This github repository contains the code use to perform the analyses and generate the figures associated with the manuscript titled "Evolutionary diversification of ancestral genes across vertebrates and insects" by Federica Mantica and Manuel Irimia (submitted for publication).
Vertebrates and insects diverged approximately 700 million years ago, and yet they retain a large core of conserved genes from their last common ancestor. These ancient genes likely present strong evolutionary constraints, which limit their overall sequence and expression divergence. However, evolutionary constraints can greatly vary across ancestral gene families. In few cases, sequence and expression changes resulting from looser constraints mediate functional evolution, as it has been demonstrated for many paralogous genes in closely related species. However, overall patterns of sequence and expression divergence and their potential functional outcome have never been explored in a genome-wide manner across large evolutionary distances in animals. In this study, we focus on approximately 7,000 highly conserved genes shared between vertebrates and insects, investigating global patterns of molecular diversification driven by changes in sequence and expression profiles. We identified molecular features generally linked to higher or lower diversification rates, together with gene groups with similar diversification profiles in both clades. However, we also discovered that some genes underwent differential diversification during vertebrate and insect evolution, potentially contributing to the emergence of unique phenotypes in each clade.
This folder contains 4 subfolders, each containing a different snakemake pipeline and relative files.
This folder contains snakemake pipeline (i.e., Snakefile) used to run the majority of computational analyses, together with the relative configuration file (config.yml) and a file with the parameters needed for cluster job submission (cluster.json). All relevant scripts can be found in the bin subfolder. The Snakefile includes rules to:
- Compute the relative expression across tissues for all the bilaterian-conserved, protein-coding genes of the 16 vertebrates and insect species included in our dataset.
- Compute all pairwise sequence similarities between all possible pairs of genes (from different species) in an orthogroup.
- Compute all pairwise expression similarities between all possible pairs of genes (from different species) in an orthogroup, starting from their relative expression across tissues.
This folder contains snakemake pipeline (i.e., Snakefile) used to run the majority of computational analyses, together with the relative configuration file (config.yml) and a file with the parameters needed for cluster job submission (cluster.json). All relevant scripts can be found in the bin subfolder. The Snakefile includes rules to:
- Compute average protein sequence similarities for each gene orthogroups, starting from all the all species-pairwise similarities between its representative orthologs.
- Compute pairwise and average expression similarities for each gene orthogroups, starting from the relative expression across tissues of all its representative orthologs.
- Define groups containing 500 most and least conserved gene orthogroups in terms of sequence or expression similarities between either vertebrates or insects.
- Generate inputs for GO enrichments of common lowly or highly diversified genes (see Fig.4 from Figures/All_Figures.Rmd).
- NB: These rules are also use to generate the corresponding files upon all the alternative setup scenarios (see Analyses/3_ALTERNATIVE_SEQ_EXPR_METRICS and Figure/Alternative_setups_Figures.Rmd).
This folder contains snakemake pipeline (i.e., Snakefile) used to run the majority of computational analyses, together with the relative configuration file (config.yml) and a file with the parameters needed for cluster job submission (cluster.json). All relevant scripts can be found in the bin subfolder. The Snakefile includes rules to:
- Compute z-scores of the average sequence or expression similarity per orthogroup and clade computed in Analyses/2_PARALOGOUS_SETS_SELECTION.
- Select all extra paralogous sets (BA-seq, BD-seq, BA-expr, BD-exr) based on the most extreme similarity values across orthogroups: the highest for BA sets (Best-Ancestral) and the lowest for BD sets (Best-Divergent).
- Define vertebrate housekeeping genes.
This folder contains snakemake pipeline a (i.e., Snakefile) used to run the majority of computational analyses, together with the relative configuration file (config.yml) and a file with the parameters needed for cluster job submission (cluster.json). All relevant scripts can be found in the bin subfolder. The Snakefile includes rules to:
- Compute all pairwise expression correlations (spearman's rho) between all possible pairs of genes (from different species) in an orthogroup, starting from their relative expression across tissues.
- Compute all pairwise expression distances (euclidean distance) between all possible pairs of genes (from different species) in an orthogroup, starting from their relative expression across tissues.
- Compute all pairwise sequence similarities between all possible pairs of genes (from different species) in an orthogroup, directly using values from blosum62.
- Compute all pairwise sequence similarities between all possible pairs of genes (from different species) in an orthogroup, directly using values from blosum45.
- Compute all pairwise sequence similarities between all possible pairs of genes (from different species) in an orthogroup, as in the main approach (see Analyses/0_ALL_PAIRWISE_SIMILARITIES) but removing leading/trailing gaps from the alignments.
- Compute all pairwise expression similarities between all possible pairs of genes (from different species) in an orthogroup, starting from their relative expression across tissues computed from summed paralogs expression.
- Compute the average phastCons across the coding sequence of all human genes.
This folder contains snakemake pipeline a (i.e., Snakefile) used to run the majority of computational analyses, together with the relative configuration file (config.yml) and a file with the parameters needed for cluster job submission (cluster.json). All relevant scripts can be found in the bin subfolder. The Snakefile includes rules to:
- Generate multiple alignments of all the genes included in the considered orthogroups.
- Build gene trees starting from these alignments.
- Parse the gene trees to date the origin of all paralogs through a species-overal approach.
This folder contains two Rmarkdown files used to generate the majority of the figure panels associated with the publication, and perform very few of the less demanding computational analyses.
The code to generate the following figures is available in All_Figures.Rmd.
- Figure 1: Framework overview and definition of sequence and expression similarities.
- Figure 2: Correlation of sequence and expression similarities between and within clades.
- Figure 3: Characterization of fast and slow evolving genes.
- Figure 4: Functional categories with common molecular diversification patterns between clades.
- Figure 5: Functional categories with molecular diversification biases between clades.
- Supplementary Figure 1: Schematics for computation of sequence/expression similarity and definition of extra 1:1 orthogroup sets.
- Supplementary Figure 2: GO enrichments and GSEA performed with fruit fly based GO annotations.
- Supplementary Figure 3: Deltas of sequence and expression similarities between vertebrates and insects.
- Supplementary Figure 4: Comparison between alternative measures of sequence conservation.
- Supplementary Figure 5: Comparison between sequence similarities computation methods.
- Supplementary Figure 9: Comparison of sequence similarities computed upon different phylogenetic setups.
- Supplementary Figure 10: Influence of paralog number and paralog origin on sequence similarities.
- Supplementary Figure 11: Comparison between alternative measures of expression conservation.
The code to generate the following figures is available in Alternative_setups_Figures.Rmd.
- Supplementary Figure 6: Key results repeated by computing sequence similarities with the blosum62 computation method.
- Supplementary Figure 7: Key results repeated by computing sequence similarities with the blosum45 computation method.
- Supplementary Figure 8: Key results repeated by computing sequence similarities not considering leading and trailing gaps.
- Supplementary Figure 12: Key results repeated by computing expression similarities from summed paralog expression.
- Supplementary Figures 13-16: Key results repeated with extra paralogous sets (BA-seq, BD-seq, BA-expr, BD-expr).