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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

Ploidy and gene ontology analysis of chromosome 31. From the 41 CL Brener chromosomes, chromosome 31 was the only one that was supernumerary in all the studied strains based on the SCoPE analysis (a). The ploidy of chromosome 31 from each strain, estimated by the ratio of the alleles in the heterozygous SNP positions, classifies Arequipa, Colombiana, Sylvio, Esmeraldo and Y as tetraploid and 231 as triploid (b). Gene ontology analysis shows that this chromosome is enriched in genes involved in the glycosylation and glycoprotein biosynthetic processes (c)
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Fig7: Ploidy and gene ontology analysis of chromosome 31. From the 41 CL Brener chromosomes, chromosome 31 was the only one that was supernumerary in all the studied strains based on the SCoPE analysis (a). The ploidy of chromosome 31 from each strain, estimated by the ratio of the alleles in the heterozygous SNP positions, classifies Arequipa, Colombiana, Sylvio, Esmeraldo and Y as tetraploid and 231 as triploid (b). Gene ontology analysis shows that this chromosome is enriched in genes involved in the glycosylation and glycoprotein biosynthetic processes (c)

Mentions: From all the 41 CL Brener chromosomes, chromosome 31 was the only one that was supernumerary in all the strains analyzed, in both SCoPE (Fig. 7a) and heterozygous SNP analyses (Fig. 7b). To identify gene functions that were overrepresented in this chromosome when compared to the whole genome, a gene ontology analysis of both Esmeraldo-like and non-Esmeraldo-like CL Brener chromosome 31 was performed (Fig. 7c, Additional file 5: Table S3). This analysis shows that this chromosome is enriched in genes involved in glycosylation and glycoprotein biosynthetic processes in both CL Brener haplotypes.Fig. 7


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)

Ploidy and gene ontology analysis of chromosome 31. From the 41 CL Brener chromosomes, chromosome 31 was the only one that was supernumerary in all the studied strains based on the SCoPE analysis (a). The ploidy of chromosome 31 from each strain, estimated by the ratio of the alleles in the heterozygous SNP positions, classifies Arequipa, Colombiana, Sylvio, Esmeraldo and Y as tetraploid and 231 as triploid (b). Gene ontology analysis shows that this chromosome is enriched in genes involved in the glycosylation and glycoprotein biosynthetic processes (c)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Ploidy and gene ontology analysis of chromosome 31. From the 41 CL Brener chromosomes, chromosome 31 was the only one that was supernumerary in all the studied strains based on the SCoPE analysis (a). The ploidy of chromosome 31 from each strain, estimated by the ratio of the alleles in the heterozygous SNP positions, classifies Arequipa, Colombiana, Sylvio, Esmeraldo and Y as tetraploid and 231 as triploid (b). Gene ontology analysis shows that this chromosome is enriched in genes involved in the glycosylation and glycoprotein biosynthetic processes (c)
Mentions: From all the 41 CL Brener chromosomes, chromosome 31 was the only one that was supernumerary in all the strains analyzed, in both SCoPE (Fig. 7a) and heterozygous SNP analyses (Fig. 7b). To identify gene functions that were overrepresented in this chromosome when compared to the whole genome, a gene ontology analysis of both Esmeraldo-like and non-Esmeraldo-like CL Brener chromosome 31 was performed (Fig. 7c, Additional file 5: Table S3). This analysis shows that this chromosome is enriched in genes involved in glycosylation and glycoprotein biosynthetic processes in both CL Brener haplotypes.Fig. 7

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