Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

TitleComparative validation of the D. melanogaster modENCODE transcriptome annotation.
Publication TypeJournal Article
Year of Publication2014
AuthorsChen, Z-X, Sturgill, D, Qu, J, Jiang, H, Park, S, Boley, N, Suzuki, AMaria, Fletcher, AR, Plachetzki, DC, FitzGerald, PC, Artieri, CG, Atallah, J, Barmina, O, Brown, JB, Blankenburg, KP, Clough, E, Dasgupta, A, Gubbala, S, Han, Y, Jayaseelan, JC, Kalra, D, Kim, Y-A, Kovar, CL, Lee, SL, Li, M, Malley, JD, Malone, JH, Mathew, T, Mattiuzzo, NR, Munidasa, M, Muzny, DM, Ongeri, F, Perales, L, Przytycka, TM, Pu, L-L, Robinson, G, Thornton, RL, Saada, N, Scherer, SE, Smith, HE, Vinson, C, Warner, CB, Worley, KC, Wu, Y-Q, Zou, X, Cherbas, P, Kellis, M, Eisen, MB, Piano, F, Kionte, K, Fitch, DH, Sternberg, PW, Cutter, AD, Duff, MO, Hoskins, RA, Graveley, BR, Gibbs, RA, Bickel, PJ, Kopp, A, Carninci, P, Celniker, SE, Oliver, B, Richards, S
JournalGenome Res
Date Published2014 Jul
KeywordsAnimals, Cluster Analysis, Computational Biology, Drosophila melanogaster, Evolution, Molecular, Exons, Female, Gene Expression Profiling, Genome, Insect, Humans, Male, Molecular Sequence Annotation, Nucleotide Motifs, Phylogeny, Position-Specific Scoring Matrices, Promoter Regions, Genetic, Reproducibility of Results, RNA Editing, RNA Splice Sites, RNA Splicing, Transcription Initiation Site, Transcriptome

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.

Alternate JournalGenome Res
PubMed ID24985915
PubMed Central IDPMC4079975
Grant ListZ01 DK015600 / / Intramural NIH HHS / United States
R01 HG004037 / HG / NHGRI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
R01 GM100140 / GM / NIGMS NIH HHS / United States
1R0IGM082843 / / PHS HHS / United States
ZIA DK015600-18 / / Intramural NIH HHS / United States
U01HB004271 / HB / NHLBI NIH HHS / United States
DK015600-18 / DK / NIDDK NIH HHS / United States

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