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Background  The three epidemiologically important Opisthorchiidae liver flukes  Opisthorchis felineus ,  O. viverrini , and  Clonorchis sinensis , are believed to harbour similar potencies to provoke hepatobiliary diseases in their definitive hosts, although their populations have substantially different ecogeographical aspects including habitat, preferred hosts, population structure. Lack of  O. felineus  genomic data is an obstacle to the development of comparative molecular biological approaches necessary to obtain new knowledge about the biology of Opisthorchiidae trematodes, to identify essential pathways linked to parasite-host interaction, to predict genes that contribute to liver fluke pathogenesis and for the effective prevention and control of the disease.    Results  Here we present the first draft genome assembly of  O. felineus  and its gene repertoire accompanied by a comparative analysis with that of  O. viverrini  and  Clonorchis sinensis . We observed both noticeably high heterozygosity of the sequenced individual and substantial genetic diversity in a pooled sample. This indicates that potency of  O. felineus  population for rapid adaptive response to control and preventive measures of opisthorchiasis is higher than in  O. viverrini  and  C. sinensis . We also have found that all three species are characterized by more intensive involvement of trans-splicing in RNA processing compared to other trematodes.    Conclusion  All revealed peculiarities of structural organization of genomes are of extreme importance for a proper description of genes and their products in these parasitic species. This should be taken into account both in academic and applied research of epidemiologically important liver flukes. Further comparative genomics studies of liver flukes and non-carcinogenic flatworms allow for generation of well-grounded hypotheses on the mechanisms underlying development of cholangiocarcinoma associated with opisthorchiasis and clonorchiasis as well as species-specific mechanisms of these diseases.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5752-8) contains supplementary material, which is available to authorized users.

New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes