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Detection of positive selection using resequencing data to understand adaptive evolution has been applied to a variety of pathogens, including <jats:italic>S. japonicum<\/jats:italic>. However, the contribution of the Z chromosome to evolution and adaptation is often neglected.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>We obtained 1,077,526 high-quality SNPs on the Z chromosome in 72 <jats:italic>S. japonicum<\/jats:italic> using re-sequencing data publicly. To examine the faster Z effect, we compared the sequence divergence of <jats:italic>S. japonicum<\/jats:italic> with two closely related species, <jats:italic>Schistosoma haematobium<\/jats:italic> and <jats:italic>S. mansoni<\/jats:italic>. Genetic diversity was compared between the Z chromosome and autosomes in <jats:italic>S. japonicum<\/jats:italic> by calculating the nucleotide diversity (\u03c0) and Dxy values. Population structure was also assessed based on PCA and structure analysis. Besides, we employed multiple methods including Tajima\u2019s <jats:italic>D<\/jats:italic>, F<jats:sub>ST<\/jats:sub>, iHS, XP-EHH, and CMS to detect positive selection signals on the Z chromosome. Further RNAi knockdown experiments were performed to investigate the potential biological functions of the candidate genes.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Our study found that the Z chromosome of <jats:italic>S. japonicum<\/jats:italic> showed faster evolution and more pronounced genetic divergence than autosomes, although the effect may be smaller than the variation among genes. Compared with autosomes, the Z chromosome in <jats:italic>S. japonicum<\/jats:italic> had a more pronounced genetic divergence of sub-populations. Notably, we identified a set of candidate genes associated with host-parasite co-evolution. In particular, <jats:italic>LCAT<\/jats:italic> exhibited significant selection signals within the Taiwan population. Further RNA interference experiments suggested that <jats:italic>LCAT<\/jats:italic> is necessary for <jats:italic>S. japonicum<\/jats:italic> survival and propagation in the definitive host. In addition, we identified several genes related to the specificity of the intermediate host in the C-M population, including <jats:italic>Rab6<\/jats:italic> and <jats:italic>VCP<\/jats:italic>, which are involved in adaptive immune evasion to the host.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Our study provides valuable insights into the adaptive evolution of the Z chromosome in <jats:italic>S. japonicum<\/jats:italic> and further advances our understanding of the co-evolution of this medically important parasite and its hosts.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-024-06250-4","type":"journal-article","created":{"date-parts":[[2024,5,8]],"date-time":"2024-05-08T12:01:46Z","timestamp":1715169706000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Characterizing genetic variation on the Z chromosome in Schistosoma japonicum reveals host-parasite co-evolution"],"prefix":"10.1186","volume":"17","author":[{"given":"An","family":"Zhou","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueling","family":"Ge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuhua","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,8]]},"reference":[{"key":"6250_CR1","unstructured":"Geneva. 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