Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Zhen Xia Chen, David Sturgill, Jiaxin Qu, Huaiyang Jiang, Soo Park, Nathan Boley, Ana Maria Suzuki, Anthony R. Fletcher, David C. Plachetzki, Peter C. FitzGerald, Carlo G. Artieri, Joel Atallah, Olga Barmina, James B. Brown, Kerstin P. Blankenburg, Emily Clough, Abhijit Dasgupta, Sai Gubbala, Yi Han, Joy C. JayaseelanDivya Kalra, Yoo Ah Kim, Christie L. Kovar, Sandra L. Lee, Mingmei Li, James D. Malley, John H. Malone, Tittu Mathew, Nicolas R. Mattiuzzo, Mala Munidasa, Donna M. Muzny, Fiona Ongeri, Lora Perales, Teresa M. Przytycka, Ling Ling Pu, Garrett Robinson, Rebecca L. Thornton, Nehad Saada, Steven E. Scherer, Harold E. Smith, Charles Vinson, Crystal B. Warner, Kim C. Worley, Yuan Qing Wu, Xiaoyan Zou, Peter Cherbas, Manolis Kellis, Michael B. Eisen, Fabio Piano, Karin Kionte, David H. Fitch, Paul W. Sternberg, Asher D. Cutter, Michael O. Duff, Roger A. Hoskins, Brenton R. Graveley, Richard A. Gibbs, Peter J. Bickel, Artyom Kopp, Piero Carninci, Susan E. Celniker, Brian Oliver, Stephen Richards

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1209-1223
Number of pages15
JournalGenome Research
Volume24
Issue number7
DOIs
StatePublished - 2014

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Transcriptome
Genome
Drosophila
Molecular Sequence Annotation
Genetic Testing
Gene Expression Profiling
Human Genome
Phylogeny
Genomics
Gene Expression
Messenger RNA

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)
  • Medicine(all)

Cite this

Chen, Z. X., Sturgill, D., Qu, J., Jiang, H., Park, S., Boley, N., ... Richards, S. (2014). Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research, 24(7), 1209-1223. https://doi.org/10.1101/gr.159384.113

Comparative validation of the D. melanogaster modENCODE transcriptome annotation. / Chen, Zhen Xia; Sturgill, David; Qu, Jiaxin; Jiang, Huaiyang; Park, Soo; Boley, Nathan; Suzuki, Ana Maria; Fletcher, Anthony R.; Plachetzki, David C.; FitzGerald, Peter C.; Artieri, Carlo G.; Atallah, Joel; Barmina, Olga; Brown, James B.; Blankenburg, Kerstin P.; Clough, Emily; Dasgupta, Abhijit; Gubbala, Sai; Han, Yi; Jayaseelan, Joy C.; Kalra, Divya; Kim, Yoo Ah; Kovar, Christie L.; Lee, Sandra L.; Li, Mingmei; Malley, James D.; Malone, John H.; Mathew, Tittu; Mattiuzzo, Nicolas R.; Munidasa, Mala; Muzny, Donna M.; Ongeri, Fiona; Perales, Lora; Przytycka, Teresa M.; Pu, Ling Ling; Robinson, Garrett; Thornton, Rebecca L.; Saada, Nehad; Scherer, Steven E.; Smith, Harold E.; Vinson, Charles; Warner, Crystal B.; Worley, Kim C.; Wu, Yuan Qing; Zou, Xiaoyan; Cherbas, Peter; Kellis, Manolis; Eisen, Michael B.; Piano, Fabio; Kionte, Karin; Fitch, David H.; Sternberg, Paul W.; Cutter, Asher D.; Duff, Michael O.; Hoskins, Roger A.; Graveley, Brenton R.; Gibbs, Richard A.; Bickel, Peter J.; Kopp, Artyom; Carninci, Piero; Celniker, Susan E.; Oliver, Brian; Richards, Stephen.

In: Genome Research, Vol. 24, No. 7, 2014, p. 1209-1223.

Research output: Contribution to journalArticle

Chen, ZX, Sturgill, D, Qu, J, Jiang, H, Park, S, Boley, N, Suzuki, AM, 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, YA, 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, LL, Robinson, G, Thornton, RL, Saada, N, Scherer, SE, Smith, HE, Vinson, C, Warner, CB, Worley, KC, Wu, YQ, 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 2014, 'Comparative validation of the D. melanogaster modENCODE transcriptome annotation', Genome Research, vol. 24, no. 7, pp. 1209-1223. https://doi.org/10.1101/gr.159384.113
Chen, Zhen Xia ; Sturgill, David ; Qu, Jiaxin ; Jiang, Huaiyang ; Park, Soo ; Boley, Nathan ; Suzuki, Ana Maria ; Fletcher, Anthony R. ; Plachetzki, David C. ; FitzGerald, Peter C. ; Artieri, Carlo G. ; Atallah, Joel ; Barmina, Olga ; Brown, James B. ; Blankenburg, Kerstin P. ; Clough, Emily ; Dasgupta, Abhijit ; Gubbala, Sai ; Han, Yi ; Jayaseelan, Joy C. ; Kalra, Divya ; Kim, Yoo Ah ; Kovar, Christie L. ; Lee, Sandra L. ; Li, Mingmei ; Malley, James D. ; Malone, John H. ; Mathew, Tittu ; Mattiuzzo, Nicolas R. ; Munidasa, Mala ; Muzny, Donna M. ; Ongeri, Fiona ; Perales, Lora ; Przytycka, Teresa M. ; Pu, Ling Ling ; Robinson, Garrett ; Thornton, Rebecca L. ; Saada, Nehad ; Scherer, Steven E. ; Smith, Harold E. ; Vinson, Charles ; Warner, Crystal B. ; Worley, Kim C. ; Wu, Yuan Qing ; Zou, Xiaoyan ; Cherbas, Peter ; Kellis, Manolis ; Eisen, Michael B. ; Piano, Fabio ; Kionte, Karin ; Fitch, David H. ; Sternberg, Paul W. ; Cutter, Asher D. ; Duff, Michael O. ; Hoskins, Roger A. ; Graveley, Brenton R. ; Gibbs, Richard A. ; Bickel, Peter J. ; Kopp, Artyom ; Carninci, Piero ; Celniker, Susan E. ; Oliver, Brian ; Richards, Stephen. / Comparative validation of the D. melanogaster modENCODE transcriptome annotation. In: Genome Research. 2014 ; Vol. 24, No. 7. pp. 1209-1223.
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AU - Suzuki, Ana Maria

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