ArticleMolecular biology and evolution2012
Allelic imbalance in Drosophila hybrid heads: exons, isoforms, and evolution.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Cis-regulatory Variation in Relation to Sex and Sexual Dimorphism in Drosophila melanogaster.Genome biology and evolution · 2024Article
- Mechanisms of transcriptional regulation inProceedings. Biological sciences · 2024Article
- Mechanisms of transcriptional regulation inbioRxiv : the preprint server for biology · 2023Article
- Transcriptional misexpression in hybrids between species linked by gene flow is associated with patterns of sequence divergence.Genome biology and evolution · 2023Article
- Sex-Biased Expression Is Associated With Chromatin State in Drosophila melanogaster and Drosophila simulans.Molecular biology and evolution · 2023Article
- Sex-biased expression is associated with chromatin state inbioRxiv : the preprint server for biology · 2023Article
- Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Power calculator for detecting allelic imbalance using hierarchical Bayesian model.BMC research notes · 2021Article
- Testcrosses are an efficient strategy for identifying cis-regulatory variation: Bayesian analysis of allele-specific expression (BayesASE).G3 (Bethesda, Md.) · 2021Article
- Trajectories of Homoeolog-Specific Expression in AllotetraploidFrontiers in plant science · 2021Article
- The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions.Journal of experimental botany · 2020Article
- The Genetic Architecture of Post-Zygotic Reproductive Isolation BetweenFrontiers in genetics · 2020Article
- Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization.Frontiers in genetics · 2020Article
- Review
- Perturbation of IIS/TOR signaling alters the landscape of sex-differential gene expression in Drosophila.BMC genomics · 2018Article
- A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids.Genetics · 2018Article
- Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.G3 (Bethesda, Md.) · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation within and between species. Regulatory mechanisms are often highly conserved, yet differences between species in gene expression are extensive. What evolutionary forces explain widespread divergence in cis regulation? AI was assessed in Drosophila melanogaster-Drosophila simulans hybrid female heads using RNA-seq technology. Mapping bias was virtually eliminated by using genotype-specific references. Allele representation in DNA sequencing was used as a prior in a novel Bayesian model for the estimation of AI in RNA. Cis regulatory divergence was common in the organs and tissues of the head with 41% of genes analyzed showing significant AI. Using existing population genomic data, the relationship between AI and patterns of sequence evolution was examined. Evidence of positive selection was found in 30% of cis regulatory divergent genes. Genes involved in defense, RNAi/RISC complex genes, and those that are sex regulated are enriched among adaptively evolving cis regulatory divergent genes. For genes in these groups, adaptive evolution may play a role in regulatory divergence between species. However, there is no evidence that adaptive evolution drives most of the cis regulatory divergence that is observed. The majority of genes showed patterns consistent with stabilizing selection and neutral evolutionary processes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.