A new plant sex-linked gene with high sequence diversity and possible introgression of the X copy

Abstract

We describe patterns of DNA sequence diversity in a newly identified sex-linked gene, SlX9/SlY9, in Silene latifolia (Caryophyllaceae). The copies on both sex chromosomes seem to be functional, and each maps close to the respective X- and Y-linked copy of another sex-linked gene pair, SlCypX/SlCypY. The Y-linked copy has low diversity, similar to what has been found for several other Y-linked genes in S. latifolia, and consistent with the theoretical expectations of hitch-hiking processes occurring on a non-recombining chromosome. However, SlX9 has higher diversity than other genes on the S. latifolia X chromosome. We evaluate the hypothesis of introgression from the closely related species S. dioica as an explanation for the high sequence diversity observed.

Figure 1

Schematic view of the alignment of SlX9, SdX9, SlY9 and Sv9. Sizes of introns and exons are not drawn to scale. Both X-linked intronic variants are shown (SlX9_hap_1 and SlX9_hap_2). Thick lines around exons: sequences available for at least one individual. (The original S. latifolia cDNA clone from which the gene was identified contained the whole open reading frame; sizes of exons for which we do not have complete sequences are drawn based on the assumption that exon sizes are the same as for the cDNA.) Note: sequences used in the diversity studies of SlX9, SdX9 and SlY9 only cover parts of the gene sequences, as indicated.

Figure 2

Neighbour-joining tree of SlX9 and SdX9. The tree was constructed in MEGA, based on all sites, with complete deletion. Bootstrap support values >70% are shown at the branches. The S. latifolia male individuals (blue shading) are identified by their numbers in Table 1, and the S. dioica plants are identified by their populations of origin when known.