Project description:These arrays measure gene expression across eight Y introgression lines in Drosophila simulans. Four lines (Ya19, Ya23, Ya24, Ya26) carry a D. simulans Y chromosome (from a Cameroon population) and four lines (Sec01, Sec03, Sec08, Sec27) carry a D. sechellia Y chromosome. All lines are otherwise identical with a D. simulans background (UCSD stock center line 14021-0251.092).
Project description:We generated RNA-seq data of Drosophila simulans and Drosophila mauritiana developing male genitalia in order to identify expression level differences between these species. These species are closely related, yet have dramatic differences in their male genital morphologies. Three independent RNA-seq library replicates were generated for Dsim w501 and Dmau D1 developing male genitalia. Flies were reared under the above conditions, and white pre-pupae collected. Males were selected using gonad size and allowed to develop in a humid container at 25ºC until stages 2 and 4.5 (see staging guide in (Hagen et al., 2019); tartan underlies the evolution of Drosophila male genital morphology). Between these stages, the claspers develop from a ridge structure to a distinct appendage separate from the surrounding tissue, and the posterior lobe has begun to extend outwards from the lateral plate primordia (Hagen et al., 2019). The heads of pupae were impaled with a needle onto a charcoal agar plate and submerged in 1xPBS. Dissection scissors were used to remove the distal tip of the pupal case and the outer membrane, and pressure applied to the abdomen to allow the developing genitalia to be quickly expelled from the pupal case and dissected away from the abdomen. Note that the entire genital arch, including internal genital organs (but not including abdominal tissue), was isolated for RNA extraction. The genitalia from fifteen males from each stage were collected and placed directly into TRIzol. RNA was then extracted using standard procedures. Quality and quantity of RNA was verified using a Qubit, and samples were sent to the Centre for Genomic Research at the University of Liverpool where dual-indexed, strand-specific RNA-seq libraries were prepared using NEBNext polyA selection and Ultra Directional RNA preparation kits. Samples were then sequenced using Illumina HiSeq 4000 (paired-end, 2x150 bp sequencing). Dsim w501 and Dmau D1 reads were mapped against reannotated reference coding sequences (Torres-Oliva et al., 2016).
Project description:Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. Identifying these groups of co-expressed genes is important to the functional annotation of genomes and understanding the evolutionary fates of the clustered genes. We used microarrays to measure gene expression in seven closely related Drosophila species, to identify domains clusters within a species of Drosophila (D. simulans) and that are evolving among species in the D. melanogater subgroup. Experiment Overall Design: Assays were carried out on three independent (biological) replicates per species for a single line of the following five species: D.yakuba (Tuscon Stock Center Number: 14021-0261.00), D.santomea (TSCN: 14021-0271.00), D.teissieri (TSCN: 14021-0257.00), D.mauritiana (David 105, TSCN: 14021-0241.01), D.sechellia (Roberstson, TSCN: 14021-0248.21). Three biological replicates for D.melanogaster. The samples assayed for D.melanogaster reflect an even genotypic contribution of 10 isogenic lines developed from a wild population (Winters, CA) and crossed in a round-robin design.For D. simulans, three replicate arrays were used to assay each of 10 round-robin crosses between 10 isogenic lines developed from the same population. the entire data set therefore included a total of 48 independent transcript assays covering seven Drosophila species in the D.melanogaster subgroup
Project description:These arrays measure gene expression across eight Y introgression lines in Drosophila simulans. Four lines (Ya19, Ya23, Ya24, Ya26) carry a D. simulans Y chromosome (from a Cameroon population) and four lines (Sec01, Sec03, Sec08, Sec27) carry a D. sechellia Y chromosome. All lines are otherwise identical with a D. simulans background (UCSD stock center line 14021-0251.092). Four biological replicates of each of eight lines, plus two technical replicates (dye swap), for a total of 32 arrays. Full methods are described in the accompanying publication.
Project description:see publication, arrays from 4 sterile genotypes containing homozygous segments with a Hybrid Male Sterility factor and 1 fertile strain in which the region is a Drosophila simulans and D. mauritiana heterozygous
