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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

Methodologies to determinate the chromosomal copy number in T. cruzi strains. To estimate the chromosome ploidy of T. cruzi strains, two approaches were evaluated by mapping reads from the Y strain on the 41 CL Brener chromosomes. a The Whole Chromosome Ploidy Estimations (WCPE) predicts the ploidy based on the mean coverage of the whole-chromosome sequence. b The single-copy genes ploidy estimations (SCoPE) predict the chromosomal ploidy based only on the coverage of the 1563 Esmo-like/Non-Esmo single-copy genes present in each chromosome. The read depth was scaled to give a value of 2 for disomic chromosomes. c The 41 T. cruzi chromosome gene distribution is shown. Multicopy gene families are represented as blue boxes and the hypothetical and housekeeping genes as black boxes. The red arrows highlight the chromosomes with a higher content of multigene families or with the largest proportion of gap regions. Chromosomes with a higher density of multigene families or that present large gap regions tend to have a biased lower predicted ploidy in the WCPE when compared to the SCoPE method. Similar results were obtained for all the other strains evaluated
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Fig2: Methodologies to determinate the chromosomal copy number in T. cruzi strains. To estimate the chromosome ploidy of T. cruzi strains, two approaches were evaluated by mapping reads from the Y strain on the 41 CL Brener chromosomes. a The Whole Chromosome Ploidy Estimations (WCPE) predicts the ploidy based on the mean coverage of the whole-chromosome sequence. b The single-copy genes ploidy estimations (SCoPE) predict the chromosomal ploidy based only on the coverage of the 1563 Esmo-like/Non-Esmo single-copy genes present in each chromosome. The read depth was scaled to give a value of 2 for disomic chromosomes. c The 41 T. cruzi chromosome gene distribution is shown. Multicopy gene families are represented as blue boxes and the hypothetical and housekeeping genes as black boxes. The red arrows highlight the chromosomes with a higher content of multigene families or with the largest proportion of gap regions. Chromosomes with a higher density of multigene families or that present large gap regions tend to have a biased lower predicted ploidy in the WCPE when compared to the SCoPE method. Similar results were obtained for all the other strains evaluated

Mentions: Approximately 50 % of the T. cruzi genome corresponds to repetitive sequences, including multigene families that account for much of the differences in the gene content of the assembled genomes of CL Brener (TcVI) and Sylvio (TcI) [20, 21]. The chromosomal sequence representation of the CL Brener non-Esmeraldo-like and Esmeraldo-like haplotypes [33] also contains large internal gap regions that may reduce the accuracy of the predicted ploidy based on RDC. To reveal the best methodology to determine the T. cruzi chromosome ploidy based on RDC, two approaches were evaluated. In the Whole Chromosome Ploidy Estimations (WCPE) approach, the chromosomal ploidy prediction for each chromosome was estimated based on the ratio between the mean RDC of each chromosome position and the genome coverage (Fig. 2a). This approach accounts for the coverage of all positions in a given chromosome to estimate its copy number, including repetitive and gap regions. In the single-copy genes ploidy estimations (SCoPE) approach, estimations of the chromosomal ploidy for each chromosome were based on the ratio between the mean coverage of all single-copy genes in a given chromosome and the genome coverage (Fig. 2b). This approach infers the copy number for each chromosome based only on the RDC of the 1563 1:1 orthologs between CL Brener Esmeraldo-like and non-Esmeraldo-like haplotypes, which were assumed to be single-copy genes in the haploid CL Brener genome content (Additional file 1: Table S1). As shown in Fig. 2, chromosomes that are rich in multigene families, repetitive sequences and gaps, such as chromosomes 18, 28, 38 and 41 (Fig. 2c), tend to have a lower predicted ploidy as determined using WCPE methodology when compared to the SCoPE approach using the Y strain reads. Similar results were obtained by mapping reads from the other T. cruzi strains on the 41 CL Brener chromosomes (data not shown). As the SCoPE approach is less prone to bias toward chromosomal repetitive content, this methodology was chosen to estimate the chromosomal ploidy for each of the strains used in this study.Fig. 2


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)

