Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta

Robert M Nowak,Wiktor Kuśmirek,Daniel Młocicki,Karol G Makowczenko,Rafał Płoski,Łukasz Paukszto,Rusłan Sałamatin,Jan P Jastrzębski,Vasyl V Tkach,Anna Sulima-Celińska,Agnieszka Sobczyk-Kopcioł,Katarzyna Basałaj,Małgorzata Rydzanicz

doi:10.1038/s41597-019-0311-3

Abstract

Despite the use of Hymenolepis diminuta as a model organism in experimental parasitology, a full genome description has not yet been published. Here we present a hybrid de novo genome assembly based on complementary sequencing technologies and methods. The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. Our results indicate that the hybrid sequencing approach is the method of choice for obtaining high-quality data. The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. We obtained one of the most complete cestode genome assemblies and annotated 15,169 potential protein-coding genes. The obtained data may help explain cestode gene function and better clarify the evolution of its gene families, and thus the adaptive features evolved during millennia of co-evolution with their hosts.

Highlights

Background & SummaryThe study of the genomics and transcriptomics of parasite model species has led to advances in the basic aspects of parasite biology, as well as new trends in human and veterinary medicine
We present a hybrid de novo genome assembly based on complementary sequencing technologies and methods
Especially those based on a combination of multiple methods, allow detailed analyses of genome structure

Summary

Background & Summary

The study of the genomics and transcriptomics of parasite model species has led to advances in the basic aspects of parasite biology, as well as new trends in human and veterinary medicine. We confirm that the hybrid sequencing approach is the optimal method for obtaining the high quality data resulting in determination of a complete genome sequence This cost-effective approach combining Illumina paired-end, mate-paired, and MinION Nanopore long reads allowed the retrieval of one of the most comprehensive tapeworm (or any parasitic worm) genome available, complimented by RNA sequencing data. These may result in better understanding of the biology of the parasite, its genetic diversity, adaptation to parasitic way of life and may allow new treatments and/or diagnostic tools to be identified in the near future

Methods

Findings

Code availability