TY  - JOUR
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
Y1  - 2014/07/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1209 
EP  - 1223 
DO  - 10.1101/gr.159384.113 
VL  - 24 
IS  - 7 
UR  - http://genome.cshlp.org/content/24/7/1209.abstract 
N2  - 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. 
ER  -