So far, these observations were made in isolation from each other, and generally in different species, find more info which makes the construction of a hypothetical model difficult. Here we present for the first time a comprehensive analysis of sequence compo sition, gene and repeat content, chromatin structure and repeat transcription of the sex specific chromosome regions of the Z and W chromosomes of our biological model S. mansoni. Recombination repression has been described before in this region of interest. Our data, in relation to previous reports, allows the current models for the suite of events that led to sex chromo some differentiation in S. mansoni to be refined and could represent a general model for this process in spe cies with genetic sex determination of the Z/W type.

Z and W specific sequences Criscione et al. identified a region of 20 scaffolds in which recombination repression was observed and suggested that these are Z specific sequences. We indeed found a male/female sequence reads hit and/or qPCR ratio of 1. 5 for 13 of these scaffolds, indicating an overrepresentation in the male genome. However, seven scaffolds in this region showed no disequilibrium of hit counts and/or qPCR between males and females, that is, the sequences are not specific to the Z chromosome. In other words, recombination is repressed but the homologous sequences on the sister chromosomes are still present. We find at least two blocks of sequences that are shared between the Z and W chromosome located in the large region with recombination repression.

This result was confirmed with the most recent version of the genome assembly. We see three possible conclusions that can be drawn from our results. Either the Z/W sequence blocks are inverted, and additionally or alternatively the sequences are heterochromatic, thus preventing recom bination. It is also possible that the scaffolds in the ori ginal assembly of the S. mansoni genome were chimeric. Indeed, of the 48 scaffolds originally found in linkage group Z/W, 4 are on other chromosomes in the 5. 2 assembly. It will be difficult to formally exclude the pos sibility that our results are due to misassembly. We did not find any paralogues to sex determination genes among the predicted genes on the Z specific scaf folds. The specific region of the W chromosome is lar gely composed of large satellite blocks of at least 36 different W specific repeats.

These repeats are abundant on the W chromosome but our PCR analysis on differ ent male individuals indicates that these sequences can also sometimes be found on other chromosomes. Batimastat The strength of the PCR signal suggests, however, that they are present in very low copy number there. Analysis of the genomic sequence shows that they can occur inter mingled with other repeats on autosomal scaffolds as individual sequences or as small blocks of up to five repeats in tandem.