Male Linked Genomic Region Determines Sex in Dioecious Amaranthus palmeri

Abstract

Dioecy, the separation of reproductive organs on different individuals, has evolved repeatedly in different plant families. Several evolutionary paths to dioecy have been suggested, but the mechanisms behind sex determination is not well understood. The diploid dioecious Amaranthus palmeri represents a well-suited model system to study sex determination in plants. Despite the agricultural importance of the species, the genetic control and evolutionary state of dioecy in A. palmeri is currently unknown. Early cytogenetic experiments did not identify heteromorphic chromosomes. Here, we used whole-genome sequencing of male and female pools from 2 independent populations to elucidate the genetic control of dioecy in A. palmeri. Read alignment to a close monoecious relative and allele frequency comparisons between male and female pools did not reveal significant sex-linked genes. Consequently, we employed an alignment-free k-mer comparison which enabled us to identify a large number of male-specific k-mers. We assembled male-specific contigs comprising a total of almost 2 Mb sequence, proposing a XY sex-determination system in the species. We were able to identify the potential Y chromosome in the A. palmeri draft genome sequence as 90% of our male-specific sequence aligned to a single scaffold. Based on our findings, we suggest an intermediate evolutionary state of dioecy with a young Y chromosome in A. palmeri. Our findings give insight into the evolution of sex chromosomes in plants and may help to develop sustainable strategies for weed management.

Keywords: Amaranthus; dioecy; invasive weed; sex chromosome.

Figure 1.

Differences in allele frequencies between male and female pools of the California population along the genome, relative to the A. hypochondiracus reference. Positive values would represent an increased frequency of the male allele, while negative an increased frequency of the female frequency. Red and blue lines represent 95% and 99% confidence intervals for frequency outliers.

Figure 2.

Comparison of the abundances of k-mers from the male and female sequence read pools of the Californian A. palmeri population. The color scale indicates the number distinct k-mers represented by 1 dot. The black line displays the null expectation for k-mer frequency in males and females, corrected for the number of individuals present in the male (n = 35) and female (n = 32) pool.

Figure 3.

Alignment of male-specific sequences to Scaffold 20 of the draft genome sequence of a male A. palmeri. (A) Alignment of assembled male-specific regions to draft genome sequence. (B) Mapping depth of male (blue) and female (red) specific reads to the draft sequence. Showing sites with depth ≥ 50X depth.