Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil.
Programa de Pós Graduação em Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil.
Methods Mol Biol. 2022;2525:409-423. doi: 10.1007/978-1-0716-2473-9_32.
Next-generation sequencing (NGS) has dominated the scene of genomics and evolutionary biology as a great amount of genomic data have been accumulated for a diverse set of species. At the same time, phylogenetic approaches and programs are in development to allow better use of such large-size datasets. Phylogenomics appears as a promising field to accommodate and explore all the information of NGS data in phylogenetic methods, being an important approach to investigate the evolution of bioluminescence in different organisms. To guarantee accurate results in phylogenomic studies, it is mandatory to correctly identify orthologous genes in phylogenetic reconstruction. Here, we show a simplified step-by-step framework to perform phylogenetic analysis along with divergence time estimation, beginning with an orthologous search. As empirical data, we exemplify transcriptome sequences of six species of the Elateroidea superfamily (Coleoptera). We introduce several bioinformatics tools for handling genomic data, especially those available in the software OrthoFinder, IQTREE, BEAST2, and TreePL.
下一代测序（NGS）在基因组学和进化生物学领域占据主导地位，因为已经积累了大量的基因组数据，涵盖了多种不同的物种。与此同时，也在开发系统发生方法和程序，以更好地利用这些大数据集。系统发生基因组学似乎是一个很有前途的领域，可以在系统发生方法中容纳和探索 NGS 数据的所有信息，是研究不同生物发光进化的重要方法。为了保证系统发生基因组学研究的准确性，在系统发生重建中正确识别直系同源基因是必不可少的。在这里，我们展示了一个简化的分步框架，用于进行系统发育分析和分歧时间估计，从直系同源搜索开始。作为经验数据，我们以 6 种 Elateroidea 超科（鞘翅目）的转录组序列为例。我们介绍了几种处理基因组数据的生物信息学工具，特别是 OrthoFinder、IQ-TREE、BEAST2 和 TreePL 等软件中的工具。
