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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 the six T. cruzi strains. The predicted ploidy of each chromosome from the T. cruzi strains Arequipa (a), Colombiana (b) and Sylvio (c) from the TcI DTU; Y (d) and Esmeraldo (e) from the TcII DTU; and 231 (f) from the TcIII DTU, using as a reference the 41 CL Brener chromosome sequences, was estimated with the SCoPE approach. Each black bar corresponds to the ratio between the single-copy gene mean RDC in the chromosome and the single-copy gene mean RDC of the whole genome, representing its predicted chromosome copy number. The overall ploidy of each strain was estimated by the proportion of the alleles in heterozygous SNP positions, where a tendency of 0.4-0.5 represents a diploid chromosome and a proportion of 0.3 and/or 0.7 corresponds to a triploid chromosome (red line)
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Fig3: Predicted ploidy of the six T. cruzi strains. The predicted ploidy of each chromosome from the T. cruzi strains Arequipa (a), Colombiana (b) and Sylvio (c) from the TcI DTU; Y (d) and Esmeraldo (e) from the TcII DTU; and 231 (f) from the TcIII DTU, using as a reference the 41 CL Brener chromosome sequences, was estimated with the SCoPE approach. Each black bar corresponds to the ratio between the single-copy gene mean RDC in the chromosome and the single-copy gene mean RDC of the whole genome, representing its predicted chromosome copy number. The overall ploidy of each strain was estimated by the proportion of the alleles in heterozygous SNP positions, where a tendency of 0.4-0.5 represents a diploid chromosome and a proportion of 0.3 and/or 0.7 corresponds to a triploid chromosome (red line)

Mentions: The SCoPE approach was used to estimate the chromosome ploidy of the T. cruzi Arequipa, Colombiana, Sylvio, Esmeraldo, Y and 231 strains. Initially, based on the mean RDC of 1563 CL Brener single-copy genes, the genome coverage was estimated for each strain: 47× for Arequipa, 28× for Colombiana, 9× for Sylvio, 52× for Esmeraldo, 34× for Y and 76× for 231. The normalized read depth coverage and the percentage of length coverage of each single-copy gene in each chromosome are provided in Additional file 2: Table S2. To determine the overall chromosome ploidy of each T. cruzi strain, the allele frequencies were estimated for each predicted heterozygous site. To this end, the proportion of each allele in the heterozygous sites divided by the total read depth for the site was determined and rounded to the first decimal place. Based on this estimation, a diploid chromosome usually has a tendency of 0.4-0.5 and a triploid of 0.3 and 0.6. A tetraploid chromosome has a more complex pattern, which can be 0.4-0.5, 0.2 and 0.8 or a combination of both. As the majority of the heterozygous SNPs show a proportion of 0.4-0.5, the overall ploidy of all the strains was assumed to be diploid (Fig. 3).Fig. 3


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 the six T. cruzi strains. The predicted ploidy of each chromosome from the T. cruzi strains Arequipa (a), Colombiana (b) and Sylvio (c) from the TcI DTU; Y (d) and Esmeraldo (e) from the TcII DTU; and 231 (f) from the TcIII DTU, using as a reference the 41 CL Brener chromosome sequences, was estimated with the SCoPE approach. Each black bar corresponds to the ratio between the single-copy gene mean RDC in the chromosome and the single-copy gene mean RDC of the whole genome, representing its predicted chromosome copy number. The overall ploidy of each strain was estimated by the proportion of the alleles in heterozygous SNP positions, where a tendency of 0.4-0.5 represents a diploid chromosome and a proportion of 0.3 and/or 0.7 corresponds to a triploid chromosome (red line)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Predicted ploidy of the six T. cruzi strains. The predicted ploidy of each chromosome from the T. cruzi strains Arequipa (a), Colombiana (b) and Sylvio (c) from the TcI DTU; Y (d) and Esmeraldo (e) from the TcII DTU; and 231 (f) from the TcIII DTU, using as a reference the 41 CL Brener chromosome sequences, was estimated with the SCoPE approach. Each black bar corresponds to the ratio between the single-copy gene mean RDC in the chromosome and the single-copy gene mean RDC of the whole genome, representing its predicted chromosome copy number. The overall ploidy of each strain was estimated by the proportion of the alleles in heterozygous SNP positions, where a tendency of 0.4-0.5 represents a diploid chromosome and a proportion of 0.3 and/or 0.7 corresponds to a triploid chromosome (red line)
Mentions: The SCoPE approach was used to estimate the chromosome ploidy of the T. cruzi Arequipa, Colombiana, Sylvio, Esmeraldo, Y and 231 strains. Initially, based on the mean RDC of 1563 CL Brener single-copy genes, the genome coverage was estimated for each strain: 47× for Arequipa, 28× for Colombiana, 9× for Sylvio, 52× for Esmeraldo, 34× for Y and 76× for 231. The normalized read depth coverage and the percentage of length coverage of each single-copy gene in each chromosome are provided in Additional file 2: Table S2. To determine the overall chromosome ploidy of each T. cruzi strain, the allele frequencies were estimated for each predicted heterozygous site. To this end, the proportion of each allele in the heterozygous sites divided by the total read depth for the site was determined and rounded to the first decimal place. Based on this estimation, a diploid chromosome usually has a tendency of 0.4-0.5 and a triploid of 0.3 and 0.6. A tetraploid chromosome has a more complex pattern, which can be 0.4-0.5, 0.2 and 0.8 or a combination of both. As the majority of the heterozygous SNPs show a proportion of 0.4-0.5, the overall ploidy of all the strains was assumed to be diploid (Fig. 3).Fig. 3

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