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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

Predicted ploidy of chromosome 11 of the T. cruzi Y strain. The blue line corresponds to the normalized RDC of each position of chromosome 11, estimated by the ratio between the RDC and the genome coverage. Below, the protein-coding genes are depicted as rectangles drawn in proportion to their length, and their coding strand is indicated by their position above (top strand) or below (bottom strand) the central line. Black and cyan rectangles represent the housekeeping/hypothetical and multicopy gene families, respectively. Gaps are represented by gene-less regions with no read coverage. The red line corresponds to the 248-kb position in this chromosome, which separates the regions of low RDC and high RDC (a). The non-normalized mean RDC estimated based on the SCoPE approach of the genes that were upstream and downstream of the 248-kb position was estimated (b)
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Fig6: Predicted ploidy of chromosome 11 of the T. cruzi Y strain. The blue line corresponds to the normalized RDC of each position of chromosome 11, estimated by the ratio between the RDC and the genome coverage. Below, the protein-coding genes are depicted as rectangles drawn in proportion to their length, and their coding strand is indicated by their position above (top strand) or below (bottom strand) the central line. Black and cyan rectangles represent the housekeeping/hypothetical and multicopy gene families, respectively. Gaps are represented by gene-less regions with no read coverage. The red line corresponds to the 248-kb position in this chromosome, which separates the regions of low RDC and high RDC (a). The non-normalized mean RDC estimated based on the SCoPE approach of the genes that were upstream and downstream of the 248-kb position was estimated (b)

Mentions: Chromosome 11 from the Y strain has some interesting features. As shown in Fig. 3, this chromosome displayed a smaller ploidy than disomic but a greater ploidy than monosomic. This led us to investigate whether this pattern occurs due to the loss of a chromosomal region instead of the loss of a chromosome copy. As showed in Fig. 6, there is a drastic change in the RDC starting at the 248-kb position in this chromosome that corresponds to a strand switch region. The first 248 kb of this chromosome has a smaller predicted ploidy when compared to the rest of the chromosome sequence (Fig. 6a). To further confirm this chromosomal region loss, the mean RDC of the single-copy genes located upstream and downstream of the 248-kb coordinate were estimated. The single-copy genes that were upstream of the 248-kb position had a non-normalized mean RDC of 20, while the single-copy genes downstream had an approximate mean RDC of 40 (Fig. 6b). This reduction of the RDC in the 5′ region when compared to the rest of the chromosome and the estimated genome coverage of 34× suggest a segmental loss of the 248 kb at the 5′ region in one copy of this chromosome in the Y strain. Alternatively, this pattern may be due to differences in the structure of chromosome 11 among the different cells of the parasite population because Y is not a cloned line.Fig. 6


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)

Predicted ploidy of chromosome 11 of the T. cruzi Y strain. The blue line corresponds to the normalized RDC of each position of chromosome 11, estimated by the ratio between the RDC and the genome coverage. Below, the protein-coding genes are depicted as rectangles drawn in proportion to their length, and their coding strand is indicated by their position above (top strand) or below (bottom strand) the central line. Black and cyan rectangles represent the housekeeping/hypothetical and multicopy gene families, respectively. Gaps are represented by gene-less regions with no read coverage. The red line corresponds to the 248-kb position in this chromosome, which separates the regions of low RDC and high RDC (a). The non-normalized mean RDC estimated based on the SCoPE approach of the genes that were upstream and downstream of the 248-kb position was estimated (b)
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4491234&req=5

Fig6: Predicted ploidy of chromosome 11 of the T. cruzi Y strain. The blue line corresponds to the normalized RDC of each position of chromosome 11, estimated by the ratio between the RDC and the genome coverage. Below, the protein-coding genes are depicted as rectangles drawn in proportion to their length, and their coding strand is indicated by their position above (top strand) or below (bottom strand) the central line. Black and cyan rectangles represent the housekeeping/hypothetical and multicopy gene families, respectively. Gaps are represented by gene-less regions with no read coverage. The red line corresponds to the 248-kb position in this chromosome, which separates the regions of low RDC and high RDC (a). The non-normalized mean RDC estimated based on the SCoPE approach of the genes that were upstream and downstream of the 248-kb position was estimated (b)
Mentions: Chromosome 11 from the Y strain has some interesting features. As shown in Fig. 3, this chromosome displayed a smaller ploidy than disomic but a greater ploidy than monosomic. This led us to investigate whether this pattern occurs due to the loss of a chromosomal region instead of the loss of a chromosome copy. As showed in Fig. 6, there is a drastic change in the RDC starting at the 248-kb position in this chromosome that corresponds to a strand switch region. The first 248 kb of this chromosome has a smaller predicted ploidy when compared to the rest of the chromosome sequence (Fig. 6a). To further confirm this chromosomal region loss, the mean RDC of the single-copy genes located upstream and downstream of the 248-kb coordinate were estimated. The single-copy genes that were upstream of the 248-kb position had a non-normalized mean RDC of 20, while the single-copy genes downstream had an approximate mean RDC of 40 (Fig. 6b). This reduction of the RDC in the 5′ region when compared to the rest of the chromosome and the estimated genome coverage of 34× suggest a segmental loss of the 248 kb at the 5′ region in one copy of this chromosome in the Y strain. Alternatively, this pattern may be due to differences in the structure of chromosome 11 among the different cells of the parasite population because Y is not a cloned line.Fig. 6

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