book of abstracts

XIII X IIII th S LO L O VAK V AK K AN D C ZEC C H PA PARAS A RAS S IT O LO O GIC C AL A L DAY DA AY S XIIII. SLLOVE ENSK KÉ A ČE ESKÉ PA ARAZIT TOLOGICK KÉ DN NI

Parasites P arassite es in n the e Heart Heaart of of Europe Euro ope e2

BOOK OF ABSTRACTS

Košice, Slovakia, Sl ki Congress C g Hotel H t l Centrum C

May 21 – 25, 2018

The editors hold no responsibility for any content, inaccuracy or language errors in the abstracts.

EDITORS MARTINA MITERPÁKOVÁ, ZUZANA VASILKOVÁ GRAPHIC DESIGN ZUZANA VASILKOVÁ

ISBN 978 – 80 - 968473 – 9 – 6 ©SLOVAK SOCIETY FOR PARASITOLOGY AT SAS KOŠICE, MAY 2018

513 bp), NADH dehydrogenase 1 (nad1, 471 bp), and 12S rRNA (rrnS, 295 bp). In five E. multilocularis isolates from humans in north-eastern Romania, resulting cox1 haplotypes of four Romanian isolates were identical to the E5 isolate (described by Nakao et al., 2009), which represents the most common European species variant. For the R5 isolate derived from Vaslui county, three nucleotide substitutions were recorded. One of these mutations (411T/G) corresponded to previously described N1 and N2 haplotypes from North America. The peculiar genetic composition of this E. multilocularis isolate coupled with the discontinuous distribution of the parasite in recent European territory support a hypothesis that the European clade has been derived from isolated populations in glacial refugia. The data provide first molecular evidence of E. multilocularis in clinical samples in Romania. In analyses focused on CE causative agents, in 16 pigs and 2 humans from Slovakia exclusively E. canadensis (G7 genotype) was detected. In Hungary, E. granulosus s.s. (G1 genotype) was firstly documented in humans, being found in liver and lung cysts of patient from Békés county (south-eastern Hungary). In six CE samples originated from Romania, two human isolates from western part of the country were identified as E. granulosus s.s. (G1, G3 genotypes), and two as E. canadensis G7. In addition, both human isolates from eastern Romania possessed E. granulosus s.s. G1 characteristics. Pig and cattle isolates from western Romania were allocated to E. canadensis G7 and E. granulosus s.s. G1. In Ukraine, E. canadensis G7 was detected in two pig samples (Sumy oblast in north-eastern Ukraine) and in one human isolate recovered from Volyn oblast in north-western Ukraine. The results obtained support the circumstantial evidence that E. canadensis, which is regarded as species with low infectivity for humans, is highly prevalent (or exclusive) in Poland, Slovakia and the forest-steppe zone of Ukraine. On the other hand, highly infectious E. granulosus s.s. was indicated as the primary causative agent for CE in Romania. The study was supported by the Grant Agency VEGA (project No. 2/0162/17).

Hybrid de novo assembly of the model tapeworm Hymenolepis diminuta genome Wiktor Kuśmirek1, Robert Nowak1, Małgorzata Rydzanicz2, Rafał Płoski2, Rusłan Sałamatin3,4, Agnieszka Sobczyk-Kopcioł3, Daniel Młocicki3,5 Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland 3 Department of General Biology and Parasitology, Medical University of Warsaw, Warsaw, Poland 4 Department of Parasitology and Vector-Borne Diseases, National Institute of Public Health – National Institute of Hygiene, Warsaw, Poland 5 W. Stefański Institute of Parasitology, Polish Academy of Sciences, Warsaw, Poland 1 2

The aim of this study was to isolate Hymenolepis diminuta (HD) genome, sequence and assemble it de novo. DNA was isolated from laboratory strain WMS-il1 underwent Next Generation Sequencing using the Illumina HiSeq 1500 platform. Additional sequencing was performed using a MinION sequencer from Oxford Nanopore Technologies (ONT) and mentioned earlier Illumina HiSeq 1500 system. For Illumina sequencer two types of data were obtained: paired-end tags (mean insert size c.a. 400 bp) and mate-pairs (mean insert size c.a. 7 kbp). The read length for both experiments carried out on Illumina system was equal to 100 bp, for ONT data the mean value of read length was greater than 7 kbp, the size of the longest DNA read reached almost 400 kbp. Obtained reads were de novo assembled in three steps. Fistly, paired-end tags were assembled by ABySS, Velvet and dnaasm applications, the results from other applications were merged by GAM-NGS tool. The number of sequences (greater than 1000 bp) was equal to 6416, value of N50 – c.a. 70 kbp, sum – 166.120 Mbp. Secondly, obtained DNA sequences were scaffolded using mate-pairs by SSPACE application. The N50 increased to c.a. 844 kbp, the number of sequences greater than 1000 bp decreased to 2342 and the sum of DNA sequences increased to 170.838 Mbp. Lastly, sequences obtained from paired-end tags and mate-pairs were joined using ONT sequencing data by LINKS tool. Final value of N50 was equal to 2537 kbp, the number of sequences greater than 1000 bp decreased up to 719 and the sum of the sequences increased to 177.348 Mbp.In this study we showed, that merging data from another sequencing platforms could greatly improve the final results of de novo assembling. Especially, combining short DNA reads obtained from next-generation sequencing with long DNA reads obtained from third generation sequencing could significantly improve the length and the quality of the resultant DNA sequences. Moreover, the increasing of coverage of the each sequencing technology above the certain level did not increase assembly results significantly, what we also showed in this study. Our study shows that combination of emerging genomic technologies is useful approach in producing accurate de novo assemblies of helminth genomes. This study was funded by the National Science Centre Poland (grant number: 2014/13/B/NZ6/00881).

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