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Defining species specific genome differences in malaria parasites.

Liew KJ, Hu G, Bozdech Z, Peter PR - BMC Genomics (2010)

Bottom Line: This has allowed the identification of numerous conserved genes across the different species and has significantly enhanced our understanding of parasite biology.Through analyses via comparative genome hybridizations using a newly designed pan-rodent array as well as in depth bioinformatics analysis, we were able to improve on the coverage of the draft rodent parasite genomes by detecting orthologous genes between these related rodent parasite species.More than 1,000 orthologs for P. yoelii were now newly associated with a P. falciparum gene.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.

ABSTRACT

Background: In recent years a number of genome sequences for different plasmodium species have become available. This has allowed the identification of numerous conserved genes across the different species and has significantly enhanced our understanding of parasite biology. In contrast little is known about species specific differences between the different genomes partly due to the lower sequence coverage and therefore relatively poor annotation of some of the draft genomes particularly the rodent malarias parasite species.

Results: To improve the current annotation and gene identification status of the draft genomes of P. berghei, P. chabaudi and P. yoelii, we performed genome-wide comparisons between these three species. Through analyses via comparative genome hybridizations using a newly designed pan-rodent array as well as in depth bioinformatics analysis, we were able to improve on the coverage of the draft rodent parasite genomes by detecting orthologous genes between these related rodent parasite species. More than 1,000 orthologs for P. yoelii were now newly associated with a P. falciparum gene. In addition to extending the current core gene set for all plasmodium species this analysis also for the first time identifies a relatively small number of genes that are unique to the primate malaria parasites while a larger gene set is uniquely conserved amongst the rodent malaria parasites.

Conclusions: These findings allow a more thorough investigation of the genes that are important for host specificity in malaria.

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Related in: MedlinePlus

Graphical plot showing the re-distribution of the rodent malaria parasite genes after removing the PIR genes. Most of the reduction occurs in the group Py-Pb-Pc in which all the three rodent malaria parasite species share a common gene. (Legend: Py = genes specific to P. yoelii; Py-Pb = genes common to both P. yoelii and P. berghei; Py-Pc = genes common to both P. yoelii and P. chabaudi; Py-Pb-Pc = genes common to all three species)
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Figure 6: Graphical plot showing the re-distribution of the rodent malaria parasite genes after removing the PIR genes. Most of the reduction occurs in the group Py-Pb-Pc in which all the three rodent malaria parasite species share a common gene. (Legend: Py = genes specific to P. yoelii; Py-Pb = genes common to both P. yoelii and P. berghei; Py-Pc = genes common to both P. yoelii and P. chabaudi; Py-Pb-Pc = genes common to all three species)

Mentions: Using a similar approach as in the previous section, we attempt to construct a rodent parasite specific associative table since we can also take advantage of the dataset from the genomic hybridizations. For this purpose, instead of using genes from P. falciparum as an index, the oligonucleotides were chosen as the index and then replaced with the best-hit P. yoelii gene. Next, P. falciparum - P. yoelii, P. berghei - P. yoelii and P. chabaudi - P. yoelii orthologs were appended to the list. This strategy creates a database of genes orthologous to P. yoelii and the reason for choosing this species as the index is due to it being more completely annotated than the other two rodent parasite species. This list was refined by removing matching orthologs from P. falciparum that were already present in the common 'core' set; thereby creating a filtered list that contains only genes that are specific to the rodent malaria parasites. Microarray data and bioinformatics (tBLASTn) to query the P. yoelii amino acid sequences were also employed. In order to reduce the complexity of the dataset, the PIRs, which consist of the largest multigene family and dominate the rodent specific genes, will not be discussed due to their variability of expression and gene expansion amongst the rodent malaria parasites due to its main role in antigenic variation [23,24] as well as its copy number being the most abundant in P. yoelii. Consequently, the huge reduction in genes common in all three rodent malaria parasite species is due to the removal of the PIR genes that could also confound relationships based on bioinformatics simply due to multiple matching of common conserved domains (Additional file 4: Supplemental Table S4; Figure 6).


