NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE274048 Query DataSets for GSE274048
Status Public on Oct 15, 2024
Title RNA-seq samples from male sex organs in Drosophila
Organisms Drosophila ananassae; Drosophila melanogaster; Drosophila simulans; Drosophila yakuba; Drosophila eugracilis; Drosophila takahashii; Drosophila elegans; Drosophila ficusphila; Drosophila kikkawai; Drosophila bipectinata; Drosophila biarmipes
Experiment type Expression profiling by high throughput sequencing
Summary Phenotypic evolution can result from gains and losses of genes, mutations in coding sequences, or regulatory mutations affecting gene expression. While the relative importance of these mechanisms is debated, regulatory evolution is recognized as a key driver of phenotypic diversity. In this study, we applied a phylogenetic model to discretized gene expression states (active or inactive) to investigate the evolutionary turnover of organ-specific transcriptomes, which we define as instances where gene expression is activated or deactivated in a particular organ. We focus on transcriptome turnover in two male reproductive organs in 11 species of the Drosophila melanogaster species group. Using the Bayesian inference method zigzag (Thompson et al. 2020), we estimate that testes express a higher proportion of the genome (65--75% of genes, depending on the species) compared to accessory glands (46--64%), with background expression noise producing less than 1% of transcripts in both organs. We find that many conserved genes have gained or lost expression in testes and accessory glands. Our model of joint transcriptome evolution, applied to 8,660 genes conserved as single copy families in all species (singleton genes), revealed similar turnover rates but distinct evolutionary trajectories in the two organs. We estimate that the genes in our data set transition between active and inactive expression states at rates on the order of 10^-9 yr^-1. The two organs experienced accelerated transcriptome turnover on different branches of the Drosophila phylogeny. The accessory glands exhibit greater variation in turnover rates among lineages, suggesting a lower baseline rate with bursts of rapid evolution in a subset of branches on the phylogeny. We do not observe significant differences in turnover rates between X-linked and autosomal genes. Genes that encode transcription factors transition between active and inactive states slower than non-TF genes in the accessory gland, but slightly faster in the testis. The results are robust to the choice of probability cut-offs used to discretize gene expression states, and there is good agreement between the estimates of expression states from zigzag and the inferences from the phylogenetic model. Overall, our study highlights the complex dynamics of transcriptome evolution in male reproductive organs. We discuss the benefits and challenges associated with investigating the evolution of gene expression as a binary trait and suggest potentially fruitful avenues for further methodological development.
 
Overall design To investigate the evolution of gene expression in drosophila male sex organs, we purified mRNA from the accessory glands and testis of pooled samples of about 25 adult male flies from two biological replicates from each of two different strains in 11 species. Libraries with insufficient read (< about 30 million) were augmented with additional sequencing runs.
Relative expression was quantified and expression state inferred using latent mixture models.
An evolutionay model and phylogenetic tree were fit to the comparitive data to infer evolutionary rates and history.
 
Contributor(s) Thompson A, Kopp A, Reidl N, Barmina O, Hopkins BR
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Aug 06, 2024
Last update date Oct 15, 2024
Contact name Ben Hopkins
E-mail(s) [email protected]
Organization name UC Davis
Department Evolution & Ecology
Street address One Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platforms (33)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
GPL21306 Illumina HiSeq 4000 (Drosophila melanogaster)
GPL22290 Illumina HiSeq 2500 (Drosophila ananassae)
Samples (176)
GSM8442473 Drosophila_eugracilis_ag_G_102_102b_S26
GSM8442474 Drosophila_eugracilis_ag_G_102_102_S22
GSM8442475 Drosophila_biarmipes_ag_G_106_106_S19
Relations
BioProject PRJNA1144788

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE274048_dana_ag_refonly_replicates.tpm.txt.gz 282.1 Kb (ftp)(http) TXT
GSE274048_dana_testes_refonly_replicates.tpm.txt.gz 308.6 Kb (ftp)(http) TXT
GSE274048_dbia_ag_refonly_replicates.tpm.txt.gz 325.0 Kb (ftp)(http) TXT
GSE274048_dbia_testes_refonly_replicates.tpm.txt.gz 301.3 Kb (ftp)(http) TXT
GSE274048_dbip_ag_refonly_replicates.tpm.txt.gz 276.6 Kb (ftp)(http) TXT
GSE274048_dbip_testes_refonly_replicates.tpm.txt.gz 306.2 Kb (ftp)(http) TXT
GSE274048_dele_ag_refonly_replicates.tpm.txt.gz 274.6 Kb (ftp)(http) TXT
GSE274048_dele_testes_refonly_replicates.tpm.txt.gz 301.5 Kb (ftp)(http) TXT
GSE274048_deug_ag_refonly_replicates.tpm.txt.gz 281.6 Kb (ftp)(http) TXT
GSE274048_deug_testes_refonly_replicates.tpm.txt.gz 371.5 Kb (ftp)(http) TXT
GSE274048_dfic_ag_refonly_replicates.tpm.txt.gz 276.4 Kb (ftp)(http) TXT
GSE274048_dfic_testes_refonly_replicates.tpm.txt.gz 302.7 Kb (ftp)(http) TXT
GSE274048_dkik_ag_refonly_replicates.tpm.txt.gz 275.5 Kb (ftp)(http) TXT
GSE274048_dkik_testes_refonly_replicates.tpm.txt.gz 301.0 Kb (ftp)(http) TXT
GSE274048_dmel_ag_refonly_replicates.tpm.txt.gz 309.5 Kb (ftp)(http) TXT
GSE274048_dmel_testes_refonly_replicates.tpm.txt.gz 345.9 Kb (ftp)(http) TXT
GSE274048_dsim_ag_refonly_replicates.tpm.txt.gz 330.2 Kb (ftp)(http) TXT
GSE274048_dsim_testes_refonly_replicates.tpm.txt.gz 370.3 Kb (ftp)(http) TXT
GSE274048_dtak_ag_refonly_replicates.tpm.txt.gz 333.5 Kb (ftp)(http) TXT
GSE274048_dtak_testes_refonly_replicates.tpm.txt.gz 315.7 Kb (ftp)(http) TXT
GSE274048_dyak_ag_refonly_replicates.tpm.txt.gz 286.6 Kb (ftp)(http) TXT
GSE274048_dyak_testes_refonly_replicates.tpm.txt.gz 323.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap