Proceedings of the Royal Society B: Biological Sciences
Restricted accessResearch articles

Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of tapeworm Ligula intestinalis

Masoud Nazarizadeh

Masoud Nazarizadeh

Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic

Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic

Contribution: Conceptualization, Formal analysis, Investigation, Methodology, Visualization, Writing – original draft, Writing – review & editing

Google Scholar

Find this author on PubMed

,
Milena Nováková

Milena Nováková

Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic

Contribution: Formal analysis, Investigation, Writing – review & editing

Google Scholar

Find this author on PubMed

,
Marie Drábková

Marie Drábková

Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic

Contribution: Formal analysis, Investigation, Writing – review & editing

Google Scholar

Find this author on PubMed

,
Julian Catchen

Julian Catchen

Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA

Contribution: Investigation, Supervision, Writing – review & editing

Google Scholar

Find this author on PubMed

,
Peter D. Olson

Peter D. Olson

Life Sciences Department, Natural History Museum, London, UK

Contribution: Methodology, Supervision, Writing – review & editing

Google Scholar

Find this author on PubMed

and
Jan Štefka

Jan Štefka

Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic

Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic

[email protected]

Google Scholar

Find this author on PubMed

Ligula intestinalis (Cestoda: Diphyllobothriidae) is an emerging model organism for studies on parasite population biology and host–parasite interactions. However, a well-resolved genome and catalogue of its gene content has not been previously developed. Here, we present the first genome assembly of L. intestinalis, based on Oxford Nanopore Technologies, Illumina and Omni-C sequencing methodologies. We use transcriptome profiling to compare plerocercoid larvae and adult worms and identify differentially expressed genes (DEGs) associated with these life stages. The genome assembly is 775.3 mega (M)bp in size, with scaffold N50 value of 118 Mbp and encodes 27 256 predicted protein-coding sequences. Over 60% of the genome consists of repetitive sequences. Synteny analyses showed that the 10 largest scaffolds representing 75% of the genome display high correspondence to full chromosomes of cyclophyllidean tapeworms. Mapping RNA-seq data to the new reference genome, we identified 3922 differentially expressed genes in adults compared with plerocercoids. Gene ontology analyses revealed over-represented genes involved in reproductive development of the adult stage (e.g. sperm production) and significantly enriched DEGs associated with immune evasion of plerocercoids in their fish host. This study provides the first insights into the molecular biology of L. intestinalis and provides the most highly contiguous assembly to date of a diphyllobothriid tapeworm useful for population and comparative genomic investigations of parasitic flatworms.

Footnotes

Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.7021305.

References

Reference