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.

Základní údaje

Originální název

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

Autoři

VOREL, Jiří (203 Česká republika, domácí), Pavel ROUDNICKÝ (203 Česká republika), Jana ILGOVÁ (703 Slovensko), Hana DVOŘÁKOVÁ (203 Česká republika), Lucie JEDLIČKOVÁ (203 Česká republika), Libor MIKEŠ (203 Česká republika), Petr BROŽ (203 Česká republika), Dagmar JIRSOVÁ (203 Česká republika), Roman LEONTOVYČ (203 Česká republika), Lukáš VETEŠNÍK (203 Česká republika), Pavel JURAJDA (203 Česká republika), Ewa DZIKA (616 Polsko), Božena KOUBKOVÁ (203 Česká republika), Milan GELNAR (203 Česká republika) a Martin KAŠNÝ (203 Česká republika, garant)

Vydání

5th ECIP meeting - European Centre of Ichtyoparasitology, 2016

Další údaje

Jazyk

angličtina

Typ výsledku

Prezentace na konferencích

Obor

10600 1.6 Biological sciences

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Kód RIV

RIV/00216224:14310/16:00088396

Organizační jednotka

Přírodovědecká fakulta

ISBN

978-80-210-8373-8

Klíčová slova anglicky

NGS; Monogenea; Eudiplozoon; nipponicum; genome; transcriptome

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

Anotace

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.

Návaznosti

GBP505/12/G112, projekt VaV

Název: ECIP - Evropské centrum ichtyoparazitologie

Investor: Grantová agentura ČR, ECIP - Evropské centrum ichtyoparazitologie

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 a 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 a 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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