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

Fragilariopsis cylindrus CCMP1102 is characterised by a complex genome with significant levels of heterozygosity between haplotypes, > 35% repeats, and an unknown karyotype. This complexity hindered prior assemblies, which show coverage discrepancies indicative of incompleteness. Here, we use a k-mer spectra analysis to reveal the coverage signature for a third haplotype. We applied a novel haplotype-specific assembly method to reconstruct the F. cylindrus CCMP1102 genome, producing 10 fully assembled chromosomes capped by telomeres, and a putative chromosome with a single breakpoint. Our analysis shows triploidy, two cases of aneuploidy, and several truncations. We also present evidence that F. cylindrus reproduces sexually. Taken together, our analytical approach is capable of haplotype-resolved assemblies from structurally complex, poly-ploid genomes, making it suitable for complex genomes of non-model organisms, including those with unknown karyotype. ### Competing Interest Statement The authors have declared no competing interest.