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

BMC Biology

Bernard Henrissat¹  Sergey Koren²  David Eccles³  Jodie Chandler³  Mali Camberis³  Graham Le Gros³  Jonathan J. Ewbank³ 

[1] Department of Biological Sciences, King Abdulaziz University;Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health;Malaghan Institute of Medical Research;

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

DOI  :  10.1186/s12915-017-0473-4

来源: DOAJ

【 摘 要 】

Abstract Background 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. Results Using Nippostrongylus brasiliensis as a test case, applying improved base-calling algorithms and assembly methods, we demonstrate the feasibility of de novo genome assembly matching current community standards using only MinION long reads. In doing so, we uncovered an unexpected diversity of very long and complex DNA sequences repeated throughout the N. brasiliensis genome, including massive tandem repeats of tRNA genes. Conclusion Base-calling and assembly methods have improved sufficiently that de novo genome assembly of large complex genomes is possible using only long reads. The method has the added advantage of preserving haplotypic variants and so has the potential to be used in population analyses.

【 授权许可】

Unknown