Code and metadata: Male linked genomic regions determine sex in dioecious Amaranthus palmeri

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.\textit{A. palmeri} represents a unique model system to study sex determination in plants, as dioecy is rare among successful colonizers.In addtion, \textit{A. palmeri} is one of the most troublesome weeds in the US and has evolved resistance to several herbicide classes and also successfully colonized other regions in the world. Early cytogenetic experiments did not identify heteromorphic chromosomes and the sex determining system in \textit{A. palmeri} has remained unknown.We used whole genome sequencing of male and female pools from two independent populations to elucidate the genetic control of dioecy in \textit{Amaranthus 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. Based on our findings we suggest an intermediate evolutionary state of dioecy in \textit{A. palmeri}. Our findings give insight into the evolution of sex chromosomes in plants and may help to develop sustainable strategies for weed management.