Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Abstract

BackgroundSilene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes.ResultsHere we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome.ConclusionsOur BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1698-7) contains supplementary material, which is available to authorized users.

Early sex-chromosome evolution in the diploid dioecious plantMercurialis annua

“…annua, pseudogenisation of its Y alleles (approximately 36%) was similar to that found in other species, such as R. hastatulus (28%, Hough, et al 2014) and S. latifilia (14.5%-30%, Bergero, Qiu, et al 2015;Blavet, et al 2015). This pattern points to an earlier disruption of gene expression of Y-linked genes compared to their pseudogenisation, as found in both S.…”

“…For instance, recent RNAseq studies have found that up to 28% and 14.5% of genes on the Y-chromosome have probably been lost in Rumex hastatulus (Hough, et al 2014) and S. latifilia (Bergero and Charlesworth 2011;Chibalina and Filatov 2011;Bergero, Qiu, et al 2015), respectively. Studies of S. latifolia using BACs suggest a rate of Y-linked gene loss of 30% (Blavet, et al 2015), and analysis based on a partially sequenced genome points to the loss of expression of as many as 45% of Y-linked genes and pseudogenisation through premature stop codons of 23% (Papadopulos, et al 2015).…”

A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

“…However, deletion sizes in A. thaliana chromosomes are restricted by the presence of essential genes at a high density, including genes necessary for pollen functioning (large deletions cannot be transmitted to the progeny generation 62 ), and possibly genes where two copies are required for zygote viability. In contrast, non-recombining regions such as the S. latifolia Y chromosome are predicted to accumulate repetitive sequences 63 and the Y is indeed much larger than the X chromosome 64 , and there is also direct evidence for the presence of repetitive sequences 65 66 67 . It may thus have a low density of essential genes, and there is evidence for loss of some genes 25 .…”

RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region

“…The gene density in S. vulgaris has been estimated from sequenced BAC clones to be about 74 genes/Mb (Blavet et al . ), and, assuming a low recombination rate of one cM per Mb, this would imply that the added regions could include at least a 1000 genes.…”