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

Reis-Cunha JL, Rodrigues-Luiz GF, Valdivia HO, Baptista RP, Mendes TA, de Morais GL, Guedes R, Macedo AM, Bern C, Gilman RH, Lopez CT, Andersson B, Vasconcelos AT, Bartholomeu DC - BMC Genomics (2015)

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. jaumlrc@gmail.com.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Dendrogram of the hierarchical analysis of the T. cruzi strains’ predicted ploidy. The hierarchical clustering analysis based on Euclidian distances of the predicted ploidy of each chromosome from the T. cruzi Arequipa, Colombiana, Sylvio, Esmeraldo, Y and 231 strains was performed using the Pvclust package and the R software platform. Two bootstrap resampling methods were used to assess the uncertainty in the hierarchical cluster analysis: the approximately unbiased (au) in red, and the bootstrap probability (bp) in green
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Fig5: Dendrogram of the hierarchical analysis of the T. cruzi strains’ predicted ploidy. The hierarchical clustering analysis based on Euclidian distances of the predicted ploidy of each chromosome from the T. cruzi Arequipa, Colombiana, Sylvio, Esmeraldo, Y and 231 strains was performed using the Pvclust package and the R software platform. Two bootstrap resampling methods were used to assess the uncertainty in the hierarchical cluster analysis: the approximately unbiased (au) in red, and the bootstrap probability (bp) in green

Mentions: To determine whether the ploidy profile of the six T. cruzi strains is in agreement with their phylogeny, a hierarchical clustering analysis was performed, using as input the predicted ploidy of each chromosome of each strain based on the SCoPE approach. The clustering analysis was based on their pairwise Euclidean distances using the Complete Linkage method (Fig. 5). In this analysis, all strains belonging to the TcI DTU clustered together, with Colombiana and Sylvio strains being closer to each other than to the Arequipa strain. This is likely due to the presence of exclusive aneuploidies in chromosomes 6 and 14 from Arequipa. Both TcII DTU strains showed a different pattern of chromosomal aneuploidies from each other and showed a smaller group consistency than the strains from the TcI DTU. The 231 TcIII DTU strain shows the most different pattern among the T. cruzi strains evaluated.Fig. 5


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

Reis-Cunha JL, Rodrigues-Luiz GF, Valdivia HO, Baptista RP, Mendes TA, de Morais GL, Guedes R, Macedo AM, Bern C, Gilman RH, Lopez CT, Andersson B, Vasconcelos AT, Bartholomeu DC - BMC Genomics (2015)

Dendrogram of the hierarchical analysis of the T. cruzi strains’ predicted ploidy. The hierarchical clustering analysis based on Euclidian distances of the predicted ploidy of each chromosome from the T. cruzi Arequipa, Colombiana, Sylvio, Esmeraldo, Y and 231 strains was performed using the Pvclust package and the R software platform. Two bootstrap resampling methods were used to assess the uncertainty in the hierarchical cluster analysis: the approximately unbiased (au) in red, and the bootstrap probability (bp) in green
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4491234&req=5

Fig5: Dendrogram of the hierarchical analysis of the T. cruzi strains’ predicted ploidy. The hierarchical clustering analysis based on Euclidian distances of the predicted ploidy of each chromosome from the T. cruzi Arequipa, Colombiana, Sylvio, Esmeraldo, Y and 231 strains was performed using the Pvclust package and the R software platform. Two bootstrap resampling methods were used to assess the uncertainty in the hierarchical cluster analysis: the approximately unbiased (au) in red, and the bootstrap probability (bp) in green
Mentions: To determine whether the ploidy profile of the six T. cruzi strains is in agreement with their phylogeny, a hierarchical clustering analysis was performed, using as input the predicted ploidy of each chromosome of each strain based on the SCoPE approach. The clustering analysis was based on their pairwise Euclidean distances using the Complete Linkage method (Fig. 5). In this analysis, all strains belonging to the TcI DTU clustered together, with Colombiana and Sylvio strains being closer to each other than to the Arequipa strain. This is likely due to the presence of exclusive aneuploidies in chromosomes 6 and 14 from Arequipa. Both TcII DTU strains showed a different pattern of chromosomal aneuploidies from each other and showed a smaller group consistency than the strains from the TcI DTU. The 231 TcIII DTU strain shows the most different pattern among the T. cruzi strains evaluated.Fig. 5

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. jaumlrc@gmail.com.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus