Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains

BMC Genomics

Daniella C. Bartholomeu²  Ana Tereza Vasconcelos⁶  Björn Andersson¹  Carlos Talavera Lopez¹  Robert H. Gilman⁴  Caryn Bern³  Andrea M. Macedo⁵  Rafael Guedes⁶  Guilherme Loss de Morais⁶  Tiago A. O. Mendes²  Rodrigo P. Baptista²  Hugo O. Valdivia²  Gabriela F. Rodrigues-Luiz²  João Luís Reis-Cunha² 

[1] Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden;Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil;University of California San Francisco, San Francisco, CA, USA;Universidad Cayetano Heredia, Lima, MD, Peru;Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil;Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil

关键词: Genomic plasticity;    Trypanosoma cruzi;    Chromosome copy number variation;   

Others  :  1219166
DOI  :  10.1186/s12864-015-1680-4

 received in 2015-03-03, accepted in 2015-06-01,  发布年份 2015

【 摘 要 】

Background

Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI–TcVI. CL Brener, the reference strain of the T. cruzi genome project, is a hybrid with a genome assembled into 41 putative chromosomes. Gene copy number variation (CNV) is well documented as an important mechanism to enhance gene expression and variability in T. cruzi. Chromosomal CNV (CCNV) is another level of gene CNV in which whole blocks of genes are expanded simultaneously. Although the T. cruzi karyotype is not well defined, several studies have demonstrated a significant variation in the size and content of chromosomes between different T. cruzi strains. Despite these studies, the extent of diversity in CCNV among T. cruzi strains based on a read depth coverage analysis has not been determined.

Results

We identify the CCNV in T. cruzi strains from the TcI, TcII and TcIII DTUs, by analyzing the depth coverage of short reads from these strains using the 41 CL Brener chromosomes as reference. This study led to the identification of a broader extent of CCNV in T. cruzi than was previously speculated. The TcI DTU strains have very few aneuploidies, while the strains from TcII and TcIII DTUs present a high degree of chromosomal expansions. Chromosome 31, which is the only chromosome that is supernumerary in all six T. cruzi samples evaluated in this study, is enriched with genes related to glycosylation pathways, highlighting the importance of glycosylation to parasite survival.

Conclusions

Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression, which represents a strategy that may be crucial for parasites that mainly depend on post-transcriptional mechanisms to control gene expression.

【 授权许可】

   
2015 Reis-Cunha et al.

【 图 表 】

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