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

Abstract

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.

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)

“…The presence of a schistosomula stage and dioecious amphimictic generation suggest their highly specialized and evolutionary derived state. Over the last ten years, not only the quality of genomes of schistosomes has improved [12], but the genomes of many other species such as C. sinensis [13], Echinostoma caproni Richard, 1964 [14], F. hepatica [14,15], Opisthorchis felineus (Rivolta, 1884) Blanchard, 1895 [16], O. viverrini (Poirier, 1886) Stiles & Hassal, 1896 [17], Schistosoma bovis Bilharz, 1852 [18], S. curassoni Brumpt, 1931 [14], S. haematobium Bilharz, 1852 [19], S. margrebowiei Le Roux, 1933 [14], S. mattheei Lawrence, 1978 [14], S. rodhaini Brumpt, 1931 [14] and Trichobilharzia regenti Horák, Kolářová & Dvořák, 1998 [14] were sequenced. Despite of the high importance of genomic data, analysis of gene expression changes under different conditions and in the different life cycle stages often remained outside of the main scope in the genome projects.…”

<i>Macrostomum lignano</i> as a model to study the genetics and genomics of parasitic flatworms

“…Importantly, new knowledge gained from experiments on M. lignano can be transferred to parasitic flatworms due to availability of numerous assemblies of genomes and transcriptomes for the most significant parasitic species, which are accessible at the WormBase ParaSite (https://parasite. wormbase.org/index.html) database (Berriman et al, 2009;Zheng et al, 2013;Cwiklinski et al, 2015;Ershov et al, 2019). By using modern computational tools of comparative genomics and transcriptomics, it is possible to readily identify the sequences of potential target genes revealed in M. lignano, which are homologous in different parasitic flatworm species, and to perform their comparative and phylogenetic analyses in silico.…”

“…This significantly facilitates the screening of phenotypes linked to the disruption of genes active in gonads and/or copulative organs (Grudniewska et al, 2018). Importantly, the worm (Wudarski et al, 2017;Grudniewska et al, 2018) Yes (Grohme et al, 2018) Yes (Berriman et al, 2009;Zheng et al, 2013;Ershov et al, 2019) Available research methods…”

Recent Progress in the Development of Liver Fluke and Blood Fluke Vaccines

“…An extensive overview of molecular research on Opisthorchis and opisthorchiasis is available [ 38 ]. Draft genomes are published for both O. viverrini (634.5 Mb) [ 39 ] and O. felineus (684 Mb) [ 40 ]. Furthermore, there is a wealth of available data on the transcriptome/secretome and proteome of both species providing key information that can be used for identifying potential novel antigens for vaccine development [ 24 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ].…”

“…Draft genomes are published for both O. viverrini (634.5 Mb) [ 39 ] and O. felineus (684 Mb) [ 40 ]. Furthermore, there is a wealth of available data on the transcriptome/secretome and proteome of both species providing key information that can be used for identifying potential novel antigens for vaccine development [ 24 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ]. Presumptive anti-worm and anti-fecundity vaccine candidates include glutathione S-transferase, other anti-oxidant/detoxification proteins, fatty acid binding protein, myoglobin, ferritin, various proteases (e.g., cathepsin F, B1), eggshell protein, SH3-domain containing protein, Ly6-domain containing protein, paramyosin, calreticulin and granulin-like growth factor (Ov-GRN-1) [ 41 , 44 , 48 ]; however, none appear to have been tested in the hamster vaccination model.…”