Supporting data for "An X-linked sex determination mechanism in cannabis and hop"

Genome assembly and annotations 

For the hop assemblies (Humulus lupulus) both haplotypes are labeled HAP1 or HAP2 for all files. For the cannabis assemblies (Cannabis sativa), please note that the gene annotation nomenclature changed so that HAP1 is now "a" and HAP2 is "b". For all XY males, the Y chromosome is in HAP1 and the X in HAP2, and these are named accordlying within the files. Coordinates for the male-specific region of the Y vs the pseudoautosomal region are found in the supplements of the manucript. The genome assemblies have also been deposited on NCBI; the versions provided here are in the exact form used in the analyses that support this manuscript.

Y-mer fastas

The Cannabis_only_male_kmers.txt.fasta and Humulus_only_male_kmers.txt.fasta are lists of male-specific 21-mers converted to fasta format, with each k-mer being given an arbitrary number from 1, 2, ... N in the header. 

Centromeres

Visualizations used for putative centromere identification are found in centromere_locations.tar.gz. For all genotypes presented in this manuscript, both sex chromosomes have been deposited. For the autosomes, only HAP1 is deposited here.

Phylogeny files

The Rosales_825_singlecopy_targets.fa file contains the single copy genes identified across Rosales that were used as targets for HybPiper. The hybpiper_results.xlsx file contains the stats and sequence lengths recovered for each sample used to build the species tree. species_tree.tar.gz, plastome_iqtree.zip, and BEAST.zip contain outputs for generating the species tree, plastome tree, and BEAST analyses and the contentets are further broken down below:

BEAST.zip    .xml = BEAST input file    .trees = tree replicates    .tree = highest probability tree

plastome_iqtree.zip    .fa = multiple sequence alignment used as input for IQ-TREE    - remainder of files are IQ-TREE output results, see https://iqtree.github.io/

species_tree.tar.gz    supercontig = directory with target gene assemblies from HybPiper    mafft = multiple sequence alignments for all target genes    trimal = trimmed multiple sequence alignments for all target genes    iqtree = IQ-TREE results output for separate ML gene tree analyses for all target genes

Gene trees

The OrthoGroups identified in OrthoFinder to build the sex chromosome gene trees are found in Orthofinder.txt The final gene trees used to visualize the timing of sex-linkage are found within gene_trees.tar.gz

Gene expression

The gene_count_matrix.csv and pheno.csv were used to as input for DESeq2 in R to run differential gene expression analyses. The following files are results of this analysis: 1) results_cannabis_leaf_femaleVegetativeToFlowering.csv: comparing leaves within females before and during flowering. 2) results_cannabis_meristem_maleL2tomaleL4.csv: comparing apical meristem tissue in males before flowering (L2) and after (L4). 3) results_cannabis_meristem_femaleL9tomaleL4.csv: comparing apical meristems between the sexes at flowering (L9 in females, L2 in males). 

Molecular evolution

Out files from PAML are found in paml_results.tar.gz. This also includes a key that links the results to gene names. Output from the genome-wide McDonald Kreitman test are found in MKT_results.csv. The raw output from pixy for pi within females of hop is in hop_females_pi_10kwindows.txt. The raw output from pixy for the Fst Outlier analyses in cannabis are within cannabis_chemotypes_fst_100kbwindows.txt and cannabis_femalevsmonoecious_fst_100kbwindows.txt. Results for from KaKs Calculator for one-to-one XY gametologs for each male genome (both hop and cannabis) are found within Ks_individually.xlsx.

Cannabis backcross

The floral phenotypes for sex are found within cannabis_backcross_pheno.xlsx