Genome evolution of gene families: the example of insect gustatory receptors

Directory containing the input files and scripts described in the book chapter.

Gene families, groups of genes that share common ancestry and are often functionally related, represent a substantial proportion of the protein-coding sequences within eukaryotic genomes. In insects, genes involved in chemoperception belong to gene families characterized by numerous copies that arise from episodic bursts of gene duplication. This biological process is crucial for insects survival as it perceives environmental chemical cues. In this chapter, we explore the gustatory receptors in the fire ant Solenopsis invicta and provide a protocol for bioinformatic analyses. First, we employ BITACORA to identify and annotate gene family members within a genome assembly, providing tools for the annotation and subsequent validation. Then, we use GALEON to explore the genomic arrangement in the chromosome-level assembly of gene family members and to visualize the distribution of gene clusters. To gain insights into the evolution and function of these genes, we conduct multiple sequence alignment and reconstruct the phylogeny, incorporating data from two other insects. Finally, we integrate physical and evolutionary distances of the gustatory receptors to further understand the dynamics of this gene family.

Contents

1 - Gene family annotation

2 - Gene annotation evaluation

3 - Identifying gene clusters

4 - Multiple sequence alignment

5 - Phylogenetic analyses

6 - Genetic and physical distances

Programs

BITACORA: https://github.com/molevol-ub/bitacora

GALEON: https://github.com/molevol-ub/galeon