Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS)
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 st...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Elsevier
2006
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/1404 |
| _version_ | 1855523757159874560 |
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| author | Shah, Tushaar Villiers, Etienne P. de Nene, Vishvanath M. Hass, B. Taracha, E.A. Gardner, J.M. Sansom, C. Pelle, Roger Bishop, Richard P. |
| author_browse | Bishop, Richard P. Gardner, J.M. Hass, B. Nene, Vishvanath M. Pelle, Roger Sansom, C. Shah, Tushaar Taracha, E.A. Villiers, Etienne P. de |
| author_facet | Shah, Tushaar Villiers, Etienne P. de Nene, Vishvanath M. Hass, B. Taracha, E.A. Gardner, J.M. Sansom, C. Pelle, Roger Bishop, Richard P. |
| author_sort | Shah, Tushaar |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| 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. |
| format | Journal Article |
| id | CGSpace1404 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2006 |
| publishDateRange | 2006 |
| publishDateSort | 2006 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace14042024-01-17T12:58:34Z Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS) Shah, Tushaar Villiers, Etienne P. de Nene, Vishvanath M. Hass, B. Taracha, E.A. Gardner, J.M. Sansom, C. Pelle, Roger Bishop, Richard P. animal diseases 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. 2006-01 2010-05-07T11:03:00Z 2010-05-07T11:03:00Z Journal Article https://hdl.handle.net/10568/1404 en Limited Access Elsevier Shah, T.; Villiers, E. de; Nene, V.; Hass, B.; Taracha, E.; Gardner, J.M.; Sansom, C.; Pelle, R.; Bishop, R. 2006. Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS). Gene 366(1):104-108. |
| spellingShingle | animal diseases Shah, Tushaar Villiers, Etienne P. de Nene, Vishvanath M. Hass, B. Taracha, E.A. Gardner, J.M. Sansom, C. Pelle, Roger Bishop, Richard P. Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS) |
| title | Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS) |
| title_full | Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS) |
| title_fullStr | Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS) |
| title_full_unstemmed | Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS) |
| title_short | Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS) |
| title_sort | using the transcriptome to annotate the genome revisited application of massively parallel signature sequencing mpss |
| topic | animal diseases |
| url | https://hdl.handle.net/10568/1404 |
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