Comparative validation of the D. melanogaster modENCODE transcriptome annotation
Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an...
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| Format: | Article |
| Language: | en_US |
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Cold Spring Harbor Laboratory Press
2014
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| Online Access: | http://hdl.handle.net/1721.1/89401 |
| _version_ | 1826205675958566912 |
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| author | Kellis, Manolis |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Kellis, Manolis |
| author_sort | Kellis, Manolis |
| collection | MIT |
| description | Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community. |
| first_indexed | 2024-09-23T13:17:09Z |
| format | Article |
| id | mit-1721.1/89401 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:17:09Z |
| publishDate | 2014 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | mit-1721.1/894012022-10-01T14:14:35Z Comparative validation of the D. melanogaster modENCODE transcriptome annotation Kellis, Manolis Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kellis, Manolis Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community. National Institutes of Health (U.S.) (NIDDK (DK015600-18)) National Institutes of Health (U.S.) (Extramural program (1ROIGM082843)) National Institutes of Health (U.S.) (Extramural program (U01HB004271)) 2014-09-09T19:41:42Z 2014-09-09T19:41:42Z 2014-07 Article http://purl.org/eprint/type/JournalArticle 1088-9051 http://hdl.handle.net/1721.1/89401 Chen, Z.-X., D. Sturgill, J. Qu, H. Jiang, S. Park, N. Boley, A. M. Suzuki, et al. “Comparative Validation of the D. Melanogaster modENCODE Transcriptome Annotation.” Genome Research 24, no. 7 (July 1, 2014): 1209–1223. en_US http://dx.doi.org/10.1101/gr.159384.113 Genome Research Creative Commons Attribution-Noncommercial 4.0 http://creativecommons.org/licenses/by-nc/4.0/ application/pdf Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press |
| spellingShingle | Kellis, Manolis Comparative validation of the D. melanogaster modENCODE transcriptome annotation |
| title | Comparative validation of the D. melanogaster modENCODE transcriptome annotation |
| title_full | Comparative validation of the D. melanogaster modENCODE transcriptome annotation |
| title_fullStr | Comparative validation of the D. melanogaster modENCODE transcriptome annotation |
| title_full_unstemmed | Comparative validation of the D. melanogaster modENCODE transcriptome annotation |
| title_short | Comparative validation of the D. melanogaster modENCODE transcriptome annotation |
| title_sort | comparative validation of the d melanogaster modencode transcriptome annotation |
| url | http://hdl.handle.net/1721.1/89401 |
| work_keys_str_mv | AT kellismanolis comparativevalidationofthedmelanogastermodencodetranscriptomeannotation |