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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Using the transcriptome to annotate the genome revisited: Application of massively parallel signature sequencing (MPSS)
Gene, Volume 366, No. 1, Year 2006
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Description
Transcriptome analysis can provide useful data for refining genome sequence annotation. Application of massively parallel signature sequencing (MPSS) revealed reproducible transcription, in multiple MPSS cycles, from 73% of computationally predicted genes in the Theileria parva schizont lifecycle stage. Signatures spanning consecutive exons confirmed 142 predicted introns. MPSS identified 83 putative genes, > 100 codons overlooked by annotation software, and 139 potentially incorrect gene models (with either truncated ORFs or overlooked exons) by interfacing signature locations with stop codon maps. Twenty representative models were confirmed as likely to be incorrect using reverse transcription PCR amplification from independent schizont cDNA preparations. More than 50% of the 60 putative single copy genes in T. parva that were absent from the genome of the closely related T. annulata had MPSS signatures. This study illustrates the utility of MPSS for improving annotation of small, gene-rich microbial eukaryotic genomes. © 2005 Elsevier B.V. All rights reserved.
Authors & Co-Authors
Shah, Trushar M.
Kenya, Nairobi
International Livestock Research Institute Nairobi
De Villiers, Etienne P.
Kenya, Nairobi
International Livestock Research Institute Nairobi
Nene, Vishvanath M.
United States, Rockville
J. Craig Venter Institute
Hass, Brian
United States, Rockville
J. Craig Venter Institute
Taracha, Evans L.N.
Kenya, Nairobi
International Livestock Research Institute Nairobi
Gardner, Malcolm J.
United States, Rockville
J. Craig Venter Institute
Sansom, Clare
United Kingdom, London
Birkbeck, University of London
Pellé, Roger
Kenya, Nairobi
International Livestock Research Institute Nairobi
Bishop, Richard Peter
Kenya, Nairobi
International Livestock Research Institute Nairobi
Statistics
Citations: 13
Authors: 9
Affiliations: 3
Identifiers
Doi:
10.1016/j.gene.2005.08.011
ISSN:
03781119
Research Areas
Genetics And Genomics