Gene loss from a plant sex chromosome system

Sex chromosomes have evolved independently in numerous animal and plant lineages. After recombination becomes suppressed between two homologous sex chromosomes, genes on the non-recombining Y chromosomes (and W chromosomes in ZW systems) undergo genetic degeneration, losing functions retained by their X- or Z-linked homologs, changing their expression, and becoming lost [1, 2]. Adaptive changes may also occur, both on the
non-recombining Y chromosome, to shut down expression of maladapted genes [3], and on the X chromosome (or the Z in ZW systems), which may evolve dosage compensation to increase low expression or compensate for poor protein function in the heterogametic sex [2, 4, 5]. Although empirical approaches to studying genetic degeneration have been developed for model species [3, 6], the onset and dynamics of these changes are still poorly understood, particularly in de novo evolving sex chromosomes. Sex chromosomes of some plants evolved much more recently than those of mammals, birds, and Drosophila [7–9], making them suitable for studying the early stages of genetic degeneration in
de novo evolving sex chromosomes. In plants, haploid selection should oppose gene loss from Y chromosomes, but recent work on sex chromosomes of two plant species has estimated that Y-linked transcripts are lacking for 10%–30% of
X-linked genes [10–12]. Here, we provide evidence that, in Silene latifolia, this largely involved losses of Y-linked genes, and not suppressed expression of
Y-linked alleles, or gene additions to the X chromosome. Our results also suggest that chromosomewide dosage compensation does not occur in this
plant.