GALEON: A pipeline for the identification, analysis, and visualization of gene clusters within chromosome-level genomes

V. A. Pisarenco, J. Vizueta and J. Rozas
Universitat de Barcelona
Current Release: Version 1.0 (April 15, 2024)

Motivation: Gene clusters, defined as a set of genes encoding functionally-related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.
To facilitate the identification, analysis, and visualisation of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families, and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.

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Downloads (not finished)

• Workflow (PDF)

• Visualization tools (PDF)

• Poster 2023 (PDF)

• GitHub Repository

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References

Pisarenco, V. A., Vizueta, J., Rozas, J. (2024). GALEON: A Comprehensive Bioinformatic Tool to Analyse and Visualise Gene Clusters in Complete Genomes. In preparation.

Application

A preliminary version of the pipeline has been used in:

Escuer et al. (2022). The chromosome-scale assembly of the Canary Islands endemic spider Dysdera silvatica (Arachnida, Araneae) sheds light on the origin and genome structure of chemoreceptor gene families in chelicerates. Mol. Ecol. Res. 22: 375-390. 10.1111/1755-0998.13471.

Rondón et al. (2024). Comparative genomic analysis of chemosensory-related gene families in gastropods. Molecular Phylogenet. Evol. 192: 107986. doi:10.1016/j.ympev.2023.107986.

Bug Reports

Please send your questions, comments and bug reports to Vadim A. Pisarenco, via GitHub.