Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- Zhen-Xia Chen1,18,
- David Sturgill1,18,
- Jiaxin Qu2,
- Huaiyang Jiang2,
- Soo Park3,
- Nathan Boley4,
- Ana Maria Suzuki5,
- Anthony R. Fletcher6,
- David C. Plachetzki7,
- Peter C. FitzGerald8,
- Carlo G. Artieri1,
- Joel Atallah7,
- Olga Barmina7,
- James B. Brown4,
- Kerstin P. Blankenburg2,
- Emily Clough1,
- Abhijit Dasgupta9,
- Sai Gubbala2,
- Yi Han2,
- Joy C. Jayaseelan2,
- Divya Kalra2,
- Yoo-Ah Kim10,
- Christie L. Kovar2,
- Sandra L. Lee2,
- Mingmei Li2,
- James D. Malley6,
- John H. Malone1,
- Tittu Mathew2,
- Nicolas R. Mattiuzzo1,
- Mala Munidasa2,
- Donna M. Muzny2,
- Fiona Ongeri2,
- Lora Perales2,
- Teresa M. Przytycka10,
- Ling-Ling Pu2,
- Garrett Robinson4,
- Rebecca L. Thornton2,
- Nehad Saada2,
- Steven E. Scherer2,
- Harold E. Smith1,
- Charles Vinson8,
- Crystal B. Warner2,
- Kim C. Worley2,
- Yuan-Qing Wu2,
- Xiaoyan Zou2,
- Peter Cherbas11,
- Manolis Kellis12,
- Michael B. Eisen13,
- Fabio Piano14,
- Karin Kionte14,
- David H. Fitch14,
- Paul W. Sternberg15,
- Asher D. Cutter16,
- Michael O. Duff17,
- Roger A. Hoskins3,
- Brenton R. Graveley17,
- Richard A. Gibbs2,
- Peter J. Bickel4,
- Artyom Kopp7,
- Piero Carninci5,
- Susan E. Celniker3,
- Brian Oliver1,19 and
- Stephen Richards2
- 1National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
- 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
- 3Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
- 4Department of Statistics, University of California, Berkeley, California 94720, USA;
- 5Technology Development Group, RIKEN Omics Science Center and RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama City, Kanagawa, Japan 230-0045;
- 6Division of Computational Bioscience, Center For Information Technology, National Institutes of Health, Bethesda, Maryland 20814, USA;
- 7Department of Evolution and Ecology, University of California, Davis, California 95616, USA;
- 8National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
- 9Clinical Trials and Outcomes Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
- 10National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA;
- 11Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
- 12Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, USA;
- 13Molecular and Cell Biology, University of California, Berkeley, California 94720, USA;
- 14Department of Biology, New York University, New York, New York 10003, USA;
- 15HHMI and Division of Biology, California Institute of Technology, Pasadena, California 91125, USA;
- 16Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada;
- 17Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
-
↵18 These authors contributed equally to this work.
Abstract
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.
Footnotes
-
↵19 Corresponding author
E-mail briano{at}helix.nih.gov
-
[Supplemental material is available for this article.]
-
Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.159384.113.
Freely available online through the Genome Research Open Access option.
- Received April 29, 2013.
- Accepted December 2, 2013.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
