Dataset Information

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

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.

SUBMITTER: Chen ZX

PROVIDER: S-EPMC4079975 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Chen Zhen-Xia ZX Sturgill David D Qu Jiaxin J Jiang Huaiyang H Park Soo S Boley Nathan N Suzuki Ana Maria AM Fletcher Anthony R AR Plachetzki David C DC FitzGerald Peter C PC Artieri Carlo G CG Atallah Joel J Barmina Olga O Brown James B JB Blankenburg Kerstin P KP Clough Emily E Dasgupta Abhijit A Gubbala Sai S Han Yi Y Jayaseelan Joy C JC Kalra Divya D Kim Yoo-Ah YA Kovar Christie L CL Lee Sandra L SL Li Mingmei M Malley James D JD Malone John H JH Mathew Tittu T Mattiuzzo Nicolas R NR Munidasa Mala M Muzny Donna M DM Ongeri Fiona F Perales Lora L Przytycka Teresa M TM Pu Ling-Ling LL Robinson Garrett G Thornton Rebecca L RL Saada Nehad N Scherer Steven E SE Smith Harold E HE Vinson Charles C Warner Crystal B CB Worley Kim C KC Wu Yuan-Qing YQ Zou Xiaoyan X Cherbas Peter P Kellis Manolis M Eisen Michael B MB Piano Fabio F Kionte Karin K Fitch David H DH Sternberg Paul W PW Cutter Asher D AD Duff Michael O MO Hoskins Roger A RA Graveley Brenton R BR Gibbs Richard A RA Bickel Peter J PJ Kopp Artyom A Carninci Piero P Celniker Susan E SE Oliver Brian B Richards Stephen S

Genome research 20140701 7

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 Dro ...[more]

PMID: 24985915

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Dataset Information

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Publications

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

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