“Omics” and population genetic tools applied on selected
species from the class Monogenea

k 2015

“Omics” and population genetic tools applied on selected species from the class Monogenea

VOREL, Jiří; Dagmar JIRSOVÁ; Jana ILGOVÁ; Pavel ROUDNICKÝ; Lucie JEDLIČKOVÁ et. al.

Základní údaje

Originální název

“Omics” and population genetic tools applied on selected species from the class Monogenea

Autoři

VOREL, Jiří (203 Česká republika, domácí); Dagmar JIRSOVÁ (203 Česká republika); Jana ILGOVÁ (703 Slovensko); Pavel ROUDNICKÝ (203 Česká republika); Lucie JEDLIČKOVÁ (203 Česká republika); Hana DVOŘÁKOVÁ (203 Česká republika); Roman LEONTOVYČ (203 Česká republika); Libor MIKEŠ (203 Česká republika); Hynek STRNAD (203 Česká republika); Božena KOUBKOVÁ (203 Česká republika); Milan GELNAR (203 Česká republika) a Martin KAŠNÝ (203 Česká republika, garant)

Vydání

4th ECIP meeting - European Centre of Ichtyoparasitology, 2015

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/00216224:14310/15:00094520

Organizační jednotka

Přírodovědecká fakulta

ISBN

978-80-210-8016-4

Klíčová slova anglicky

NGS; AFLP; Monogenea; genome; transcriptome; population genetics

Změněno: 16. 2. 2018 14:51, Mgr. Jiří Vorel, Ph.D.

Anotace

V originále

Our study is focused on three model organisms Eudiplozoon nipponicum, Paradiplozoon homoion and Paradiplozoon gracile all of them are representing blood sucking fish ectoparasites from group Monogenea: Diplozoidae. Our project consists of two parts according to the used methods. The first part combining the modern pyro-sequencing methods and computer databases for the faster and more accurately identification of numerous sets of protein molecules, which are essential for life of monogeneans. The second part of study is more focused on population genetics and description of each sample at the individual level. In order to obtain this type of data, we decided to use amplified fragment length polymorphism technique (AFLP). Our four aims are realized; (i) compare the genetic diversity in populations of monogenean species, (ii) determine the level of genetic variability of the two permanently fused worms isolated from the same fish (“sex factor”), (iii) reveal the intra- and inter-population patterns and (iv) evaluate the effect of different host species on genetic plasticity of monogenea with generalist life strategy. We started the preliminary analyses leading to generation of E. nipponicum genome, transcriptome and proteome databases. We would like to use data platforms for identification and further characterization of protein molecules involved into the interaction between host and parasite. In the order to check the volume of obtained genomic data vs. reality we used the DNA fluorescent double staining method, which represents simple and easy checking point for obtained bioinformatics data. This method was designed for single-celled organisms and therefore we had to optimise the dying protocol and we are currently working on analysis settings for multi-celled organisms. The mRNA E. nipponicum adult in the form of sort reads/transcripts was analyzed using specific software tools. e.g. Trimmomatic, SPAdes, TopHat, Bowtie2, Trinity, SOAPdenovo and Velvet-Oases.

Návaznosti

GBP505/12/G112, projekt VaV

Název: ECIP - Evropské centrum ichtyoparazitologie

Investor: Grantová agentura ČR, ECIP - Evropské centrum ichtyoparazitologie

Citovat

VOREL, Jiří; Dagmar JIRSOVÁ; Jana ILGOVÁ; Pavel ROUDNICKÝ; Lucie JEDLIČKOVÁ; Hana DVOŘÁKOVÁ; Roman LEONTOVYČ; Libor MIKEŠ; Hynek STRNAD; Božena KOUBKOVÁ; Milan GELNAR a Martin KAŠNÝ. “Omics” and population genetic tools applied on selected species from the class Monogenea. In 4th ECIP meeting - European Centre of Ichtyoparasitology. 2015. ISBN 978-80-210-8016-4.

@proceedings{1318673,
   author = {Vorel, Jiří and Jirsová, Dagmar and Ilgová, Jana and Roudnický, Pavel and Jedličková, Lucie and Dvořáková, Hana and Leontovyč, Roman and Mikeš, Libor and Strnad, Hynek and Koubková, Božena and Gelnar, Milan and Kašný, Martin},
   booktitle = {4th ECIP meeting - European Centre of Ichtyoparasitology},
   keywords = {NGS; AFLP; Monogenea; genome; transcriptome; population genetics},
   language = {eng},
   isbn = {978-80-210-8016-4},
   title = {“Omics” and population genetic tools applied on selected species from the class Monogenea},
   year = {2015}
}

TY  - CONF
ID  - 1318673
AU  - Vorel, Jiří - Jirsová, Dagmar - Ilgová, Jana - Roudnický, Pavel - Jedličková, Lucie - Dvořáková, Hana - Leontovyč, Roman - Mikeš, Libor - Strnad, Hynek - Koubková, Božena - Gelnar, Milan - Kašný, Martin
PY  - 2015
TI  - “Omics” and population genetic tools applied on selected species from the class Monogenea
SN  - 9788021080164
KW  - NGS
KW  - AFLP
KW  - Monogenea
KW  - genome
KW  - transcriptome
KW  - population genetics
N2  - Our study is focused on three model organisms Eudiplozoon nipponicum, Paradiplozoon homoion and Paradiplozoon gracile all of them are representing blood sucking fish ectoparasites from group Monogenea: Diplozoidae. Our project consists of two parts according to the used methods. The first part combining the modern pyro-sequencing methods and computer databases for the faster and more accurately identification of numerous sets of protein molecules, which are essential for life of monogeneans. The second part of study is more focused on population genetics and description of each sample at the individual level. In order to obtain this type of data, we decided to use amplified fragment length polymorphism technique (AFLP). Our four aims are realized; (i) compare the genetic diversity in populations of monogenean species, (ii) determine the level of genetic variability of the two permanently fused worms isolated from the same fish (“sex factor”), (iii) reveal the intra- and inter-population patterns and (iv) evaluate the effect of different host species on genetic plasticity of monogenea with generalist life strategy. We started the preliminary analyses leading to generation of E. nipponicum genome, transcriptome and proteome databases. We would like to use data platforms for identification and further characterization of protein molecules involved into the interaction between host and parasite. In the order to check the volume of obtained genomic data vs. reality we used the DNA fluorescent double staining method, which represents simple and easy checking point for obtained bioinformatics data. This method was designed for single-celled organisms and therefore we had to optimise the dying protocol and we are currently working on analysis settings for multi-celled organisms. The mRNA E. nipponicum adult in the form of sort reads/transcripts was analyzed using specific software tools. e.g. Trimmomatic, SPAdes, TopHat, Bowtie2, Trinity, SOAPdenovo and Velvet-Oases.
ER  -

VOREL, Jiří; Dagmar JIRSOVÁ; Jana ILGOVÁ; Pavel ROUDNICKÝ; Lucie JEDLIČKOVÁ; Hana DVOŘÁKOVÁ; Roman LEONTOVYČ; Libor MIKEŠ; Hynek STRNAD; Božena KOUBKOVÁ; Milan GELNAR a Martin KAŠNÝ. “Omics” and population genetic tools applied on selected species from the class Monogenea. In \textit{4th ECIP meeting - European Centre of Ichtyoparasitology}. 2015. ISBN~978-80-210-8016-4.

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