The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of .

BACKGROUND

is a worldwide invasive species with serious economic impacts. Herein, we are presenting the first project of sequencing and assembling the whole genomes of two lines of derived from Romanian local populations using exclusively Oxford Nanopore Technologies data.

METHODS

We implemented both MinION and Flongle flow-cells and tested the impact of various basecalling models and assembly strategies on the quality of the sought-after representative genome assemblies.

RESULTS

We demonstrate that the sup-basecalling model significantly improved the read quality and that adding a relatively small collection of reads had a significant positive impact over the assembly quality. The novel dScaff bioinformatics prototype tool allowed us to perform sequence-level quality tests, as well as to represent assembly selections and display both the contig redundancy and the repeats-enriched genomic sub-sequences. Moreover, we used dScaff to propose a minimal assembly variant corresponding to one of our lines, GB-ls-coga4, which assured a basic linear coverage of the genome and exhibited quality parameters comparable with those particular to the current reference genome assembly.

CONCLUSIONS

The study presents the first sequencing and assembly of a line in Romania and argues the efficiency of long-read sequencing strategies.