Vizueta Joel, Pisarenco Vadim A, Rozas Julio
Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.
Methods Mol Biol. 2025;2935:179-209. doi: 10.1007/978-1-0716-4583-3_8.
Gene families, which are groups of genes that share common ancestry and are often functionally related, constitute 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 insect survival, as it enables the perception of environmental chemical cues. In this chapter, we analyze the gustatory receptors in the fire ant Solenopsis invicta and present a protocol for bioinformatic analyses. First, we employ BITACORA to identify and annotate gene family members in the genome assembly, providing tools for the annotation and subsequent validation. Then, we use GALEON to explore the genomic arrangement of gene family members in the chromosome-level assembly and 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.
基因家族是一组具有共同祖先且通常在功能上相关的基因，它们在真核生物基因组的蛋白质编码序列中占相当大的比例。在昆虫中，参与化学感知的基因属于基因家族，其特征是有许多通过基因复制的偶发爆发而产生的拷贝。这一生物学过程对昆虫的生存至关重要，因为它能使昆虫感知环境中的化学信号。在本章中，我们分析了红火蚁（Solenopsis invicta）的味觉受体，并提出了一种生物信息学分析方案。首先，我们使用BITACORA在基因组组装中识别和注释基因家族成员，提供注释和后续验证的工具。然后，我们使用GALEON在染色体水平组装中探索基因家族成员的基因组排列，并可视化基因簇的分布。为了深入了解这些基因的进化和功能，我们进行多序列比对并重建系统发育，纳入另外两种昆虫的数据。最后，我们整合味觉受体的物理距离和进化距离，以进一步了解这个基因家族的动态变化。
