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Protease inhibitors are crucial for the survival of both <jats:italic>Echinococcus spp<\/jats:italic>. Kunitz-type inhibitors play a regulatory role in the control of protease activity. In this study,we identified Kunitz-type domain protease inhibitors(KDPIs) present in the genomes of these two tapeworms and analyzed the gene sequences using computational, structural bioinformatics and phylogenetic approaches to evaluate the evolutionary relationships of these genes. Hi-seq transcriptome analysis showed that <jats:italic>E. granulosus<\/jats:italic><jats:italic>s.s.<\/jats:italic>\u00a0KDPIs were differentially expressed in the different developmental stages. We validated some of the genes expressed in adult worm, protoscolex and cyst germinal membrane of <jats:italic>E. granulosus<\/jats:italic><jats:italic>s.s.<\/jats:italic>\u00a0and <jats:italic>E. multilocularis<\/jats:italic> by quantitative PCR.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>A total of 19 genes from <jats:italic>E. multilocularis<\/jats:italic> and 23 genes from <jats:italic>E. granulosus<\/jats:italic><jats:italic>s.s.<\/jats:italic>\u00a0were predicted to be KDPIs with the most containing a single Kunitz-domain. A maximum likelihood method phylogenetic tree indicated that the <jats:italic>E. granulosus<\/jats:italic><jats:italic>s.s.<\/jats:italic>\u00a0and <jats:italic>E. multilocularis<\/jats:italic> Kunitz domain peptides were divided into three branches containing 9 clusters. The ratio of positively charged residues and neutral residues are different between <jats:italic>E. multilocularis<\/jats:italic> and <jats:italic>E. granulosus<\/jats:italic><jats:italic>s.s.<\/jats:italic>\u00a0KDPIs. We also found that <jats:italic>E. multilocularis<\/jats:italic> had higher percentage of sequences containing signal peptides (17\/19, 89.47%) than that of <jats:italic>E. granulosus<\/jats:italic><jats:italic>s.s.<\/jats:italic>\u00a0(14\/23, 60.87%). Transcript analysis showed all the <jats:italic>E. granulosus<\/jats:italic><jats:italic>s.s.<\/jats:italic>\u00a0KDPI genes were expressed differentially in four developmental stages of the worm. Transcription analysis showed that 9 KDPIs (including EG_07244,EGR_08716 and EGR_10096) were highly upregulated in adult worm, and 2 KDPIs (EG_09268 and EG_09490) were highly expressed in the cyst germinal membrane. Quantitative gene expression analysis(qPCR) of four genes confirmed the expression of these genes. EGR_08716 and its homologous gene (EmuJ_001137000) were highly and specifically expressed in adult worms of the two worms.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>A total 19 and 23 KDPIs were identified in the genomes of <jats:italic>E. multilocularis<\/jats:italic> and <jats:italic>E. granulosus\u00a0s.s.\u00a0<\/jats:italic>, respectively. The differential expression of these KDPIs in different stages may indicate their different roles in the different hosts. The difference in characterization of KDPIs may be associated with the different pathology of metacestode stage of these two parasites.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-021-08219-4","type":"journal-article","created":{"date-parts":[[2021,12,18]],"date-time":"2021-12-18T19:02:19Z","timestamp":1639854139000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Bioinformatic comparison of Kunitz protease inhibitors in Echinococcus granulosus sensu stricto\u00a0and E. multilocularis and the genes expressed in different developmental stages of E. granulosus\u00a0s.s."],"prefix":"10.1186","volume":"22","author":[{"given":"Hui","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengxiao","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjing","family":"Qi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huajun","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gang","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiwanthi L.","family":"Ranasinghe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donald P.","family":"McManus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenbao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,12,18]]},"reference":[{"key":"8219_CR1","doi-asserted-by":"crossref","unstructured":"Wen H, Vuitton L, Tuxun T, Li J, Vuitton DA, Zhang W, McManus DP. 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