Methodologies to determinate the chromosomal copy number in T. cruzi strains. To estimate the chromosome ploidy of T. cruzi strains, two approaches were evaluated by mapping reads from the Y strain on the 41 CL Brener chromosomes. a The Whole Chromosome Ploidy Estimations (WCPE) predicts the ploidy based on the mean coverage of the whole-chromosome sequence. b The single-copy genes ploidy estimations (SCoPE) predict the chromosomal ploidy based only on the coverage of the 1563 Esmo-like/Non-Esmo single-copy genes present in each chromosome. The read depth was scaled to give a value of 2 for disomic chromosomes. c The 41 T. cruzi chromosome gene distribution is shown. Multicopy gene families are represented as blue boxes and the hypothetical and housekeeping genes as black boxes. The red arrows highlight the chromosomes with a higher content of multigene families or with the largest proportion of gap regions. Chromosomes with a higher density of multigene families or that present large gap regions tend to have a biased lower predicted ploidy in the WCPE when compared to the SCoPE method. Similar results were obtained for all the other strains evaluated
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4491234&req=5

Fig2: Methodologies to determinate the chromosomal copy number in T. cruzi strains. To estimate the chromosome ploidy of T. cruzi strains, two approaches were evaluated by mapping reads from the Y strain on the 41 CL Brener chromosomes. a The Whole Chromosome Ploidy Estimations (WCPE) predicts the ploidy based on the mean coverage of the whole-chromosome sequence. b The single-copy genes ploidy estimations (SCoPE) predict the chromosomal ploidy based only on the coverage of the 1563 Esmo-like/Non-Esmo single-copy genes present in each chromosome. The read depth was scaled to give a value of 2 for disomic chromosomes. c The 41 T. cruzi chromosome gene distribution is shown. Multicopy gene families are represented as blue boxes and the hypothetical and housekeeping genes as black boxes. The red arrows highlight the chromosomes with a higher content of multigene families or with the largest proportion of gap regions. Chromosomes with a higher density of multigene families or that present large gap regions tend to have a biased lower predicted ploidy in the WCPE when compared to the SCoPE method. Similar results were obtained for all the other strains evaluated
Mentions: Approximately 50 % of the T. cruzi genome corresponds to repetitive sequences, including multigene families that account for much of the differences in the gene content of the assembled genomes of CL Brener (TcVI) and Sylvio (TcI) [20, 21]. The chromosomal sequence representation of the CL Brener non-Esmeraldo-like and Esmeraldo-like haplotypes [33] also contains large internal gap regions that may reduce the accuracy of the predicted ploidy based on RDC. To reveal the best methodology to determine the T. cruzi chromosome ploidy based on RDC, two approaches were evaluated. In the Whole Chromosome Ploidy Estimations (WCPE) approach, the chromosomal ploidy prediction for each chromosome was estimated based on the ratio between the mean RDC of each chromosome position and the genome coverage (Fig. 2a). This approach accounts for the coverage of all positions in a given chromosome to estimate its copy number, including repetitive and gap regions. In the single-copy genes ploidy estimations (SCoPE) approach, estimations of the chromosomal ploidy for each chromosome were based on the ratio between the mean coverage of all single-copy genes in a given chromosome and the genome coverage (Fig. 2b). This approach infers the copy number for each chromosome based only on the RDC of the 1563 1:1 orthologs between CL Brener Esmeraldo-like and non-Esmeraldo-like haplotypes, which were assumed to be single-copy genes in the haploid CL Brener genome content (Additional file 1: Table S1). As shown in Fig. 2, chromosomes that are rich in multigene families, repetitive sequences and gaps, such as chromosomes 18, 28, 38 and 41 (Fig. 2c), tend to have a lower predicted ploidy as determined using WCPE methodology when compared to the SCoPE approach using the Y strain reads. Similar results were obtained by mapping reads from the other T. cruzi strains on the 41 CL Brener chromosomes (data not shown). As the SCoPE approach is less prone to bias toward chromosomal repetitive content, this methodology was chosen to estimate the chromosomal ploidy for each of the strains used in this study.Fig. 2

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