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

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

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.
Author Robert Marek Nowak (FEIT / IN)
Robert Marek Nowak,,
- The Institute of Computer Science
, Jakub Jastrzębski
Jakub Jastrzębski,,
-
, Wiktor Kuśmirek (FEIT / IN)
Wiktor Kuśmirek,,
- The Institute of Computer Science
, Rusłan Sałamatin
Rusłan Sałamatin,,
-
, Małgorzata Rydzanicz
Małgorzata Rydzanicz,,
-
, Agnieszka Sobczyk-Kopcioł
Agnieszka Sobczyk-Kopcioł,,
-
, Anna Sulima-Celińska
Anna Sulima-Celińska,,
-
, Łukasz Paukszto
Łukasz Paukszto,,
-
, Karol G. Makowczenko
Karol G. Makowczenko,,
-
, Rafał Płoski
Rafał Płoski,,
-
et al.`
Journal seriesScientific data, ISSN 2052-4463, (N/A 140 pkt)
Issue year2019
Vol6
No1
Pages1-6
Publication size in sheets0.5
Keywords in EnglishMitochondrial genome, Eukaryote, DNA sequencing
ASJC Classification1804 Statistics, Probability and Uncertainty; 3304 Education; 3309 Library and Information Sciences; 1706 Computer Science Applications; 1710 Information Systems; 2613 Statistics and Probability
DOIDOI:10.1038/s41597-019-0311-3
URL http://dx.doi.org/10.1038/s41597-019-0311-3
Languageen angielski
File
s41597-019-0311-3.pdf 8.47 MB
Score (nominal)140
Score sourcejournalList
ScoreMinisterial score = 140.0, 01-01-2020, ArticleFromJournal
Publication indicators WoS Citations = 0; Scopus SNIP (Source Normalised Impact per Paper): 2018 = 2.629; WoS Impact Factor: 2017 = 5.305 (2) - 2017=5.862 (5)
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