The Drosophila melanogaster transcriptome by paired-end RNA sequencing.

TitleThe Drosophila melanogaster transcriptome by paired-end RNA sequencing.
Publication TypeJournal Article
Year of Publication2011
AuthorsDaines, B, Wang, H, Wang, L, Li, Y, Han, Y, Emmert, D, Gelbart, W, Wang, X, Li, W, Gibbs, RA, Chen, R
JournalGenome Res
Date Published2011 Feb
KeywordsAlternative Splicing, Animals, Drosophila melanogaster, Female, Gene Expression Profiling, Genes, Y-Linked, Male, Molecular Sequence Annotation, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Sequence Analysis, RNA

RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on the Illumina GA II yielding 356× sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events. A total of 319 novel transcripts were identified, representing a 2% increase over the current annotation. Alternate splicing was observed in 31% of D. melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms. Much of this splicing is subtle such as tandem alternate splice sites.

Alternate JournalGenome Res
PubMed ID21177959
PubMed Central IDPMC3032934
Grant ListT32 EYO7102-16 / / PHS HHS / United States
F32 EY019430 / EY / NEI NIH HHS / United States
5U54HG003273 / HG / NHGRI NIH HHS / United States
EY19430-01 / EY / NEI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
R01 EY016853 / EY / NEI NIH HHS / United States
R01EY016853 / EY / NEI NIH HHS / United States
T32 EY007102 / EY / NEI NIH HHS / United States

Similar Publications

Chin C-S, Behera S, Khalak A, Sedlazeck FJ, Sudmant PH, Wagner J, et al.. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nat Methods. 2023;20(8):1213-1221.
Schlosser P, Zhang J, Liu H, Surapaneni AL, Rhee EP, Arking DE, et al.. Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage. Genome Biol. 2023;24(1):150.
Harris RA, McAllister JM, Strauss JF. Single-Cell RNA-Seq Identifies Pathways and Genes Contributing to the Hyperandrogenemia Associated with Polycystic Ovary Syndrome. Int J Mol Sci. 2023;24(13).
Lu J, Zheng KQ, Bertrand RElaine, Quinlan J, Ferdous S, Srinivasan T, et al.. Gene augmentation therapy to rescue degenerative photoreceptors in a Cwc27 mutant mouse model. Exp Eye Res. 2023;234:109596.
Calame DG, Guo T, Wang C, Garrett L, Jolly A, Dawood M, et al.. Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. Am J Hum Genet. 2023;110(8):1394-1413.
Qian X, Srinivasan T, He J, Lu J, Jin Y, Gu H, et al.. Ceramide compensation by ceramide synthases preserves retinal function and structure in a retinal dystrophy mouse model. Dis Model Mech. 2023;16(7).
Sisoudiya SDushyant, Mishra P, Li H, Schraw JM, Scheurer ME, Salvi S, et al.. Identification of USP9X as a leukemia susceptibility gene. Blood Adv. 2023;7(16):4563-4575.
Einson J, Glinos D, Boerwinkle E, Castaldi P, Darbar D, de Andrade M, et al.. Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. Genetics. 2023;224(4).
Yang L, Chen X, Lee C, Shi J, Lawrence EB, Zhang L, et al.. Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer. J Exp Clin Cancer Res. 2023;42(1):113.
Elbendary HM, Marafi D, Saad AK, Elhossini R, Duan R, Rafat K, et al.. Novel LSS variants in alopecia and intellectual disability syndrome: New case report and clinical spectrum of LSS-related rare disease traits. Clin Genet. 2023;104(3):344-349.