty about the exact genome size, the variability in clonability and the higher frequency of repeat sequences in larger chromosomes. Chromosome III- and IV-specific cosmids were analyzed on Southern blots of chromosomal separations. For strain CL Brener, all clones tested exhibited cross-hybridization to a homologous chromosome larger than 1 Mbp, supporting the assumption of the respective chromosome couple being diploid pairs.

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“…Here we focus on a physical mapping strategy based on hybridization experiments Scholler et al, 1995;Hanke et al, 1998). This procedure starts with a library of clones which correspond to subintervals of a larger contiguous piece of DNA G, all subintervals having the same size.…”

Section: Heber Et Almentioning

confidence: 99%

Contig Selection in Physical Mapping

Heber

Stoye

Frohme

et al. 2000

Journal of Computational Biology

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In physical mapping, one orders a set of genetic landmarks or a library of cloned fragments of DNA according to their position in the genome. Our approach to physical mapping divides the problem into smaller and easier subproblems by partitioning the probe set into independent parts (probe contigs). For this purpose we introduce a new distance function between probes, the averaged rank distance (ARD) derived from bootstrap resampling of the raw data. The ARD measures the pairwise distances of probes within a contig and smoothes the distances of probes across different contigs. It shows distinct jumps at contig borders. This makes it appropriate for contig selection by clustering. We have designed a physical mapping algorithm that makes use of these observations and seems to be particularly well suited to the delineation of reliable contigs. We evaluated our method on data sets from two physical mapping projects. On data from the recently sequenced bacterium Xylella fastidiosa, the probe contig set produced by the new method was evaluated using the probe order derived from the sequence information. Our approach yielded a basically correct contig set. On this data we also compared our method to an approach which uses the number of supporting clones to determine contigs. Our map is much more accurate. In comparison to a physical map of Pasteurella haemolytica that was computed using simulated annealing, the newly computed map is considerably cleaner. The results of our method have already proven helpful for the design of experiments aimed at further improving the quality of a map.

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Hybridization mapping of Trypanosoma cruzi chromosomes III and IV

Cited by 14 publications

References 11 publications

Physical Mapping of a 670-kb Region of Chromosomes XVI and XVII from the Human Protozoan Parasite Trypanosoma cruzi Encompassing the Genes for Two Immunodominant Antigens

Physical Mapping of a 670-kb Region of Chromosomes XVI and XVII from the Human Protozoan Parasite Trypanosoma cruzi Encompassing the Genes for Two Immunodominant Antigens

Selective generation of chromosomal cosmid libraries within the Trypanosoma cruzi genome project

Contig Selection in Physical Mapping

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