Supplementary Data: Genomic insights into the sex-linked region in Phytelephas aequatorialis.

This repository contains the Supplementary Data for the article entitled: "Genomic insights into sex-linked regions and dioecy in the ivory palm (Phytelephas aequatorialis)". It includes five figures and ten tables. Figure S1: Relatedness (A) and genetic structure (B) of Phytelephas aequatorialis studied individual from the population (Pop-ExC). Figure S2: Synteny maps among the three publicly available genomes: P. dactylifera BC4, Chamaerops humilis CHM, and Elaeis guineensis EGP. The sex-linked region identified in Phytelephas is conserved across the three genomes and is highlighted in green. Figure S3: Sex linkage XY (blue) and autosomal (red) posterior probabilities for each gene mapped on the reference P. dactylifera (BC4) genome. Figure S4: Distribution of the total number of SNPs and sex-fixed SNPs for each gene analyzed by SDpop using Phytelephas exon capture data, mapped across the chromosomes of the P. dactylifera (BC4) reference genome. Figure S5: Agarose gel electrophoresis of SNP-based markers designed from three candidate high-confidence sex-linked (HCSL) genes: (A) LOC103722625 (Dimet) (B) LOC103720606 (POLY) (C) LOC103722617 (SKP) showing PCR amplification products exclusively in males and not in females thereby enabling sex discrimination among Phytelephas individuals. Two autosomal markers were included as controls: (D) LOC103703289 (PEThyr) (E) LOC103696848 (Pestr) exhibiting PCR amplification products in individuals of both sexes. Phytelephas samples used are from VSLG population (Supplementary Data Table S1). Individuals 1–11 are females (individuals in order are: 1: Pa13, 2: Pa28, 3: Pa39, 4: Pa50, 5: Pa51, 6: Pa56, 7: Pa85, 8: Pa86, 9: Pa7, 10: Pa21, and 11: Pa25), and individuals 12–22 are males (individuals in order are: 12: Pa11, 13: Pa52, 14: Pa88, 15: Pa89, 16: Pa124, 17: Pa145, 18: Pa189, 19: Pa8, 20: Pa106, and 21: Pa12). Number 22 stands for the negative control. The DNA ladder is 100 bp. Table S1: List of analyzed Phytelephas aequatorialis samples from Ecuador. F and M denote female and male individuals, respectively. VSLG indicates samples used exclusively for validation of selected candidate sex-linked genes, whereas Pop-ExC refers to samples used for detecting sex-linked SNPs and genes. Table S2 : Classification criteria for sex-linked genes bases on SDpop, synonymous divergence (dS) , and iKISS Evidence. HCSL stands for high-confidence sex-linked, PSL for probably sex-linked, NSL for not sex-linked, and NA not applicable. Table S3: Measurements of DNA concentration and quality by nanodrop of the Phytelephas samples used for the validation of three selected candidate sex-linked genes. F and M stands for female and male individuals, respectively. Primers sequences of the autosomal and high-confidence sex-linked genes along with their expected sequence size amplification and the amplification presence (yes) or absence (no) are represented by green and red color for each individual, respectively. Table S4: Exon capture data evaluation and summary. Table S5: Pairwise relatedness estimates between Phytelephas individuals.Values around 0.5 indicate identical samples, ca.0.25 first degree relatives, and lower values reflect decreasing relatedness. The columns N_AaAa and N_AAaa represent the number of sites where both individuals are heterozygous and the number of sites where they are opposite homozygotes, respectively. Table S6: Optimized proportions and the Bayesian Information Criterion (BIC) of SDpop models XY, ZW, and No sex chromosome. Table S7: Genomic coordinates, functional annotation, and sex-linkage or autosomal-linkage of Phytelephas aequatorialis genes mapped to the Phoenix dactylifera 'Barhee' BC4 reference genome. Gene IDs were inferred from the reference genome annotation of P. dactylifera (BC4). HCSL stands for high-confidence sex-linked genes, PSL for probably sex-linked genes, NSL for not sex-linked genes, and synonymous divergence (dS). XY_prior and noprior_autosomal values refer to the posterior probabilities for sex-linked and autosomal calculated by SDpop, respectively. Table S8: Calculated heterozygosity per gene. Table S9: Sex-linked contigs identified by iKISS and their genomic location and gene correspondence in the Phoenix dactylifera reference genome (BC4). Table S10: Total number of SNPs detected for each gene and the number of sex fixed SNPs.