Could nanopore sequencing help us improve genome assembly of
Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)?

k 2017

Could nanopore sequencing help us improve genome assembly of Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)?

VOREL, Jiří, Marie JANKŮJOVÁ, Jan OPPELT, Filip PARDY, Pavel ROUDNICKÝ et. al.

Basic information

Original name

Could nanopore sequencing help us improve genome assembly of Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)?

Authors

VOREL, Jiří (203 Czech Republic, 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), Hana DVOŘÁKOVÁ (203 Czech Republic), Lucie JEDLIČKOVÁ (203 Czech Republic), Libor MIKEŠ (203 Czech Republic), Dagmar JIRSOVÁ (203 Czech Republic), Božena KOUBKOVÁ (203 Czech Republic), Milan GELNAR (203 Czech Republic) and Martin KAŠNÝ (203 Czech Republic, guarantor)

Edition

6th ECIP meeting - European Centre of Ichtyoparasitology, 2017

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

References:

URL

RIV identification code

RIV/00216224:14310/17:00095265

Organization unit

Faculty of Science

ISBN

978-80-210-8799-6

Keywords in English

NGS; nanopore; Monogenea; Eudiplozoon; nipponicum; genome

Změněno: 13/12/2017 14:53, Mgr. Jiří Vorel, Ph.D.

Abstract

V originále

Ectoparasitic flatworms from the family Diplozoidae (Platyhelminthes, Monogenea) represent a serious bloodfeeding fish pathogens. Until now, 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. To this date only two monogenean genomes are deposited in public sequence databases. Genomes of Gyrodactylus salaris (Monopisthocotylea, Gyrodactylidae) and Protopolystoma xenopodis (Polyopisthocotylea, Polystomatidae). Therefore, we designed whole-genomic sequencing of selected monogenean representative - Eudiplozoon nipponicum Goto 1891, which was performed by three sequencing techniques. 454/Roche (Junior sequencing platform), Illumina (MiSeq and HiSeq sequencing platforms) and modern Oxford Nanopore technique (MinION sequencing platform). Using 454/Roche Junior and both Illumina sequencing platforms, 164,773,962 short raw reads were originally generated. After trimming of low quality reads (Trimmomatic v. 0.36) and removing contaminatinon - reads given by fish host (Cyprinus carpio), 130,741,241 reads were used for the draft of genome assembly. Finally, 766,162 scaffolds were generated in total length 1,322,576,402 base pairs (1.3 Gb). But most of assembled scaffolds were identified as a Spiroplasma sp. or Emticicia oligotrophica (bacterial contaminations), which could mean that significant number of E. nipponicum reads could be unintentionally filtered out and final scaffold is incomplete. For purpose to improve E. nipponicum genome draft, we have additionally included reads generated by modern third generation sequencing method – nanopore sequencing. The MinION platform is a small and portable, real time working, low-cost USB device, producing long-read (theoretically up to 250 Kb). 500 working channels produced 1,097,634 reads with length up to 198,101 base pairs.

Links

GBP505/12/G112, research and development project

Name: ECIP - Evropské centrum ichtyoparazitologie

Investor: Czech Science Foundation

Citovat

VOREL, Jiří, Marie JANKŮJOVÁ, Jan OPPELT, Filip PARDY, Pavel ROUDNICKÝ, Jana ILGOVÁ, Hana DVOŘÁKOVÁ, Lucie JEDLIČKOVÁ, Libor MIKEŠ, Dagmar JIRSOVÁ, Božena KOUBKOVÁ, Milan GELNAR and Martin KAŠNÝ. Could nanopore sequencing help us improve genome assembly of Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)? In 6th ECIP meeting - European Centre of Ichtyoparasitology. 2017. ISBN 978-80-210-8799-6.

@proceedings{1399070,
   author = {Vorel, Jiří and Jankůjová, Marie and Oppelt, Jan and Pardy, Filip and Roudnický, Pavel and Ilgová, Jana and Dvořáková, Hana and Jedličková, Lucie and Mikeš, Libor and Jirsová, Dagmar and Koubková, Božena and Gelnar, Milan and Kašný, Martin},
   booktitle = {6th ECIP meeting - European Centre of Ichtyoparasitology},
   keywords = {NGS; nanopore; Monogenea; Eudiplozoon; nipponicum; genome},
   language = {eng},
   isbn = {978-80-210-8799-6},
   title = {Could nanopore sequencing help us improve genome assembly of Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)?},
   url = {http://ecip.cz/home},
   year = {2017}
}

TY  - CONF
ID  - 1399070
AU  - Vorel, Jiří - Jankůjová, Marie - Oppelt, Jan - Pardy, Filip - Roudnický, Pavel - Ilgová, Jana - Dvořáková, Hana - Jedličková, Lucie - Mikeš, Libor - Jirsová, Dagmar - Koubková, Božena - Gelnar, Milan - Kašný, Martin
PY  - 2017
TI  - Could nanopore sequencing help us improve genome assembly of Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)?
SN  - 9788021087996
KW  - NGS
KW  - nanopore
KW  - Monogenea
KW  - Eudiplozoon
KW  - nipponicum
KW  - genome
UR  - http://ecip.cz/home
N2  - Ectoparasitic flatworms from the family Diplozoidae (Platyhelminthes, Monogenea) represent a serious bloodfeeding fish pathogens. Until now, 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. To this date only two monogenean genomes are deposited in public sequence databases. Genomes of Gyrodactylus salaris (Monopisthocotylea, Gyrodactylidae) and Protopolystoma xenopodis (Polyopisthocotylea, Polystomatidae). Therefore, we designed whole-genomic sequencing of selected monogenean representative - Eudiplozoon nipponicum Goto 1891, which was performed by three sequencing techniques. 454/Roche (Junior sequencing platform), Illumina (MiSeq and HiSeq sequencing platforms) and modern Oxford Nanopore technique (MinION sequencing platform). Using 454/Roche Junior and both Illumina sequencing platforms, 164,773,962 short raw reads were originally generated. After trimming of low quality reads (Trimmomatic v. 0.36) and removing contaminatinon - reads given by fish host (Cyprinus carpio), 130,741,241 reads were used for the draft of genome assembly. Finally, 766,162 scaffolds were generated in total length 1,322,576,402 base pairs (1.3 Gb). But most of assembled scaffolds were identified as a Spiroplasma sp. or Emticicia oligotrophica (bacterial contaminations), which could mean that significant number of E. nipponicum reads could be unintentionally filtered out and final scaffold is incomplete. For purpose to improve E. nipponicum genome draft, we have additionally included reads generated by modern third generation sequencing method – nanopore sequencing. The MinION platform is a small and portable, real time working, low-cost USB device, producing long-read (theoretically up to 250 Kb). 500 working channels produced 1,097,634 reads with length up to 198,101 base pairs.
ER  -

VOREL, Jiří, Marie JANKŮJOVÁ, Jan OPPELT, Filip PARDY, Pavel ROUDNICKÝ, Jana ILGOVÁ, Hana DVOŘÁKOVÁ, Lucie JEDLIČKOVÁ, Libor MIKEŠ, Dagmar JIRSOVÁ, Božena KOUBKOVÁ, Milan GELNAR and Martin KAŠNÝ. Could nanopore sequencing help us improve genome assembly of Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)? In \textit{6th ECIP meeting - European Centre of Ichtyoparasitology}. 2017. ISBN~978-80-210-8799-6.

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