Scripts and analyses for R. hastatulus XYY male genome paper

Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution in Rumex hastatulus. Sacchi, Humphries et al. 2024

Ks Plots

• input: anchorwave dot plots, Ks output from coge
• comparing haplotype A and B assemblies of a rumex hastatulus xyy male genome

Genespace

• synteny plots and pangene annotations

Gene loss

• tabulating gametologs present and absent between X and Y

NCmaleHaplotypeTEs

Purpose: understand where TEs are in the genome

Specific goals for this file:

• Windows MAKER and EDTA data (summarizes along chromosomes)
• For the X and Y chromosomes, categorizes areas based on when they lost recombination: Pseudoautosomal Regions (PAR), old sex-linked, and new sex-linked
• Visualises the chromosomal "landscape": proportion of 1Mb windows occupied by genes/TEs
• Visualises the fraction of sex chromosome regions occupied by TEs

RelaxedSelection

Purpose: look for signs of TE insertion/retention near genes

Specific goals for this file:

• Combine output files from =bedtools coverage= (1kb upstream, 1kb downstream, introns, exons)
• Visualise the chromosomal landscape of TEs near 1:1:1 orthologous genes
• Visualise the fraction of genes with nearby TE insertions, categorized by chromosomal location
• Per gene, understand whether it's more likely to be near TEs if on the X or Ys