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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

PCR screening of a random sample of newly discovered genes. Screenings were performed pair-wise with the PCR products of the species containing the known gene of interest loaded in odd-numbered wells while the corresponding PCR screen of the other species whereby sequence is absent or the gene is not predicted are in the even-numbered wells. The Genbank accession numbers of these novel orthologs are indicated in parentheses in the following description. (1&2): PY00632 screen with Py and Pb gDNA (GU390534); (3&4): PY03414 screen with Py and Pb gDNA (GU390535); (5&6): PY04600 screen with Py and Pb gDNA (GU390540); (7&8): PY04485 screen with Py and Pb gDNA (GU390538); (9&10): PY02086 screen with Py and Pc gDNA (GU390539); (11&12): PY04869 with Py and Pc gDNA; (13&14): PY06972 screen with Py and Pc gDNA (GU390536); (15&16): PY05482 screen with Py and Pc gDNA (GU390537). (Legend: M = 100 bp DNA ladder)
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Figure 3: PCR screening of a random sample of newly discovered genes. Screenings were performed pair-wise with the PCR products of the species containing the known gene of interest loaded in odd-numbered wells while the corresponding PCR screen of the other species whereby sequence is absent or the gene is not predicted are in the even-numbered wells. The Genbank accession numbers of these novel orthologs are indicated in parentheses in the following description. (1&2): PY00632 screen with Py and Pb gDNA (GU390534); (3&4): PY03414 screen with Py and Pb gDNA (GU390535); (5&6): PY04600 screen with Py and Pb gDNA (GU390540); (7&8): PY04485 screen with Py and Pb gDNA (GU390538); (9&10): PY02086 screen with Py and Pc gDNA (GU390539); (11&12): PY04869 with Py and Pc gDNA; (13&14): PY06972 screen with Py and Pc gDNA (GU390536); (15&16): PY05482 screen with Py and Pc gDNA (GU390537). (Legend: M = 100 bp DNA ladder)

Mentions: A selection of genes that were detected via the microarray data were randomly selected for polymerase chain reaction (PCR) screening (Figure 3) and direct sequencing in order to establish the confidence of this group of newly discovered genes. PCR primer pairs were designed flanking the oligonucleotide sequence to the species where there is known sequence information and these were used to amplify a newly predicted gene in another species where it is not annotated/predicted or where the sequence is absent. All screens were performed on regions where sequence information for the newly discovered orthologous genes is not present (i.e. missing sequence) except for PY00632 and PY03414 where a corresponding P. berghei contig is present but the gene is not predicted. In summary, 7 of the 8 PCR reactions gave a product around the predicted size and the one sample that was PCR negative could be due to sequence polymorphisms at the primer sites. Sequence analysis of the PCR product confirmed that the PCR product did indeed represent the predicted gene (data not shown). Some PCR products also exhibit a change in the predicted size, for example different PCR product sizes of PY00632 and its P. berghei ortholog are expected based on the currently available sequence information. Differences in PCR product size are due to variations in sequence length in the region bounded by the primers. The differences in PCR product size in the PY06972 screen of P. yoelii and P. chabaudi genomes are also due to the same reason. The high congruence of PCR-positive screens showed the power of the array in detecting homologous sequences currently absent from the available genome sequences of the other species. Additional microarray investigations pertaining to the detection and validation of polymorphic genes and differential transcription profiles between related parasite clones have further validated the performance of the oligonucleotide probes (unpublished).


Defining species specific genome differences in malaria parasites.

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

PCR screening of a random sample of newly discovered genes. Screenings were performed pair-wise with the PCR products of the species containing the known gene of interest loaded in odd-numbered wells while the corresponding PCR screen of the other species whereby sequence is absent or the gene is not predicted are in the even-numbered wells. The Genbank accession numbers of these novel orthologs are indicated in parentheses in the following description. (1&2): PY00632 screen with Py and Pb gDNA (GU390534); (3&4): PY03414 screen with Py and Pb gDNA (GU390535); (5&6): PY04600 screen with Py and Pb gDNA (GU390540); (7&8): PY04485 screen with Py and Pb gDNA (GU390538); (9&10): PY02086 screen with Py and Pc gDNA (GU390539); (11&12): PY04869 with Py and Pc gDNA; (13&14): PY06972 screen with Py and Pc gDNA (GU390536); (15&16): PY05482 screen with Py and Pc gDNA (GU390537). (Legend: M = 100 bp DNA ladder)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: PCR screening of a random sample of newly discovered genes. Screenings were performed pair-wise with the PCR products of the species containing the known gene of interest loaded in odd-numbered wells while the corresponding PCR screen of the other species whereby sequence is absent or the gene is not predicted are in the even-numbered wells. The Genbank accession numbers of these novel orthologs are indicated in parentheses in the following description. (1&2): PY00632 screen with Py and Pb gDNA (GU390534); (3&4): PY03414 screen with Py and Pb gDNA (GU390535); (5&6): PY04600 screen with Py and Pb gDNA (GU390540); (7&8): PY04485 screen with Py and Pb gDNA (GU390538); (9&10): PY02086 screen with Py and Pc gDNA (GU390539); (11&12): PY04869 with Py and Pc gDNA; (13&14): PY06972 screen with Py and Pc gDNA (GU390536); (15&16): PY05482 screen with Py and Pc gDNA (GU390537). (Legend: M = 100 bp DNA ladder)
Mentions: A selection of genes that were detected via the microarray data were randomly selected for polymerase chain reaction (PCR) screening (Figure 3) and direct sequencing in order to establish the confidence of this group of newly discovered genes. PCR primer pairs were designed flanking the oligonucleotide sequence to the species where there is known sequence information and these were used to amplify a newly predicted gene in another species where it is not annotated/predicted or where the sequence is absent. All screens were performed on regions where sequence information for the newly discovered orthologous genes is not present (i.e. missing sequence) except for PY00632 and PY03414 where a corresponding P. berghei contig is present but the gene is not predicted. In summary, 7 of the 8 PCR reactions gave a product around the predicted size and the one sample that was PCR negative could be due to sequence polymorphisms at the primer sites. Sequence analysis of the PCR product confirmed that the PCR product did indeed represent the predicted gene (data not shown). Some PCR products also exhibit a change in the predicted size, for example different PCR product sizes of PY00632 and its P. berghei ortholog are expected based on the currently available sequence information. Differences in PCR product size are due to variations in sequence length in the region bounded by the primers. The differences in PCR product size in the PY06972 screen of P. yoelii and P. chabaudi genomes are also due to the same reason. The high congruence of PCR-positive screens showed the power of the array in detecting homologous sequences currently absent from the available genome sequences of the other species. Additional microarray investigations pertaining to the detection and validation of polymorphic genes and differential transcription profiles between related parasite clones have further validated the performance of the oligonucleotide probes (unpublished).

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