A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

Amit Bahl, Paul H Davis, Michael Behnke, Florence Dzierszinski, Manjunatha Jagalur, Feng Chen, Dhanasekaran Shanmugam, Michael W. White, David Kulp, David S. Roos

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

Background: Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators.Results: Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals) and Plasmodium falciparum (a related parasite responsible for severe human malaria), we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP)-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis) and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at pilot scale to inform future array designs.Conclusions: In addition to providing an initial global view of the T. gondii transcriptome across major lineages and permitting detailed resolution of recombination points in a historical sexual cross, the multifunctional nature of this array also allowed opportunities to exploit probes for purposes beyond their intended use, enhancing analyses. This array is in widespread use by the T. gondii research community, and several aspects of the design strategy are likely to be useful for other pathogens.

Original languageEnglish (US)
Article number603
JournalBMC genomics
Volume11
Issue number1
DOIs
StatePublished - Oct 25 2010

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Toxoplasma
Oligonucleotide Array Sequence Analysis
Single Nucleotide Polymorphism
Parasites
Genome
Plasmodium falciparum
Transcriptome
Genetic Recombination
Social Planning
North America
Research
Genes
Malaria
Research Personnel
Gene Expression
Costs and Cost Analysis
Population

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Bahl, A., Davis, P. H., Behnke, M., Dzierszinski, F., Jagalur, M., Chen, F., ... Roos, D. S. (2010). A novel multifunctional oligonucleotide microarray for Toxoplasma gondii. BMC genomics, 11(1), [603]. https://doi.org/10.1186/1471-2164-11-603

A novel multifunctional oligonucleotide microarray for Toxoplasma gondii. / Bahl, Amit; Davis, Paul H; Behnke, Michael; Dzierszinski, Florence; Jagalur, Manjunatha; Chen, Feng; Shanmugam, Dhanasekaran; White, Michael W.; Kulp, David; Roos, David S.

In: BMC genomics, Vol. 11, No. 1, 603, 25.10.2010.

Research output: Contribution to journalArticle

Bahl, A, Davis, PH, Behnke, M, Dzierszinski, F, Jagalur, M, Chen, F, Shanmugam, D, White, MW, Kulp, D & Roos, DS 2010, 'A novel multifunctional oligonucleotide microarray for Toxoplasma gondii', BMC genomics, vol. 11, no. 1, 603. https://doi.org/10.1186/1471-2164-11-603
Bahl, Amit ; Davis, Paul H ; Behnke, Michael ; Dzierszinski, Florence ; Jagalur, Manjunatha ; Chen, Feng ; Shanmugam, Dhanasekaran ; White, Michael W. ; Kulp, David ; Roos, David S. / A novel multifunctional oligonucleotide microarray for Toxoplasma gondii. In: BMC genomics. 2010 ; Vol. 11, No. 1.
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AU - Shanmugam, Dhanasekaran

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