De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads

David W Eccles (1) , Jodie Chandler , Mali Camberis , Bernard Henrissat (2) , Sergey Koren (3) , Graham Le Gros , Jonathan J. Ewbank (4)

1 FSU - Florida State University [Tallahassee]
2 AFMB - Architecture et fonction des macromolécules biologiques
3 National Biodefense Analysis and Countermeasures Center [Frederick]
4 CIML - Centre d'Immunologie de Marseille - Luminy

Eukaryotic genome assembly remains a challenge in part due to the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematodes are parasites and some represent a serious threat to human health. There is a pressing need for better molecular characterization of animal and plant parasitic nematodes. The advent of long-read DNA sequencing methods offers the promise of resolving complex genomes.

Keywords: DNA repeat; Genome assembly; Helminths; Next-generation sequencing; Population analysis; Base-calling

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology; Genomics [q-bio.GN]

David W Eccles, Jodie Chandler, Mali Camberis, Bernard Henrissat, Sergey Koren, et al.. De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads. BMC Biology, 2018, 16 (1), pp.6. ⟨10.1186/s12915-017-0473-4⟩. ⟨hal-02094619⟩