Eudiplozoon nipponicum (Monogenea): the molecules transcribed
by hematophagous parasite of fish

k 2016

Eudiplozoon nipponicum (Monogenea): the molecules transcribed by hematophagous parasite of fish

VOREL, Jiří, Pavel ROUDNICKÝ, Jana ILGOVÁ, Hana DVOŘÁKOVÁ, Lucie JEDLIČKOVÁ et. al.

Basic information

Original name

Eudiplozoon nipponicum (Monogenea): the molecules transcribed by hematophagous parasite of fish

Authors

VOREL, Jiří (203 Czech Republic, belonging to the institution), Pavel ROUDNICKÝ (203 Czech Republic), Jana ILGOVÁ (703 Slovakia), Hana DVOŘÁKOVÁ (203 Czech Republic), Lucie JEDLIČKOVÁ (203 Czech Republic), Libor MIKEŠ (203 Czech Republic), Petr BROŽ (203 Czech Republic), Dagmar JIRSOVÁ (203 Czech Republic), Roman LEONTOVYČ (203 Czech Republic), Lukáš VETEŠNÍK (203 Czech Republic), Pavel JURAJDA (203 Czech Republic), Ewa DZIKA (616 Poland), Božena KOUBKOVÁ (203 Czech Republic), Milan GELNAR (203 Czech Republic) and Martin KAŠNÝ (203 Czech Republic, guarantor)

Edition

5th ECIP meeting - European Centre of Ichtyoparasitology, 2016

Other information

Language

English

Type of outcome

Prezentace na konferencích

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14310/16:00088396

Organization unit

Faculty of Science

ISBN

978-80-210-8373-8

Keywords in English

NGS; Monogenea; Eudiplozoon; nipponicum; genome; transcriptome

Změněno: 25/3/2017 07:46, RNDr. Martin Kašný, Ph.D.

Abstract

V originále

Ectoparasitic flatworms from the family Diplozoidae (Platyhelminthes, Monogenea) represent a serious bloodfeeding fish pathogens. Until now, the running research is focused mainly on morphological and phylogenetical characteristics of these worms and the information related to the biochemical and molecular nature of the physiological processes is rather sporadic. Therefore we started with a first complex transcriptomic followed by genomic analysis of monogenean representative - Eudiplozoon nipponicum Goto 1891 (Monogenea, Diplozoidae), which was performed by three sequencing strategies - 454/Roche, MiSeq Illumina and HiSeq Illumina. The mRNA of E. nipponicum adults, in the form cDNA was sequenced (454/Roche, MiSeq Illumina) and raw reads were processed in order to get high quality transcriptomics sequences for further annotation. Raw reads were filtered and low quality bases were removed as well as contaminations – reads related to host organisms (common carp). Sequencing errors and mismatches were corrected and finally the processed reads were assembled into the form individual transcripts. 454/Roche and Illumina sequences were pooled and several further bioinformatics approaches (especially searching for the closest homologous in non-redundant databases and prediction of proteins key properties) were used. We identified number of molecules of our interest (e.g. those related to hematophagy - proteolytic enzymes and their inhibitors, anticoagulant agents and immunomodulators). Some of these molecules are subjects of our further research. In order to reach the complete information of all E. nipponicum genes, the reads related to genomic DNA were generated by adoption of Illumina HiSeq platform. Quality of reads was checked, low quality reads were removed and total genome size and sequencing coverage were estimated. The estimation of genome size was performed also experimentally using DNA fluorescent double staining method, which represents simple and easy pointbased measurement of intensity of fluorescent signal given by amount of DNA. This method was originally designed for single-celled organisms and therefore we are optimizing the protocol for multicellular organism E. nipponicum. All obtained sequences on E. nipponicum have been compared with sporadic nucleotide sequential datasets from other members of the class Monogenea.

Links

GBP505/12/G112, research and development project

Name: ECIP - Evropské centrum ichtyoparazitologie

Investor: Czech Science Foundation

Citovat

VOREL, Jiří, Pavel ROUDNICKÝ, Jana ILGOVÁ, Hana DVOŘÁKOVÁ, Lucie JEDLIČKOVÁ, Libor MIKEŠ, Petr BROŽ, Dagmar JIRSOVÁ, Roman LEONTOVYČ, Lukáš VETEŠNÍK, Pavel JURAJDA, Ewa DZIKA, Božena KOUBKOVÁ, Milan GELNAR and Martin KAŠNÝ. Eudiplozoon nipponicum (Monogenea): the molecules transcribed by hematophagous parasite of fish. In 5th ECIP meeting - European Centre of Ichtyoparasitology. 2016. ISBN 978-80-210-8373-8.

