A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees

摘要

The large scale genome datasets that are now available can provide unprecedented insight into the evolution of genes and gene families. Nevertheless, handling and transforming such datasets into the desired format for downstream analyses is often a difficult and time-consuming task for researchers without a background in informatics. Here, we present a simple and fast protocol for data preparation and high quality phylogenetic tree inferences using simple to install cross-platform software applications with rich graphical interfaces. To illustrate its potential, this protocol was used to provide insight into the evolution of GULO gene in animals, a gene that encodes the enzyme responsible for the last step of vitamin C synthesis in this group of organisms. We find that GULO is always a single copy gene in all animal groups with the exception of Echinodermata. Surprisingly, we find potentially functional GULO genes in several Prostotomian groups such as Molluscs, Priapulida and Arachnida. To our knowledge, this is the first time a putative functional GULO gene is reported in Protostomians. All previously reported GULO gene losses were easily identified using the presented protocol.