Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Chen, Z. -X.; Sturgill, D.; Qu, J.; Jiang, H.; Park, S.; Boley, N.; Suzuki, A. M.; Fletcher, A. R.; Plachetzki, D. C.; FitzGerald, P. C.; Artieri, C. G.; Atallah, J.; Barmina, O.; Brown, J. B.; Blankenburg, K. P.; Clough, E.; Dasgupta, A.; Gubbala, S.; Han, Y.; Jayaseelan, J. C.; Kalra, D.; Kim, Y. -A.; Kovar, C. L.; Lee, S. L.; Li, M.; Malley, J. D.; Malone, J. H.; Mathew, T.; Mattiuzzo, N. R.; Munidasa, M.; Muzny, D. M.; Ongeri, F.; Perales, L.; Przytycka, T. M.; Pu, L. -L.; Robinson, G.; Thornton, R. L.; Saada, N.; Scherer, S. E.; Smith, H. E.; Vinson, C.; Warner, C. B.; Worley, K. C.; Wu, Y. -Q.; Zou, X.; Cherbas, P.; Kellis, M.; Eisen, M. B.; Piano, F.; Kionte, K.; Fitch, D. H.; Sternberg, P. W.; Cutter, A. D.; Duff, M. O.; Hoskins, R. A.; Graveley, B. R.; Gibbs, R. A.; Bickel, P. J.; Kopp, A.; Carninci, P.; Celniker, S. E.; Oliver, B.; Richards, S.

doi:10.1101/gr.159384.113

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Journal Article · Tue Jul 01 00:00:00 EDT 2014 · Genome Research

DOI:https://doi.org/10.1101/gr.159384.113· OSTI ID:1625626

Chen, Z. -X. ^[1]; Sturgill, D. ^[2]; Qu, J. ^[3]; Jiang, H. ^[3]; Park, S. ^[4]; Boley, N. ^[5]; Suzuki, A. M. ^[6]; Fletcher, A. R. ^[7]; Plachetzki, D. C. ^[8]; FitzGerald, P. C. ^[9]; Artieri, C. G. ^[2]; Atallah, J. ^[8]; Barmina, O. ^[8]; Brown, J. B. ^[5]; Blankenburg, K. P. ^[3]; Clough, E. ^[2]; Dasgupta, A. ^[10]; Gubbala, S. ^[3]; Han, Y. ^[3]; Jayaseelan, J. C. ^[3] more »

National Institutes of Health (NIH), Bethesda, MD (United States). National Inst. of Diabetes and Digestive and Kidney Diseases; DOE/OSTI
National Institutes of Health (NIH), Bethesda, MD (United States). National Inst. of Diabetes and Digestive and Kidney Diseases
Baylor Univ., Houston, TX (United States). College of Medicine. Human Genome Sequencing Center
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division. Dept. of Genome Dynamics
Univ. of California, Berkeley, CA (United States). Dept. of Statistics
RIKEN Omics Science Center Yokohama City (Japan). RIKEN Center for Life Science Technologies. Division of Genomic Technologies. Technology Development Group
National Institutes of Health (NIH), Bethesda, MD (United States). Center for Information Technology. Division of Computational Bioscience
Univ. of California, Davis, CA (United States). Dept. of Evolution and Ecology
National Cancer Institute, Bethesda, MD (United States)
National Institutes of Health (NIH), Bethesda, MD (United States). National Inst. of Arthritis and Musculoskeletal and Skin Diseases. Clinical Trials and Outcomes Branch
National Library of Medicine (NLM), Bethesda, MD (United States)
Indiana Univ., Bloomington, IN (United States). Dept. of Biology
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Computer Science and Artificial Intelligence Lab.
Univ. of California, Berkeley, CA (United States). Molecular and Cell Biology
New York Univ. (NYU), NY (United States). Dept. of Biology
California Institute of Technology (CalTech), Pasadena, CA (United States). HHMI and Division of Biology
Univ. of Toronto, ON (Canada). Dept. of Ecology and Evolutionary Biology
Univ. of Connecticut, Farmington, CT (United States). Health Center. Inst. for Systems genomics. Dept. of Genetics and Developmental Biology
RIKEN Omics Science Center Yokohama City (Japan). RIKEN Center for Life Science Technologies. Division of Genomic Technologies. Technology Development Group

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625626

Journal Information:: Genome Research, Journal Name: Genome Research Journal Issue: 7 Vol. 24; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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