Evidence of Recombination Suppression Blocks on the Y Chromosome of Date Palm (Phoenix dactylifera)

Abstract

The genus Phoenix includes the fruit producing date palm tree among 14 species that are all dioecious. Females produce the fruit that are high in sugar content and used in multiple countries ranging from North Africa to South Asia, especially from the Phoenix dactylifera, Phoenix sylvestris, and Phoenix canariensis species. While females produce the fruit, understanding of the genetic basis of sex control only began recently. Through genus-wide sequencing of males and females we recently identified three genes that are conserved in all males and absent in all females of the genus and confirmed an XY sex chromosome system. While our previous study focused on conservation of male-specific sequences at the genus-level, it would be of interest to better understand the spread of male-specific sequences away from the core conserved male genes on the Y chromosome during speciation. To this end, we enumerated male-specific 16 bp sequences using three male/female pairs from the western subpopulation of date palm and documented the density of these sequences in contigs of a phased date palm genome assembly. Here we show that male specific sequences in the date palm Y chromosome have likely spread in defined events that appear as blocks of varying density with significant changes in density between them. Collinearity of genes in these blocks with oil palm shows high synteny with chromosome 10 between megabase 15 and 23 and reveals that large sections of the date palm Y chromosome have maintained the ancestral structure even as recombination has stopped between X and Y.

Keywords: Y chromosome strata; date palm; phased sequencing; recombination suppression; sex determination.

FIGURE 1

A proposed step-wise model of evolution in the Phoenix (including Date Palm) sex-determination region compared with the two-gene model for sex determination (adapted from Charlesworth et al., 2005). Two genes are deleted from Proto-X (white pentagons with red x), a later rearrangement (gray triangles) relocates multiple genes and a final duplication and translocation of a gene (pentagon with blue lines) with potential female-suppressing characteristics (LOG^Su) creates males and females. Gene abbreviations and gene IDs MYB: LOC105059740, MAP: LOC105059742, CDA: LOC105059743, MYB-A: LOC105059783, GPAT (GPAT3): LOC105059961, TIF2: LOC105059784, CYP (CYP703): LOC105059962, BAG: LOC105059785. Cytidine deaminase (CDA) was the only gene with male-conserved kmers present in both male and female individuals.

FIGURE 2

Workflow used in this study. (A) A phased male date palm genome was used as reference. While Y specific contigs are clear by the absence of a second allele, which alleles are X or Y linked for the remainder is unclear. (B) Three male/female pairs of the western date palm subpopulation were used to identify male-specific 16 bp k-mers. (C) Contigs with one allele showing higher density of male-specific k-mers were selected as Y-linked. (D) The density of male specific k-mers was noted and (E) groups of contigs ordered by blocks of shared k-mer density (KDB). (F) The ordering was compared to oil palm and conserved ordering or rearrangements noted.

FIGURE 3

The ratio of male-specific kmers between both haplotypes of the phased Deglet Noor male assembly. Most contigs did not show a difference in the numbers of male-specific kmers matching each contig suggesting a lack of phasing separation or that the kmers are not truly Y chromosome specific. Contigs with greater than 2.5X difference in numbers of male-specific kmers between the two phases were considered for future analysis.

FIGURE 4

A plot of male-specific kmer density in contigs with significant differences between each assembled haplotype for three date palm male/female combinations. The density on the haplotype with the most kmers is plotted as base pairs of sequence per male-specific kmer. To identify regions of significant changes in the density, the running average of the leading five to trailing five contigs male-specific kmer density is plotted.

FIGURE 5

Alignment of the date palm male-rich kmer contigs to the current oil palm reference genome from kmer density blocks 1 and 2 (A) and all with significant alignment against the new oil palm assembly (B). For panel (A) Rectangles at the top represent date palm contigs with high similarity (light blue) or no similarity with any oil palm transcript (white). Black rectangles represent contigs with similarity to other oil palm chromosomes The smaller rectangles at the bottom represent oil palm genes and the numbers indicate their predicted position within the scaffold. Homology between date palm contigs (top) and oil palm (bottom) is represented by light-gray rectangles. The orange block represents chromosome 10 and the numbers indicate approximate locations of the transcripts with homology to date palm contigs. For panel (B) the rectangles represent date palm contigs with high similarity with oil palm chromosome 10 (GeneBank accession GK000085.1). Large regions of homology between date palm contigs and oil palm are represented by gray trapezoids. The numbers below each contig indicate their approximate location in chromosome 10. The dark blue rectangles represent contigs within kmer density block 1 (KDB1). Lighter blue, green and yellow rectangles represent contigs within KDB2, KDB3, and KDB4, respectively. Asterisks appear next to dpB2Y alignments that split across the region. KDB, Kmer Density Block. FEN: LOC105059737; AARF: LOC105059738; GPI: LOC105059739; MYB: LOC105059740; MAP: LOC105059742; CDA: LOC105059743; GDLS: LOC105059768; DBP: LOC105059770; BEACH: LOC105059782; MYB-A: LOC105059783; GPAT: LOC105059961; TIF2: LOC105059784; CYP: LOC105059962; BAG: LOC105059785. Gene 61: LOC105059787; Gene 62: LOC105059788; Gene 63: LOC105059789; Gene 69: LOC105059792; Gene 74:LOC105059800; Gene 75: LOC105059801; Gene 77: LOC105059803; Gene 78: LOC105059804; Gene 79: LOC105059805; Gene 81: LOC105059809; Gene 86: LOC105059813; Gene 87: LOC105059814; Gene 92: LOC105059820.