TreeExp1.0 – R Package for Analyzing Expression Evolution Based on RNA-Seq Data

Recent innovation of RNA-seq technology has shed insightful light on the transcriptomic evolution studies, especially on researches of tissue-specific expression evolution. Phylogenetic analysis of transcriptome data may help to identify causal gene expression differences underlying the evolutionary changes in morphological, physiological, and developmental characters of interest. However, there is a deficiency of software to phylogenetically analyze transcriptome data.

To address this need, researchers at Fudan University have developed an R package TreeExp that can perform comparative expression evolution analysis based on RNA-seq data, which includes optimized input formatting, normalization, pairwise expression distance estimation, expression character tree inference, and preliminary expression phylogenetic network analysis. TreeExp also enables user to map expression distance onto a customized phylogenetic tree.

By applying TreeExp on two cases of mammalian gene expression evolution, the researchers observed that:

1. expression trees of brain and testis are largely consistent with known mammalian species tree with minor discrepancies;
2. intertissues expression divergences (brain and testis) are more substantial than interspecies expression divergences across mammalian species; and
3. expression pattern of gene modules related to nervous system development exhibits specific expression pattern in brain of primates compared to housekeeping genes. These tissue-specific expression patterns might give insights underlying evo-devo mechanisms of complex organisms.

(A) Expression divergences of human–mouse–brain–testis quartet, representing developmental factor (internal branch length γ_D) and evolutionary factor (internal branch length γ_E) of expression divergences, as well as independent divergences factors (external branch length a–d). (B) γ_D and γ_E combinations of human with other eight amniotes’ brain and testis based on pairwise expression divergence calculated by Pearson distance measure (numbered from recently diverged species to remotely diverged species).

Availability – TreeExp is released under the GPL v3 open source license, and its current stable version 1.0 is freely available at the Github developer site (https://github.com/hr1912/TreeExp).