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| Status |
Public on Aug 06, 2011 |
| Title |
Widespread, focal copy number variations (CNV) in Trypanosoma cruzi strains |
| Organism |
Trypanosoma cruzi |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Trypanosoma cruzi is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America. T. cruzi is diploid, almost exclusively asexual, and displays an extraordinarily diverse population structure both genetically and phenotypically. Yet, to date the genotypic diversity of T. cruzi and its relationship, if any, to biological diversity have not been studied at the whole genome level. In this study, we used whole genome oligonucleotide tiling arrays to compare gene content in biologically disparate T. cruzi strains by comparative genomic hybridization (CGH). We observed that T. cruzi strains display widespread and focal copy number variations (CNV) and a substantially greater level of diversity than can be adequately defined by the current genetic typing methods. As expected, CNV were particularly frequent in gene family-rich regions containing mucins and trans-sialidases but were also evident in core genes. Gene groups that showed little variation in copy numbers among the strains tested included those encoding protein kinases and ribosomal proteins, suggesting these loci were less permissive to CNV. Moreover, frequent variation in chromosome copy numbers were observed, and chromosome-specific CNV signatures were shared by genetically divergent T. cruzi strains, suggesting a greater degree of chromosome exchange than previously thought.
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| Overall design |
Genomic DNA samples from 16 T. cruzi strains were compared to genomic DNA from the CL Brener strain by competitive hybridizations on whole genome oligonucleotide tiling arrays.
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| Contributor(s) |
Minning TA, Weatherly DB, Tarelton RL, Flibotte S |
| Citation(s) |
21385342 |
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| Submission date |
Aug 11, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Todd A Minning |
| E-mail(s) |
tminning@uga.edu
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| Phone |
706-542-3155
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| Fax |
706-542-3582
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| URL |
http://paige.ctegd.uga.edu/
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| Organization name |
University of Georgia
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| Department |
CTEGD
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| Lab |
Tarleton Research Group
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| Street address |
Rm 310 Coverdell
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platforms (1) |
| GPL10781 |
Nimblegen T. cruzi 290K version 1.0 |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA130919 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23576_RAW.tar |
210.8 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
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