Detailed Information on Publication Record

VOREL, Jiří, Marie JANKŮJOVÁ, Jan OPPELT, Filip PARDY, Pavel ROUDNICKÝ, Jana ILGOVÁ, Libor MIKEŠ, Milan GELNAR and Martin KAŠNÝ. Monogeneans in the pores. In 24th Helminthological Days. 2018. ISBN 978-80-7444-057-1.

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TY  - CONF
ID  - 1416798
AU  - Vorel, Jiří - Jankůjová, Marie - Oppelt, Jan - Pardy, Filip - Roudnický, Pavel - Ilgová, Jana - Mikeš, Libor - Gelnar, Milan - Kašný, Martin
PY  - 2018
TI  - Monogeneans in the pores
SN  - 9788074440571
KW  - Parasites
KW  - Monogenea
KW  - Sequencing
KW  - Genome
KW  - Nanopores
N2  - Ectoparasitic flatworms from the group Monogenea represent serious fish pathogens. Their presence in stocks can lead to significant losses in fish host populations. Despite this fact, the running research has been 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. Up to now, we performed whole-genomic sequencing of selected monogenean representative Eudiplozoon nipponicum by three sequencing techniques. 454/Roche (Junior sequencing platform), Illumina (MiSeq and HiSeq sequencing platforms) and recently by Oxford Nanopore (MinION sequencing platform). Using 454/Roche Junior and both Illumina sequencing platforms, 164,773,962 short genomic reads were originally generated. After quality processing of raw reads (trimming, removing contaminants, errors correction, etc.), 130,741,241 reads were used for the draft of genome assembly. Finally, 524,914 contigs were generated by MaSuRCA assembler in total length 1,109,208,298 base pairs (1.1 Gb). Unfortunately, the final assembly was fragmented and significant number of contigs was identified as a bacterial contamination. In order to improve E. nipponicum draft genome, especially to fill the missing genome gaps, we generated long reads using modern third generation sequencing method nanopore sequencing (MinION). The MinION platform (Oxford Nanopore Technologies, UK) is a small and portable, real time working, low-cost USB device, producing very long-reads (theoretically up to 250 Kb). The results of our analysis with E. nipponicum DNA showed, that 500 active channels/pores (from max. 512) produced 1,091,445 reads with length up to 198,101 base pairs (average 2,588 base pairs). In total, more than 2,8 Gb were generated in two days run, it significantly helped us to improve genome information by merging a relevant percentage of contigs (9.7 %), from 524,914 to 474,134.
ER  -

Basic information
Original name	Monogeneans in the pores
Authors	VOREL, Jiří (203 Czech Republic, guarantor, belonging to the institution), Marie JANKŮJOVÁ (203 Czech Republic), Jan OPPELT (203 Czech Republic), Filip PARDY (203 Czech Republic), Pavel ROUDNICKÝ (203 Czech Republic), Jana ILGOVÁ (703 Slovakia), Libor MIKEŠ (203 Czech Republic), Milan GELNAR (203 Czech Republic) and Martin KAŠNÝ (203 Czech Republic).
Edition	24th Helminthological Days, 2018.

Other information
Original language	English
Type of outcome	Presentations at conferences
Field of Study	10600 1.6 Biological sciences
Country of publisher	Czech Republic
Confidentiality degree	is not subject to a state or trade secret
RIV identification code	RIV/00216224:14310/18:00100930
Organization unit	Faculty of Science
ISBN	978-80-7444-057-1
Keywords in English	Parasites; Monogenea; Sequencing; Genome; Nanopores
Changed by	Changed by: Mgr. Jiří Vorel, Ph.D., učo 376321. Changed: 13/5/2018 12:09.

Abstract
Ectoparasitic flatworms from the group Monogenea represent serious fish pathogens. Their presence in stocks can lead to significant losses in fish host populations. Despite this fact, the running research has been 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. Up to now, we performed whole-genomic sequencing of selected monogenean representative Eudiplozoon nipponicum by three sequencing techniques. 454/Roche (Junior sequencing platform), Illumina (MiSeq and HiSeq sequencing platforms) and recently by Oxford Nanopore (MinION sequencing platform). Using 454/Roche Junior and both Illumina sequencing platforms, 164,773,962 short genomic reads were originally generated. After quality processing of raw reads (trimming, removing contaminants, errors correction, etc.), 130,741,241 reads were used for the draft of genome assembly. Finally, 524,914 contigs were generated by MaSuRCA assembler in total length 1,109,208,298 base pairs (1.1 Gb). Unfortunately, the final assembly was fragmented and significant number of contigs was identified as a bacterial contamination. In order to improve E. nipponicum draft genome, especially to fill the missing genome gaps, we generated long reads using modern third generation sequencing method nanopore sequencing (MinION). The MinION platform (Oxford Nanopore Technologies, UK) is a small and portable, real time working, low-cost USB device, producing very long-reads (theoretically up to 250 Kb). The results of our analysis with E. nipponicum DNA showed, that 500 active channels/pores (from max. 512) produced 1,091,445 reads with length up to 198,101 base pairs (average 2,588 base pairs). In total, more than 2,8 Gb were generated in two days run, it significantly helped us to improve genome information by merging a relevant percentage of contigs (9.7 %), from 524,914 to 474,134.

Abstract

Ectoparasitic flatworms from the group Monogenea represent serious fish pathogens. Their presence in stocks can lead to significant losses in fish host populations. Despite this fact, the running research has been 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. Up to now, we performed whole-genomic sequencing of selected monogenean representative Eudiplozoon nipponicum by three sequencing techniques. 454/Roche (Junior sequencing platform), Illumina (MiSeq and HiSeq sequencing platforms) and recently by Oxford Nanopore (MinION sequencing platform). Using 454/Roche Junior and both Illumina sequencing platforms, 164,773,962 short genomic reads were originally generated. After quality processing of raw reads (trimming, removing contaminants, errors correction, etc.), 130,741,241 reads were used for the draft of genome assembly. Finally, 524,914 contigs were generated by MaSuRCA assembler in total length 1,109,208,298 base pairs (1.1 Gb). Unfortunately, the final assembly was fragmented and significant number of contigs was identified as a bacterial contamination. In order to improve E. nipponicum draft genome, especially to fill the missing genome gaps, we generated long reads using modern third generation sequencing method nanopore sequencing (MinION). The MinION platform (Oxford Nanopore Technologies, UK) is a small and portable, real time working, low-cost USB device, producing very long-reads (theoretically up to 250 Kb). The results of our analysis with E. nipponicum DNA showed, that 500 active channels/pores (from max. 512) produced 1,091,445 reads with length up to 198,101 base pairs (average 2,588 base pairs). In total, more than 2,8 Gb were generated in two days run, it significantly helped us to improve genome information by merging a relevant percentage of contigs (9.7 %), from 524,914 to 474,134.

Links
GBP505/12/G112, research and development project	Name: ECIP - Evropské centrum ichtyoparazitologie
GBP505/12/G112, research and development project	Investor: Czech Science Foundation
MUNI/A/0816/2017, interní kód MU	Name: Výzkum ekologicko-evolučních vztahů bezobratlých živočichů (Acronym: EKOLINKS)
MUNI/A/0816/2017, interní kód MU	Investor: Masaryk University, Category A