About the 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.
Papers:
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Cool paper using the bipectinata data that has been published by Thad Seher in the Kopp lab: Genetic Basis of a Violation of Dollo’s Law: Re-Evolution of Rotating Sex Combs in Drosophila bipectinata
The aim is to better identify and annotate conserved sequences within the Drosophila genome.
The modEncode comparative genomics white paper also requests the sequencing of the Oregon R fly strain used for many of the modEncode lab experiments.
We sequenced isolates of the strains used in three modENCODE laboratories (Bloomington, Elgin laboratory, Orr-Weaver laboratory) using an illumina re-sequencing approach. Raw sequences are available on the NCBI BioProject: Drosophila melanogaster page.
Genomic Resources
Eight genome assemblies now available on the NCBI website
Additional resources
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BCM-HGSC data: raw RNAseq data is available here. This includes sampling from adult males, adult females and mixed embryos for each of the eight species.
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BCM-HGSC data: raw sequence reads can be found here. This includes BAM alignment files, and vcf files with SNP and indel calls.
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Twenty fly alignment files produced by Brian Raney as part of the alignathon project, which includes the alignathon fly set tree.
Web Apollo: A web-based sequence annotation editor for community annotation
For information about Web Apollo, please contact Monica Poelchau.
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Web Apollo annotation tool (requires log in)
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Web Apollo Jbrowse viewing of the automated annotation tracks (no log in required)
Listserve
Updates about the modENCODE genome sequencing are being posted to the modENCODE genomics listserv. Please contact Stephen Richards with your email address to sign up.