Drosophila Genome Project

Drosophila
Image source: Wikimedia Commons

The BCM-HGSC has been involved in several Drosophila genome sequence projects.

Drosophila Genetic Reference Panel

In association with Trudy Mackay (North Carolina State University) we are sequencing a number of phenotyped inbred strains of D. melanogaster using new technologies. The aim is to allow whole genome association studies, and make both the fly lines and the sequences available to the entire Drosophila community. As a start to this process, sequences will be made available here as well as in the usual public depositories.

Drosophila melanogaster genome sequence

The BCM-HGSC was a member of the Berkeley Drosophila Genome Project (BDGP), and responsible for sequencing and finishing approximately one third of the D. melanogaster reference sequence. The reference has since been published (Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-95 (2000).) and further refined (Celniker, S. E. et al. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol 3, RESEARCH0079 (2002)).

Find the most recent data at flybase.

Drosophila pseudoobscura genome sequence

A draft genome sequence of the fruitfly (D. pseudoobscura) was performed by the BCM-HGSC, and published in January 2005 (Richards et al. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Research 15:1-18).

Drosophila modENCODE Project

As part of the Drosophila modENCODE project, we are studying the comparative genomics of eight additional species of Drosophila: biarmipes, bipectinata, elegans, eugracillis, ficusphila, kikkawai, rhopaloa and takahashii.


 

Related Publications

Ellis LL, Huang W, Quinn AM, Ahuja A, Alfrejd B, Gomez FE, et al. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity. PLoS Genet. 2014 ;10(7):e1004522.

Chen Z-X, Sturgill D, Qu J, Jiang H, Park S, Boley N, et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 ;24(7):1209-23.

Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, et al.. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res. 2014 ;24(7):1193-208.

Jusiak B, Karandikar UC, Kwak S-J, Wang F, Wang H, Chen R, et al. Regulation of Drosophila eye development by the transcription factor Sine oculis. PLoS One. 2014 ;9(2):e89695.

Jusiak B, Eblimit A, Haelterman N, Chen R, Mardon G. MAPK target sites of eyes absent are not required for eye development or survival in Drosophila. PLoS One. 2012 ;7(12):e50776.

English AC, Richards S, Han Y, Wang M, Vee V, Qu J, et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One. 2012 ;7(11):e47768.

Huang W, Richards S, Carbone MAnna, Zhu D, Anholt RRH, Ayroles JF, et al. Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci U S A. 2012 ;109(39):15553-9.

Hong X, Doddapaneni HV, Comeron JM, Rodesch MJ, Halvensleben HA, Nien CY, et al. Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissue-specific transcription in Drosophila melanogaster. G3 (Bethesda). 2012 ;2(8):873-82.