Our support of evolutionary theory depends greatly on the empirical ubiquity of its effects. Although old sex chromosomes in animal systems are well characterized, the young sex chromosomes of plants are sparsely investigated. Here, we determine the amount of chromosomal degeneration observed in the XYY chromosomal system of the dioecious annual plant Rumex hastatulus. Using both RNAseq and genomic Paired-End data, we observe both deletion and silencing of single copy hemizygous genes on the Y chromosomes, where more genes are deleted than silenced. Genes in high copy number are enriched for copies of genes from the chloroplast genome. We conclude that using transcriptome and genome data together allow for the ascertainment of the most complete set of sex-linked and hemizygous genes.