Cannon Johanna Taylor, Kocot Kevin Michael
Department of Zoology, Naturhistoriska Riksmuseet, 50007, SE-104 05, Stockholm, Sweden.
Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, 307 Mary Harmon Bryant Hall, Tuscaloosa, AL, 35487, USA.
Methods Mol Biol. 2016;1452:65-80. doi: 10.1007/978-1-4939-3774-5_4.
This chapter presents a generalized protocol for conducting phylogenetic analyses using large-scale molecular datasets, specifically using transcriptome data from the Illumina sequencing platform. The general molecular lab bench protocol consists of RNA extraction, cDNA synthesis, and sequencing, in this case via Illumina. After sequences have been obtained, bioinformatics methods are used to assemble raw reads, identify coding regions, and categorize sequences from different species into groups of orthologous genes (OGs). The specific OGs to be used for phylogenetic inference are selected using a custom shell script. Finally, the selected orthologous groups are concatenated into a supermatrix. Generalized methods for phylogenomic inference using maximum likelihood and Bayesian inference software are presented.
本章介绍了一种使用大规模分子数据集进行系统发育分析的通用方案，具体是使用来自Illumina测序平台的转录组数据。一般的分子实验室操作方案包括RNA提取、cDNA合成和测序，在这种情况下是通过Illumina进行测序。获得序列后，使用生物信息学方法组装原始读数、识别编码区域，并将来自不同物种的序列分类为直系同源基因（OG）组。使用自定义的Shell脚本选择用于系统发育推断的特定OG。最后，将选定的直系同源组连接成一个超级矩阵。还介绍了使用最大似然法和贝叶斯推断软件进行系统发育基因组推断的通用方法。
