Supporting data for: Gene-rich UV sex chromosomes harbor conserved regulators of sexual development (Carey et al., 2021)
novaseq_FASTQ_de_interlacer.pl -- splits paired-end Illumina NovaSeq data into forward and reverse files liverwort_trinity_assemblies.tar.gz -- contains all de novo Trinity assemblies for liverworts used in this study moss_trinity_assemblies.tar.gz -- contains all de novo 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 Marchantia polymorpha sexlinked_moss_alignments.tar.gz -- final, filtered cds alignments used to build gene trees of sex-linked genes in Ceratodon purpureus sexlinked_liverwort_trees.tar.gz -- RAxML gene trees with bootstrap support of sex-linked genes in Marchantia polymorpha sexlinked_moss_trees.tar.gz -- RAxML gene trees with bootstrap support of sex-linked genes in Ceratodon purpureus 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 C. purpureus sex-linked genes and the closest Physcomitrium patens outgroup prune_tree.py -- python script that uses ETE3 to identify C. purpureus sex-linked genes and prune at the closest Physcomitrium patens 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 C. purpureus 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 C. purpureus 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,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.,All methods can be found in the Material and Methods or Supplementary Materials and Methods sections of Carey et al., 2020.
Lipzen, Anna; Conrad, Roth; Schmutz, Jeremy; McBreen, Jordan; Shu, Shenqiang; Chen, Cindy; Healey, Adam; Daum, Chris; Jenkins, Jerry; Shenqiang, Avinash; Payton, Adam; Kollar, Leslie; Maumus, Florian; Lovell, John; Johnson, Matthew; Wang, Mei; Tiley, George; Wickett, Norman; Grimwood, Jane; McDaniel, Stuart; Barry, Kerrie; Huttunen, Sanna; Fernandez-Pozo, Noe; Landis, Jacob; Saski, Christopher; Carey, Sarah; Olsson, Sanna; Rensing, Stefan; Burleigh, Gordon (2020), "Supporting data for: Gene-rich UV sex chromosomes harbor conserved regulators of sexual development (Carey et al., 2021)", DRYAD, doi: 10.5061/dryad.v41ns1rsm