Genetic basis of transcriptome diversity in Drosophila melanogaster
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE67505 | GEO | 2015/10/01
SECONDARY ACCESSION(S): PRJNA280097
REPOSITORIES: GEO
Similar Datasets
Project description:Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive, but is essential for predicting adaptive evolution, selecting agriculturally important animals and crops, and personalized medicine. Here, we quantified genome-wide genetic variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel. We found that a substantial fraction of the Drosophila transcriptome is genetically variable and organized into modules of genetically correlated transcripts, which provide functional context for newly identified novel transcribed regions. We identified regulatory variants for the mean and variance of gene expression, both of which showed oligogenic genetic architecture. Expression quantitative trait loci the mean, but not the variance, of gene expression were concentrated near genes. This comprehensive characterization of transcriptomic diversity and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.
2015-10-05 | E-MTAB-3216 | biostudies-arrayexpress
Project description:Our primary objective was to characterize the amount of variation in transcript abundance among individual flies with identical genotypes. We also wanted to determine which analysis methods would be optimal for RNA-Seq data. To meet these objectives, we performed transcriptional profiling of whole adult individuals from 16 Drosophila Genetic Reference Panel (DGRP) lines. We quantified differential expression among genotypes, environments, and sexes. We randomly chose 16 DGRP lines for this experiment: DGRP-93, DGRP-229, DGRP-320, DGRP-352, DGRP-370, DGRP-563, DGRP-630, DGRP-703, DGRP-761, DGRP-787, DGRP-790, DGRP-804, DGRP-812, DGRP-822, DGRP-850, and DGRP-900. We collected 8 virgin male and 8 virgin female flies from the 16 DGRP genotypes in three replicated environments to produce RNA sequence profiles. We controlled the environmental conditions in the following ways. We seeded the fly cultures with 5 male and 5 female parents. We reared the progeny in a single incubator on standard Drosophila food (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/bloomfood.htm) at 25°C, 60% humidity, and a 12:12-hour light:dark cycle. We collected and maintained male and female virgins at 20 flies to a same-sex vial for four days prior to RNA extraction to control for social exposure. Flies were frozen for RNA extraction at the same circadian time (1:00 pm) in 96-well plates. PolyA RNA stranded libraries were prepared by modifying an existing protocol. ERCC (External RNA Controls Consortium, SRM2374, beta version, pools 78A/78B) sequences were added during the library preparation as a control. For some samples >1 library was generated to check technical variation. We performed multiplexed single-end 76 bp sequencing on an Illumina HiSeq2000. Reads were mapped to FlyBase release 5 version 57 and release 6 version 01 of the Drosophila melanogaster genome and the ERCC sequences. Mapped reads were counted at the gene level.
2015-12-21 | E-GEOD-60314 | biostudies-arrayexpress
Project description:Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive but is essential for predicting adaptive evolution, for selecting agriculturally important animals and crops, and for personalized medicine. Gene expression may provide a link between variation in DNA sequence and organismal phenotypes, and its abundance can be measured efficiently and accurately. Here we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). We found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. We found that NTRs often were negatively correlated with the expression of protein-coding genes, which we exploited to annotate NTRs functionally. We identified regulatory variants for the mean and variance of gene expression, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression were concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.
| S-EPMC4640795 | biostudies-literature
Project description:Our primary objective was to characterize the amount of variation in transcript abundance among individual flies with identical genotypes. We also wanted to determine which analysis methods would be optimal for RNA-Seq data. To meet these objectives, we performed transcriptional profiling of whole adult individuals from 16 Drosophila Genetic Reference Panel (DGRP) lines. We quantified differential expression among genotypes, environments, and sexes.
2015-12-21 | GSE60314 | GEO
Project description:Genome pool-sequencing of 30 DGRP strains
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Project description:PacBio for six Drosophila melanogaster DGRP lines
| PRJNA574592 | ENA
Project description:Variation in mitochondrial genomes in the DGRP
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Project description:Most animals restrict their activity to specific part of the day, being either diurnal, nocturnal, or crepuscular. The genetic basis underlying this diurnal preference is largely unknown. Under laboratory conditions, Drosophila melanogaster is crepuscular, showing a bi-modal activity profile. However, recent experiments in our lab indicated that high variability among individuals exist, particularly in strains that derive from different wild populations. By assembling together flies from various geographical strains, we have generated a highly diverse population whose progeny exhibited extreme diurnal preference, including diurnal and nocturnal flies. We have used this population as a starting point for an artificial selection experiment in which we selected males that show the most extreme diurnal preference and mated them to their sisters. The response to selection was strong, and already after 10 selection cycles we obtained highly diurnal (D) and nocturnal (N) strains. Another strain that was not selected and showed intermediate behaviour (crepuscular) served as a control (C). These strains provide us with a unique opportunity to understand the genetics of diurnal preference.
2020-08-17 | GSE116985 | GEO
Project description:Deep sequencing of mitochondrial genomes in the DGRP
| PRJNA504538 | ENA