title: Phylogenomics Using Transcriptome Data.
abstract: 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.
authors.affiliation: Department of Zoology, Naturhistoriska Riksmuseet, 50007, SE-104 05, Stockholm, Sweden. Johanna.cannon@nrm.se.
authors.forename: Johanna Taylor
authors.initials: JT
authors.lastname: Cannon
authors.affiliation: Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, 307 Mary Harmon Bryant Hall, Tuscaloosa, AL, 35487, USA.
authors.forename: Kevin Michael
authors.initials: KM
authors.lastname: Kocot
mesh_terms: D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000235:genetics; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018076:DNA, Complementary
keywords: Illumina; Phylogenomics; Phylogeny; RNAseq; Transcriptomes; cDNA