In turn, this implies that only the Xp end is pseudoautoso- mal. Including the probe genes, the S. 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. These BAC sequences were therefore assembled into a scaffold Additional file 1: 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. When aligning X-linked Blavet et al. Sequencing BACs should help identify genes with low expression levels, some of which were prob- ably missed by previous studies, because most sex-linked genes identified so far in S. Ortho- logs of all 10 genes have been identified in S. Sex chromosomes, Sex-linked genes, Plant, BAC, RNA-seq, Gene loss, Y degeneration, Silene latifolia,Silene vulgaris Of only a handful of plant sex chromosome systems that have been investigated at the molecular level, the XY chromosome system of Silene latifolia is one of the best- studied [1, 2].
A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. We ana- lysed the gene densities of the X-linked, Y-linked and S. When aligning X-linked Blavet et al. Recently, however, three studies used RNA-seq to identify hundreds of S. A handful of BACs from the S. These sequences are clearly not pseudoautosomal, so we infer that the S. The estimate is similar when we use BAC-located genes that have S. In contrast, the S. An alternative approach to dis- covering new sex-linked genes is to sequence BAC clones from the sex chromosomes. The results of our re-evaluation suggests that gene loss may have been underestimated based on RNA-seq alone, although more work is still needed to get a precise esti- mate of Y gene loss in S. To directly evaluate the extent of gene losses from the S. This suggests that failure to ascertain genes as sex-linked when they have low expression affects inferences using RNA-seq, in addition to absence of expression of. Only half of these genes were identified as sex-linked by any of the previous studies Table 2. Sequencing the complete S. 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. Our results therefore suggest that we have reached the end of the Xq arm in S. Their map locations in S. Gene densities in S. Tables S1 and S2. The number of sex-linked genes in S. In contrast, Blast searching found only two new Y- vulgaris gene pairs Table 1 and Additional file 3: Moreover, the RNA-seq studies focused on RNA from only one tissue flower buds and any sex-linked genes not expressed in flower buds, or expressed at low levels, must be missed [6—8]. In turn, this implies that only the Xp end is pseudoautoso- mal. Tables S1 and S2 , revealing a total of genes, 78 of which are from S. These BAC sequences were therefore assembled into a scaffold Additional file 1: An all-against-all Blast search among the BAC-located genes revealed conserved blocks of several tens of kb around each probe gene in the S. Results and discussion Obtaining S.
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