The respository contains information and code relating to the Schistosoma mansoni genome project from Matt Berriman's Parasite Genomics group (Wellcome Sanger Institute and the University of Glasgow), and supporting information to the manuscript entitled "Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system".
The manuscript is currently available on bioRxiv here and is currently under peer review.
Custom code used for the analysis and generation of figures is available here
Abstract:
Background
Schistosoma mansoni is a parasitic flatworm that causes a neglected tropical disease affecting hundreds
of millions worldwide. Most flatworms are hermaphrodites but schistosomes have genotypically determined
male (ZZ) and female (ZW) sexes. Sex is essential for pathology and transmission, however, the molecular
determinants that drive sex-specific developmental programmes remain unknown and are limited by poorly
resolved sex chromosomes in previous genome assemblies.
Results
Here we present a 391.4 Mb S. mansoni genome assembly resolved into seven single-scaffold autosomes with both Z and W sex chromosomes separately defined. Annotation of this assembly incorporating short and long-read RNAseq data together with manual curation allowed us to resolve gene and repeat arrays, trans-splicing, and UTRs, resulting in vastly improved gene models. The sex chromosomes each comprise pseudoautosomal- and sex-specific regions; the Z-specific region contains 932 genes, of which only 33 gametologues have been retained in the W-specific region, and five of these have become pseudogenes indicating that degeneration of W is ongoing. Comparative analysis between closely related Schistosoma spp. reveals an ancient chromosomal fusion within a shared ancestrally sex-specific region of Z; here, only a single protein-coding gene—encoding the large subunit of pre-mRNA splicing factor U2AF—has retained an intact copy on W. The sex-specific copies of U2AF have divergent N-termini and show sex-biased gene expression.
Conclusion
Our chromosomally-resolved assembly and curated annotation is a significant improvement on existing genetic resources for S. mansoni, an important but neglected human pathogen. Delineation of the Z and W chromosomes, together with identifying a single sex-linked gene that shows genetic and transcriptomic differences between sexes, is a major advance toward resolving the evolutionary path taken to establish two distinct sexes in schistosomes.
Any reuse of data or code is encouraged with due acknowledgement, either via citation of the published manuscript (when available) and/or GitHub repository. Comments, suggestions, and discussion are welcome.
Note: while much effort is made to make all data and code available, some of the code is very specific to the Sanger HPC environment and will need to be modified to work elsewhere. If you are interested in using any of it for your own work, but are stuck, please do get in touch.
Copyright (c) 2022, Stephen R Doyle
All rights reserved.
This source code is licensed under the BSD-style license found in the LICENSE file in the root directory of this source tree.
