Sex-determination and sex chromosomes are shared across the radiation of dioecious Nepenthes pitcher plants

Abstract

Plants with separate sexes (dioecy) represent a minority but dioecy has evolved multiple times independently in plants. Our understanding of sex determination systems in plants and of the ecological factors and molecular changes associated with the evolution of dioecy remain limited. Here, we study the sex-determination system in dioecious plants that lack heteromorphic sex chromosomes and are not amenable to controlled breeding: Nepenthes pitcher plants. We genotyped wild populations of flowering males and females of three Nepenthes taxa using ddRAD-seq, and sequenced a male inflorescence transcriptome. We developed a novel statistical tool (privacy rarefaction) to distinguish true sex-specificity from stochastic noise in high-throughput sequencing data. Our results support XY-systems in all three Nepenthes taxa and in Silene latifolia which was used as a positive control for its known XY-system. The male-specific region of the Y chromosome showed little conservation among the three Nepenthes taxa, except for the essential pollen development gene DYT1 which was also male-specific in additional taxa. Hence, this homomorphic XY sex-determination system likely has a unique origin older than the crown of the genus Nepenthes at c. 17.7 My. In addition to the characterisation of the previously unknown sex chromosomes of Nepenthes, our work contributes an innovative, highly sensitive statistical method to efficiently detect sex-specific genomic regions in wild populations in general.