A chromosome-scale reference genome for Spironucleus salmonicida

Sci Data. 2022 Sep 24;9(1):585. doi: 10.1038/s41597-022-01703-w.


Spironucleus salmonicida is a diplomonad causing systemic infection in salmon. The first S. salmonicida genome assembly was published 2014 and has been a valuable reference genome in protist research. However, the genome assembly is fragmented without assignment of the sequences to chromosomes. In our previous Giardia genome study, we have shown how a fragmented genome assembly can be improved with long-read sequencing technology complemented with optical maps. Combining Pacbio long-read sequencing technology and optical maps, we are presenting here this new S. salmonicida genome assembly in nine near-complete chromosomes with only three internal gaps at long repeats. This new genome assembly is not only more complete sequence-wise but also more complete at annotation level, providing more details into gene families, gene organizations and chromosomal structure. This near-complete reference genome will aid comparative genomics at chromosomal level, and serve as a valuable resource for the diplomonad community and protist research.

Publication types

  • Dataset

MeSH terms

  • Chromosomes / genetics
  • Diplomonadida* / genetics
  • Genome, Protozoan*
  • Genomics
  • Molecular Sequence Annotation
  • Sequence Analysis, DNA