RT Journal
A1 Chen, Zhen-Xia
A1 Sturgill, David
A1 Qu, Jiaxin
A1 Jiang, Huaiyang
A1 Park, Soo
A1 Boley, Nathan
A1 Suzuki, Ana Maria
A1 Fletcher, Anthony R.
A1 Plachetzki, David C.
A1 FitzGerald, Peter C.
A1 Artieri, Carlo G.
A1 Atallah, Joel
A1 Barmina, Olga
A1 Brown, James B.
A1 Blankenburg, Kerstin P.
A1 Clough, Emily
A1 Dasgupta, Abhijit
A1 Gubbala, Sai
A1 Han, Yi
A1 Jayaseelan, Joy C.
A1 Kalra, Divya
A1 Kim, Yoo-Ah
A1 Kovar, Christie L.
A1 Lee, Sandra L.
A1 Li, Mingmei
A1 Malley, James D.
A1 Malone, John H.
A1 Mathew, Tittu
A1 Mattiuzzo, Nicolas R.
A1 Munidasa, Mala
A1 Muzny, Donna M.
A1 Ongeri, Fiona
A1 Perales, Lora
A1 Przytycka, Teresa M.
A1 Pu, Ling-Ling
A1 Robinson, Garrett
A1 Thornton, Rebecca L.
A1 Saada, Nehad
A1 Scherer, Steven E.
A1 Smith, Harold E.
A1 Vinson, Charles
A1 Warner, Crystal B.
A1 Worley, Kim C.
A1 Wu, Yuan-Qing
A1 Zou, Xiaoyan
A1 Cherbas, Peter
A1 Kellis, Manolis
A1 Eisen, Michael B.
A1 Piano, Fabio
A1 Kionte, Karin
A1 Fitch, David H.
A1 Sternberg, Paul W.
A1 Cutter, Asher D.
A1 Duff, Michael O.
A1 Hoskins, Roger A.
A1 Graveley, Brenton R.
A1 Gibbs, Richard A.
A1 Bickel, Peter J.
A1 Kopp, Artyom
A1 Carninci, Piero
A1 Celniker, Susan E.
A1 Oliver, Brian
A1 Richards, Stephen
T1 Comparative validation of the D. melanogaster modENCODE transcriptome annotation
JF Genome Research 
JO Genome Research 
YR 2014 
FD July 01 
VO 24 
IS 7 
SP 1209 
OP 1223 
DO 10.1101/gr.159384.113 
UL http://genome.cshlp.org/content/24/7/1209.abstract 
AB 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.