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Updated: Jul 4, 2026
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
From candidate genes to omics: Unbiased approaches reshaping arthropod Evo-Devo
João Vieira1,2, Rodrigo Nunes-da-Fonseca1
1Universidade Federal do Rio de Janeiro, Instituto de Biodiversidade e Sustentabilidade, Macaé, RJ, Brazil.
Genetics and Molecular Biology
|July 3, 2026
Summary
Modern genomic tools allow detailed study of gene regulatory networks in diverse arthropods. Integrating multi-omic data and functional studies is key to understanding evolutionary developmental biology.
Area of Science:
- Evolutionary developmental biology (Evo-Devo)
- Genomics
- Arthropod biology
Background:
- The candidate-gene approach in Drosophila melanogaster historically guided arthropod Evo-Devo.
- Genome-wide methods now allow direct study of gene regulatory networks (GRNs) in non-model arthropods.
Purpose of the Study:
- To review the application of genome-wide methods in non-model arthropods.
- To critically assess the scope and limitations of current multi-omic approaches.
- To highlight future directions for mechanistic understanding of evolutionary regulation.
Main Methods:
- Bulk RNA-seq
- Single-cell/single-nucleus transcriptomics
- Chromatin profiling (ATAC-seq, CUT&Tag/CUT&RUN)
- 3D genome mapping (Hi-C)
- Multi-omic data integration
- Functional perturbations
Main Results:
- Identification of lineage-restricted regulators in diverse arthropod clades.
- Resolution of cell-type trajectories.
- Mapping of cis-regulatory landscapes.
- Uncovered challenges in linking distal regulatory elements to target genes.
Conclusions:
- High-quality genomes, annotations, and experimental design are crucial for success.
- Mitigating technical artifacts (dissociation, ambient RNA) is essential.
- Integrating multi-omic data with functional perturbations is vital for a mechanistic understanding of evolution.
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