ZW sex chromosome structure in Amborella trichopoda

Abstract

Sex chromosomes have evolved hundreds of times across the flowering plant tree of life; their recent origins in some members of this clade can shed light on the early consequences of suppressed recombination, a crucial step in sex chromosome evolution. Amborella trichopoda, the sole species of a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly contiguous assemblies of the Z and W chromosomes. We identify a ~3-megabase sex-determination region (SDR) captured in two strata that includes a ~300-kilobase inversion that is enriched with repetitive sequences and contains a homologue of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, such as repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is derived in Amborella and the sex chromosome pair has not significantly degenerated.

Fig. 1. Amborella and its genome structure.

a,b, Female (a) and male (b) Amborella flowers. c,d, The Amborella genome (c) and chromosome 9 (Chr09, d) are typical of flowering plants: gene-rich chromosome arms and repeat-dense, large pericentromeric regions. Gene positions were extracted from the protein-coding gene annotations, repeats from EDTA and exact matches of 536,985 female-specific k-mers (W-mers). Syntenic mapping was calculated using AnchorWave and processed using SyRI, only plotting inversions, insertions and deletions >10 kb. Visualization of synteny was accomplished with GENESPACE and sliding windows with gscTools. The sex-determination region of Chr09 with W-mers is highlighted in d. All chromosomes in haplotype 1 and all but four in haplotype 2 have both left and right telomeres in the assembly (flagged with red *), defined as a region of ≥150 bp made up of ≥90% plant telomere k-mers (CCCGAAA, CCCTAAA, RC) separated by no more than 100 bp. CDS, coding sequence.

Fig. 2. Sex chromosome location in Amborella.

a,b, W-mer coverage in the SDR (a) and HZR (b) using four different sampling strategies for isolates. c,d, SDR (c) and HZR (d) location and their proximity to the Chr09 centromere. Ty3 elements (dark blue) are often enriched in the pericentromeric regions of plants and correspond to the low-complexity block of tandem repeat arrays (grey shading) that also contain the high-complexity centromeric block, indicated by the satellite monomer density (light blue). Gene density (orange) also predictably decreases near the pericentromeric region. The SDR (red) is notably outside of the putative pericentromeric region and distant from the centromere. DTH, PIF Harbinger terminal inverted repeat transposon; DTA, hAT terminal inverted repeat transposon; DTM, Mutator terminal inverted repeat transposon.

Fig. 3. Molecular evolution of the Amborella sex chromosomes.

a, Evidence for two strata. For Ks, points above 0.06 were excluded. b,c, The repeat landscapes of the Amborella haplotypes 1 (b) and 2 (c) indicate similar patterns of expansion and minimal evidence of recent TE proliferation. Relative time was determined using the Kimura substitution level, with lower values closer to 0 representing more recent events and higher values approaching 40 representing older events. DTT, Tc1 Mariner terminal inverted repeat transposon; DTC, CACTA terminal inverted repeat transposon; LINE, long interspersed nuclear element; MITE miniature inverted-repeat transposable element.