Defining species specific genome differences in malaria parasites.

Liew KJ, Hu G, Bozdech Z, Peter PR - BMC Genomics (2010)

Graphical plot showing the re-distribution of the rodent malaria parasite genes after removing the PIR genes. Most of the reduction occurs in the group Py-Pb-Pc in which all the three rodent malaria parasite species share a common gene. (Legend: Py = genes specific to P. yoelii; Py-Pb = genes common to both P. yoelii and P. berghei; Py-Pc = genes common to both P. yoelii and P. chabaudi; Py-Pb-Pc = genes common to all three species)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837034&req=5

Figure 6: Graphical plot showing the re-distribution of the rodent malaria parasite genes after removing the PIR genes. Most of the reduction occurs in the group Py-Pb-Pc in which all the three rodent malaria parasite species share a common gene. (Legend: Py = genes specific to P. yoelii; Py-Pb = genes common to both P. yoelii and P. berghei; Py-Pc = genes common to both P. yoelii and P. chabaudi; Py-Pb-Pc = genes common to all three species)
Mentions: Using a similar approach as in the previous section, we attempt to construct a rodent parasite specific associative table since we can also take advantage of the dataset from the genomic hybridizations. For this purpose, instead of using genes from P. falciparum as an index, the oligonucleotides were chosen as the index and then replaced with the best-hit P. yoelii gene. Next, P. falciparum - P. yoelii, P. berghei - P. yoelii and P. chabaudi - P. yoelii orthologs were appended to the list. This strategy creates a database of genes orthologous to P. yoelii and the reason for choosing this species as the index is due to it being more completely annotated than the other two rodent parasite species. This list was refined by removing matching orthologs from P. falciparum that were already present in the common 'core' set; thereby creating a filtered list that contains only genes that are specific to the rodent malaria parasites. Microarray data and bioinformatics (tBLASTn) to query the P. yoelii amino acid sequences were also employed. In order to reduce the complexity of the dataset, the PIRs, which consist of the largest multigene family and dominate the rodent specific genes, will not be discussed due to their variability of expression and gene expansion amongst the rodent malaria parasites due to its main role in antigenic variation [23,24] as well as its copy number being the most abundant in P. yoelii. Consequently, the huge reduction in genes common in all three rodent malaria parasite species is due to the removal of the PIR genes that could also confound relationships based on bioinformatics simply due to multiple matching of common conserved domains (Additional file 4: Supplemental Table S4; Figure 6).

Bottom Line: This has allowed the identification of numerous conserved genes across the different species and has significantly enhanced our understanding of parasite biology.Through analyses via comparative genome hybridizations using a newly designed pan-rodent array as well as in depth bioinformatics analysis, we were able to improve on the coverage of the draft rodent parasite genomes by detecting orthologous genes between these related rodent parasite species.More than 1,000 orthologs for P. yoelii were now newly associated with a P. falciparum gene.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.

ABSTRACT

Background: In recent years a number of genome sequences for different plasmodium species have become available. This has allowed the identification of numerous conserved genes across the different species and has significantly enhanced our understanding of parasite biology. In contrast little is known about species specific differences between the different genomes partly due to the lower sequence coverage and therefore relatively poor annotation of some of the draft genomes particularly the rodent malarias parasite species.

Results: To improve the current annotation and gene identification status of the draft genomes of P. berghei, P. chabaudi and P. yoelii, we performed genome-wide comparisons between these three species. Through analyses via comparative genome hybridizations using a newly designed pan-rodent array as well as in depth bioinformatics analysis, we were able to improve on the coverage of the draft rodent parasite genomes by detecting orthologous genes between these related rodent parasite species. More than 1,000 orthologs for P. yoelii were now newly associated with a P. falciparum gene. In addition to extending the current core gene set for all plasmodium species this analysis also for the first time identifies a relatively small number of genes that are unique to the primate malaria parasites while a larger gene set is uniquely conserved amongst the rodent malaria parasites.

Conclusions: These findings allow a more thorough investigation of the genes that are important for host specificity in malaria.

Show MeSH
Related in: MedlinePlus