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Although aspects of sex determination, differentiation and reproduction have been studied in some <jats:italic>Schistosoma<\/jats:italic> species, almost nothing is known for <jats:italic>Schistosoma japonicum<\/jats:italic>, the causative agent of schistosomiasis japonica. This mainly reflects the lack of high\u2010quality genomic and transcriptomic resources for this species. As current genomes for <jats:italic>S. japonicum<\/jats:italic> are highly fragmented, we assembled and report a chromosome\u2010level reference genome (seven autosomes, the Z\u2010chromosome and partial W\u2010chromosome), achieving a substantially enhanced gene annotation. Utilizing this genome, we discovered that the sex chromosomes of <jats:italic>S. japonicum<\/jats:italic> and its congener <jats:italic>S. mansoni<\/jats:italic> independently suppressed recombination during evolution, forming five and two evolutionary strata, respectively. 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Collectively, these data provide a valuable resource for further functional genomic characterization of <jats:italic>S. japonicum<\/jats:italic>, shed light on the evolution of sex chromosomes in this highly virulent human blood fluke, and provide a pathway to identify novel targets for development of intervention tools against schistosomiasis.<\/jats:p>","DOI":"10.1111\/1755-0998.13689","type":"journal-article","created":{"date-parts":[[2022,7,18]],"date-time":"2022-07-18T04:13:45Z","timestamp":1658117625000},"page":"205-221","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Chromosome\u2010level genome assembly defines female\u2010biased genes associated with sex determination and differentiation in\u00a0the human blood fluke <i>Schistosoma japonicum<\/i>"],"prefix":"10.1111","volume":"23","author":[{"given":"Xindong","family":"Xu","sequence":"first","affiliation":[{"name":"Laboratory of Molecular Parasitology, Key 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