Forni Giobbe, Luchetti Andrea, Rota-Stabelli Omar
BiGeA, University of Bologna, Bologna, Italy.
Center C3A, University of Trento, San Michele all'Adige, TN, Italy.
Methods Mol Biol. 2025;2935:211-235. doi: 10.1007/978-1-0716-4583-3_9.
Phylogenomics is the inference of phylogenies using genome-scale data. In a broader sense, it is also the mapping of genomic patterns onto phylogenies. This process is inherently complex, requiring the concurrent use of genomic, bioinformatics, phylogenetics, and comparative methods expertise. Here, we provide an overview of how to plan and conduct a typical phylogenomic study of insects aimed at both producing a genome-scale phylogenetic tree and studying various genomic traits on that phylogeny. Drawing from our experience in insect phylogenomics, we offer practical recommendations to guide researchers through this effort.
系统发育基因组学是利用基因组规模的数据推断系统发育关系。从更广泛的意义上讲，它也是将基因组模式映射到系统发育树上。这个过程本质上很复杂，需要同时运用基因组学、生物信息学、系统发育学和比较方法等专业知识。在这里，我们概述了如何规划和开展一项针对昆虫的典型系统发育基因组学研究，目标是构建一个基因组规模的系统发育树，并在该系统发育树上研究各种基因组特征。基于我们在昆虫系统发育基因组学方面的经验，我们提供实用建议以指导研究人员开展这项工作。