@proceedings{1363063,
   author = {Vorel, Jiří and Roudnický, Pavel and Ilgová, Jana and Dvořáková, Hana and Jedličková, Lucie and Mikeš, Libor and Brož, Petr and Jirsová, Dagmar and Leontovyč, Roman and Vetešník, Lukáš and Jurajda, Pavel and Dzika, Ewa and Koubková, Božena and Gelnar, Milan and Kašný, Martin},
   booktitle = {5th ECIP meeting - European Centre of Ichtyoparasitology},
   keywords = {NGS; Monogenea; Eudiplozoon; nipponicum; genome; transcriptome},
   language = {eng},
   isbn = {978-80-210-8373-8},
   title = {Eudiplozoon nipponicum (Monogenea): the molecules transcribed by hematophagous parasite of fish},
   year = {2016}
}

TY  - CONF
ID  - 1363063
AU  - Vorel, Jiří - Roudnický, Pavel - Ilgová, Jana - Dvořáková, Hana - Jedličková, Lucie - Mikeš, Libor - Brož, Petr - Jirsová, Dagmar - Leontovyč, Roman - Vetešník, Lukáš - Jurajda, Pavel - Dzika, Ewa - Koubková, Božena - Gelnar, Milan - Kašný, Martin
PY  - 2016
TI  - Eudiplozoon nipponicum (Monogenea): the molecules transcribed by hematophagous parasite of fish
SN  - 9788021083738
KW  - NGS
KW  - Monogenea
KW  - Eudiplozoon
KW  - nipponicum
KW  - genome
KW  - transcriptome
N2  - Ectoparasitic flatworms from the family Diplozoidae (Platyhelminthes, Monogenea) represent a serious bloodfeeding fish pathogens. Until now, the running research is focused mainly on morphological and phylogenetical characteristics of these worms and the information related to the biochemical and molecular nature of the physiological processes is rather sporadic. Therefore we started with a first complex transcriptomic followed by genomic analysis of monogenean representative - Eudiplozoon nipponicum Goto 1891 (Monogenea, Diplozoidae), which was performed by three sequencing strategies - 454/Roche, MiSeq Illumina and HiSeq Illumina. The mRNA of E. nipponicum adults, in the form cDNA was sequenced (454/Roche, MiSeq Illumina) and raw reads were processed in order to get high quality transcriptomics sequences for further annotation. Raw reads were filtered and low quality bases were removed as well as contaminations – reads related to host organisms (common carp). Sequencing errors and mismatches were corrected and finally the processed reads were assembled into the form individual transcripts. 454/Roche and Illumina sequences were pooled and several further bioinformatics approaches (especially searching for the closest homologous in non-redundant databases and prediction of proteins key properties) were used. We identified number of molecules of our interest (e.g. those related to hematophagy - proteolytic enzymes and their inhibitors, anticoagulant agents and immunomodulators). Some of these molecules are subjects of our further research. In order to reach the complete information of all E. nipponicum genes, the reads related to genomic DNA were generated by adoption of Illumina HiSeq platform. Quality of reads was checked, low quality reads were removed and total genome size and sequencing coverage were estimated. The estimation of genome size was performed also experimentally using DNA fluorescent double staining method, which represents simple and easy pointbased measurement of intensity of fluorescent signal given by amount of DNA. This method was originally designed for single-celled organisms and therefore we are optimizing the protocol for multicellular organism E. nipponicum. All obtained sequences on E. nipponicum have been compared with sporadic nucleotide sequential datasets from other members of the class Monogenea.
ER  -

VOREL, Jiří, Pavel ROUDNICKÝ, Jana ILGOVÁ, Hana DVOŘÁKOVÁ, Lucie JEDLIČKOVÁ, Libor MIKEŠ, Petr BROŽ, Dagmar JIRSOVÁ, Roman LEONTOVYČ, Lukáš VETEŠNÍK, Pavel JURAJDA, Ewa DZIKA, Božena KOUBKOVÁ, Milan GELNAR and Martin KAŠNÝ. Eudiplozoon nipponicum (Monogenea): the molecules transcribed by hematophagous parasite of fish. In \textit{5th ECIP meeting - European Centre of Ichtyoparasitology}. 2016. ISBN~978-80-210-8373-8.

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