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Series GSE23576 Query DataSets for GSE23576
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
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.
 
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.
 
Contributor(s) Minning TA, Weatherly DB, Tarelton RL, Flibotte S
Citation(s) 21385342
Submission date Aug 11, 2010
Last update date Mar 22, 2012
Contact name Todd A Minning
E-mail(s) tminning@uga.edu
Phone 706-542-3155
Fax 706-542-3582
URL http://paige.ctegd.uga.edu/
Organization name University of Georgia
Department CTEGD
Lab Tarleton Research Group
Street address Rm 310 Coverdell
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platforms (1)
GPL10781 Nimblegen T. cruzi 290K version 1.0
Samples (16)
GSM578346 Brazil
GSM578347 Chinata
GSM578348 M78
Relations
BioProject PRJNA130919

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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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