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

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.

Complete genome sequence of lovastatin producer Aspergillus terreus ATCC 20542 and evaluation of genomic diversity among A. terreus strains

“…Genomic DNA of A. terreus ATCC 20542 was isolated using the SDS/Phenol method as described previously (Wilson 1987 ; Nowak et al 2019 ). DNA quality control was performed by measuring the absorbance at 260/230, template concentration was determined using Qubit fluorimeter (Thermo Fisher Scientific, Waltham, USA), and DNA integrity was analyzed by 0.8% agarose gel electrophoresis and by PFGE using Biorad CHEF-III instrument (BioRad, Hercules, USA).…”

Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly

“…However, if the subsampled data correspond to <30× coverage, the final assembly can be deteriorated, as we notice on Homo sapiens assembly, where chromosome 22 is missing from the primary assembly and chromosomes 16, 19, 21 and 22 from the final assembly, after the scaffolding and correction process. On the other hand, it has been reported that a hybrid assembly would need 50× Illumina short-read coverage and 30× Nanopore long-read coverage of the genome ( 15 , 51 , 52 ). In the case of the human genome, notable results with a 34× Illumina and 30× Nanopore coverage were able to be produced.…”

“…By following the hybrid assembly strategy ( 14 , 15 ), the advantages of the two generations are combined, incorporating the information contained in the two read types, overcoming their drawbacks. Recent advantages in long-read sequencing by PacBio have shown very promising results: Sequel System II was released in 2019 with an upgraded SMRT flow cell that was first introduced in 2013 ( 16 ), which was able to increase the sequencing yield up to 8-fold.…”

Nostoc edaphicum CCNP1411 from the Baltic Sea—A New Producer of Nostocyclopeptides

“…Genomic DNA of N. edaphicum CCNP1411 was isolated using SDS/Phenol method as described previously [47,48]. DNA quality control was performed by measuring the absorbance at 260/230 nm, template concentration was determined using Qubit fluorimeter (Thermo Fisher Scientific, Waltham, MA, USA), and DNA integrity was analyzed by 0.8% agarose gel electrophoresis and by PFGE using Biorad CHEF-III instrument (BioRad, Hercules, CA, USA).…”