DOI: 10.5061/dryad.v41ns1rsm
title: Supporting data for: Gene-rich UV sex chromosomes harbor conserved regulators of sexual development (Carey et al., 2021)

description: Non-recombining sex chromosomes, like the mammalian Y, often lose genes
 and accumulate transposable elements, a process termed degeneration. The
 correlation between suppressed recombination and degeneration is clear in
 animal XY systems, but the absence of recombination is confounded with
 other asymmetries between the X and Y. In contrast, UV sex chromosomes,
 like those found in bryophytes, experience symmetrical population genetic
 conditions. Here we generate and use nearly gapless female and male
 chromosome-scale reference genomes of the moss Ceratodon purpureus to test
 for degeneration in the bryophyte UV sex chromosome system. We show the
 moss sex chromosomes evolved over 300 million years ago and expanded via
 two chromosomal fusions. Although the sex chromosomes show signs of weaker
 purifying selection than autosomes, we find suppressed recombination alone
 is insufficient to drive gene loss on sex-specific chromosomes. Instead,
 the U and V sex chromosomes harbor thousands of broadly-expressed genes,
 including numerous key regulators of sexual development across land
 plants.
description: All methods can be found in the Material and Methods or
 Supplementary Materials and Methods sections of Carey et al.,
 2020.
description: novaseq_FASTQ_de_interlacer.pl -- splits paired-end
 Illumina NovaSeq data into forward and reverse files
 liverwort_trinity_assemblies.tar.gz -- contains all <em>de
 novo</em> Trinity assemblies for liverworts used in this
 study moss_trinity_assemblies.tar.gz -- contains all
 <em>de novo</em> Trinity assemblies for mosses used in this
 study all_pep_files_for_orthofinder.tar.gz -- all
 peptide files for all species used in the OrthoFinder run in this
 study Orthogroups.txt - all orthogroups identified by
 OrthoFinder clustering orthogroup_filter.pl -- perl
 script to filter orthogroups ("clusters") output by OrthoFinder
 for a minimum number of species all_cds.fa.gz and
 all_pep.fa.gz -- fasta files containing all cds and peptides,
 respectively, for all species combined to write fasta files for each
 Orthofinder gene cluster fasta_from_OrthoFinder.pl --
 perl script to write a separate fasta file for each Orthogroup
 ("cluster") output by OrthoFinder
 alignment_length_filter.pl -- perl script to filter fasta files
 by a user input minimum number of nucleotides or amino acids
 sexlinked_liverwort_alignments.tar.gz -- final, filtered cds
 alignments used to build gene trees of sex-linked genes in
 <em>Marchantia polymorpha</em> 
 sexlinked_moss_alignments.tar.gz -- final, filtered cds
 alignments used to build gene trees of sex-linked genes in
 <em>Ceratodon purpureus</em> 
 sexlinked_liverwort_trees.tar.gz -- RAxML gene trees with
 bootstrap support of sex-linked genes in <em>Marchantia polymorpha
 </em> sexlinked_moss_trees.tar.gz -- RAxML
 gene trees with bootstrap support of sex-linked genes in
 <em>Ceratodon purpureus</em> edlwtre2.pl
 -- perl script that roots gene trees and reduces isoforms of the same
 sample (within a clade) down to the longest isoform
 physco_outgroup.py -- python script that uses ETE3 to identify
 <em>C. purpureus</em> sex-linked genes and the closest
 <em>Physcomitrium patens</em> outgroup
 prune_tree.py -- python script that uses ETE3 to identify
 <em>C. purpureus</em> sex-linked genes and prune at the
 closest <em>Physcomitrium patens</em> outgroup. The script
 also randomly selects one isoform/homolog for each other species in the
 tree array_hash_extractor_fasta_unlock_tree_mod.pl --
 perl script that filters the original fasta file for those left after
 prune_tree.py paml_header_prep.pl -- perl script for
 prepping the headers in gene trees and fasta files for PAML
 paml_tree_prep.pl -- perl script for generating different
 labeled trees for the sex-linked genes evolving differently than
 autosomes for PAML paml_bash.sh -- bash script to run
 PAML on multiple genes and report the results of dN, dS, and dN/dS
 for <em>C. purpureus </em>sex-linked genes
 paml_AIC.pl -- perl script necessary to run PAML in
 paml_bash.sh array_hash_extractor_fasta_unlock_ks.pl
 -- perl script that searches for a user identified list of <em>C.
 purpureus</em> one-to-one orthologous UV genes across multiple
 alignments. The output is an individual alignment for each of the U and
 V-linked orthologous genes aln_to_axt.pl -- perl
 script that converts an alignment of one-to-one UV genes into axt format
 for KaKs Calculator ceratodon_genome_plots.R -- R
 script for generating gene tree plots, density plots, Ks on UV chromosome
 plot,  codon metrics and dN/dS plots, and gene expression
 heatmaps