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Nucleic Acids Research 2005 33(17):5503-5511; doi:10.1093/nar/gki818
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Published online 25 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage

Richard Bishop*, Trushar Shah, Roger Pelle, David Hoyle1, Terry Pearson2, Lee Haines2, Andrew Brass3, Helen Hulme3, Simon P. Graham, Evans L. N. Taracha, Simon Kanga4, Charles Lu4, Brian Hass4, Jennifer Wortman4, Owen White4, Malcolm J. Gardner4, Vishvanath Nene4 and Etienne P. de Villiers

The International Livestock Research Institute (ILRI) PO Box 30709, Nairobi, Kenya 1Department of Computer Science, University of Exeter North Park Road, Exeter EX4 4QF, UK 2Department of Biochemistry and Microbiology Petch Building, Ring Road University of Victoria Victoria BC V8W 3P6, Canada 3Department of Computer Science, University of Manchester Oxford Road, Manchester M13 9PL, UK 4The Institute for Genomic Research (TIGR) 9712 Medical Center Drive, Rockville, MD 20850, USA

*To whom correspondence should be addressed. Tel: +254 20 4223002; Email: r.bishop{at}cgiar.org

Received June 2, 2005. Revised July 19, 2005. Accepted August 19, 2005.

Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1 095 000, 20 bp sequences representing 4371 different signatures were generated from T.parva schizonts. Reproducible signatures were identified within 73% of potentially detectable predicted genes and 83% had signatures in at least one MPSS cycle. A predicted leader peptide was detected on 405 expressed genes. The quantitative range of signatures was 4–52 256 transcripts per million (t.p.m.). Rare transcripts (<50 t.p.m.) were detected from 36% of genes. Sequence signatures approximated a lognormal distribution, as in microarray. Transcripts were widely distributed throughout the genome, although only 47% of 138 telomere-associated open reading frames exhibited signatures. Antisense signatures comprised 13.8% of the total, comparable with Plasmodium. Eighty five predicted genes with antisense signatures lacked a sense signature. Antisense transcripts were independently amplified from schizont cDNA and verified by sequencing. The MPSS transcripts per million for seven genes encoding schizont antigens recognized by bovine CD8 T cells varied 1000-fold. There was concordance between transcription and protein expression for heat shock proteins that were very highly expressed according to MPSS and proteomics. The data suggests a low level of baseline transcription from the majority of protein-coding genes.


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