Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome.

Fragilariopsis cylindrus is characterised by a complex genome with significant levels of heterozygosity between haplotypes, > 35% repeats, and an unknown karyotype. This complexity led to coverage discrepancies in prior assemblies, potentially indicative of them being incomplete. Here, we use a k-mer spectra analysis to discover a third haplotype, confirming triploidy for F. cylindrus CCMP1102. A novel haplotype-specific assembly method was applied to reconstruct the F. cylindrus genome, which revealed the presence of 11 fully assembled chromosomes capped by telomeres, two cases of aneuploidy and several truncations. We also present evidence that F. cylindrus reproduces sexually. Taken together, our approach is capable of haplotype-resolved assemblies from structurally complex, polyploid genomes. Thus, we suggest our approach is suitable for complex genomes of non-model organisms, including those with unknown karyotype.