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Shotgun sequencing analysis of Trypanosoma cruzi I Sylvio X10/1 and comparison with T. cruzi VI CL Brener.

Franzén O, Ochaya S, Sherwood E, Lewis MD, Llewellyn MS, Miles MA, Andersson B - PLoS Negl Trop Dis (2011)

Bottom Line: We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1.Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes.This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite.

View Article: PubMed Central - PubMed

Affiliation: Science for Life Laboratory, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden. oscar.franzen@scilifelab.se

ABSTRACT
Trypanosoma cruzi is the causative agent of Chagas disease, which affects more than 9 million people in Latin America. We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features. We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1. Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes. There were 336 genes indicated as under positive selection, 145 unique to T. cruzi in comparison to T. brucei and Leishmania. This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite.

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Related in: MedlinePlus

Sequence identity of Sylvio X10/1 contigs compared to non-Esmeraldo and Esmeraldo.Shows the percentage identity (horizontal axis) of the best Sylvio X10/1 versus CL Brener BLAST hit and the combined alignment length on the vertical axis. The black line (triangles) represent Sylvio X10/1 compared to non-Esmeraldo and blue lines (circles) represent Sylvio X10/1 compared to Esmeraldo. Both comparisons have a similar overall distribution of identities but Sylvio X10/1 compared to non-Esmeraldo is shifted to a slightly higher sequence identity. Sylvio X10/1 compared to non-Esmeraldo has a peak at 97% sequence identity and Sylvio X10/1 compared to Esmeraldo has a peak at 96% sequence identity.
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pntd-0000984-g001: Sequence identity of Sylvio X10/1 contigs compared to non-Esmeraldo and Esmeraldo.Shows the percentage identity (horizontal axis) of the best Sylvio X10/1 versus CL Brener BLAST hit and the combined alignment length on the vertical axis. The black line (triangles) represent Sylvio X10/1 compared to non-Esmeraldo and blue lines (circles) represent Sylvio X10/1 compared to Esmeraldo. Both comparisons have a similar overall distribution of identities but Sylvio X10/1 compared to non-Esmeraldo is shifted to a slightly higher sequence identity. Sylvio X10/1 compared to non-Esmeraldo has a peak at 97% sequence identity and Sylvio X10/1 compared to Esmeraldo has a peak at 96% sequence identity.

Mentions: In the coding regions the mean nucleotide identity was higher between Sylvio X10/1 and non-Esmeraldo i.e. TcIII (98.2%) than between Sylvio X10/1 and Esmeraldo i.e. TcII (97.5%) (Table 2, Figure 1 and 2). The mean nucleotide identity between the two CL Brener haplotypes Esmeraldo and non-Esmeraldo was 97.8%. This is independent genome-wide evidence of the generally closer phylogenetic relationship between TcI (Sylvio X10/1) and TcIII (non-Esmeraldo) than with TcII (Esmeraldo). The divergence between these three T. cruzi lineages is therefore greater than between T. brucei subspecies T. brucei brucei and T. brucei gambiense (99.2%) [54] but less than between two representatives of different Leishmania species complexes, L. major and L. infantum (94%) [55].


Shotgun sequencing analysis of Trypanosoma cruzi I Sylvio X10/1 and comparison with T. cruzi VI CL Brener.

Franzén O, Ochaya S, Sherwood E, Lewis MD, Llewellyn MS, Miles MA, Andersson B - PLoS Negl Trop Dis (2011)

Sequence identity of Sylvio X10/1 contigs compared to non-Esmeraldo and Esmeraldo.Shows the percentage identity (horizontal axis) of the best Sylvio X10/1 versus CL Brener BLAST hit and the combined alignment length on the vertical axis. The black line (triangles) represent Sylvio X10/1 compared to non-Esmeraldo and blue lines (circles) represent Sylvio X10/1 compared to Esmeraldo. Both comparisons have a similar overall distribution of identities but Sylvio X10/1 compared to non-Esmeraldo is shifted to a slightly higher sequence identity. Sylvio X10/1 compared to non-Esmeraldo has a peak at 97% sequence identity and Sylvio X10/1 compared to Esmeraldo has a peak at 96% sequence identity.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3050914&req=5

pntd-0000984-g001: Sequence identity of Sylvio X10/1 contigs compared to non-Esmeraldo and Esmeraldo.Shows the percentage identity (horizontal axis) of the best Sylvio X10/1 versus CL Brener BLAST hit and the combined alignment length on the vertical axis. The black line (triangles) represent Sylvio X10/1 compared to non-Esmeraldo and blue lines (circles) represent Sylvio X10/1 compared to Esmeraldo. Both comparisons have a similar overall distribution of identities but Sylvio X10/1 compared to non-Esmeraldo is shifted to a slightly higher sequence identity. Sylvio X10/1 compared to non-Esmeraldo has a peak at 97% sequence identity and Sylvio X10/1 compared to Esmeraldo has a peak at 96% sequence identity.
Mentions: In the coding regions the mean nucleotide identity was higher between Sylvio X10/1 and non-Esmeraldo i.e. TcIII (98.2%) than between Sylvio X10/1 and Esmeraldo i.e. TcII (97.5%) (Table 2, Figure 1 and 2). The mean nucleotide identity between the two CL Brener haplotypes Esmeraldo and non-Esmeraldo was 97.8%. This is independent genome-wide evidence of the generally closer phylogenetic relationship between TcI (Sylvio X10/1) and TcIII (non-Esmeraldo) than with TcII (Esmeraldo). The divergence between these three T. cruzi lineages is therefore greater than between T. brucei subspecies T. brucei brucei and T. brucei gambiense (99.2%) [54] but less than between two representatives of different Leishmania species complexes, L. major and L. infantum (94%) [55].

Bottom Line: We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1.Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes.This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite.

View Article: PubMed Central - PubMed

Affiliation: Science for Life Laboratory, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden. oscar.franzen@scilifelab.se

ABSTRACT
Trypanosoma cruzi is the causative agent of Chagas disease, which affects more than 9 million people in Latin America. We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features. We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1. Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes. There were 336 genes indicated as under positive selection, 145 unique to T. cruzi in comparison to T. brucei and Leishmania. This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite.

Show MeSH
Related in: MedlinePlus