Code, data and plots associated with "Comparative genomics of the dynamics of chromosome evolution in Lepidoptera"

Charlotte Wright, Blaxter lab, Tree of Life, Wellcome Sanger Institute

This repository contains all of the source code - that together with the supplementary files available on Zenodo - are required to reproduce all figures presented in the manuscript.

A copy of this GitHub repository has been accessioned in Zenodo at https://doi.org/10.5281/zenodo.10373060.

Each subdirectory contains a README with descriptions of the files it contains.

The scripts were writted using R version 4.1.0 and Python version 3.9.9.

The scripts require the following R packages: phytools, dplyr, ggplot2, treeio, aplot, ggtree, tidyverse, patchwork, scales, ggpubr, reshape2, ggrepel.

1_genomes

Code and files related to the first results section ("Over two hundred chromosomally-complete lepidopteran genomes").

2_merian_elements

Code and files related to the second results section ("Thirty-two ancestral lepidopteran linkage groups").

3_interchromosomal_rearrangements

Code and files related to the third results section ("Distribution of fusion and fission events across Lepidoptera").

4_highly_rearranged_genomes

Code and files related to the fourth results section ("Extensive rearrangemets in eight independent lineages").

5_sequence_contents

Code and files related to the fifth results section ("Understanding biases in chromosomal fusions in Lepidoptera").

6_fusion_consequences

Code and files related to the sixth results section ("Consequences of fusions").

sup_tables

TSV files containing Supplementary Tables 1-11.

repeat_annotation_files

FASTA files containing the repeat libraries for each species.

gene_annotation_files

FASTA files containing the gene annotations for each species.