Three reference genomes for freshwater diatom ecology and evolution.

Diatoms are an important component of marine and freshwater ecosystems. Although the majority of described diatom species live in freshwater systems, genome sequencing efforts have focused primarily on marine species. Genomic resources for freshwater species have the potential to improve our understanding of diatom ecology and evolution, particularly in the context of major environmental shifts. We used long- and short-read sequencing platforms to assemble reference genomes for three freshwater diatom species, all in the order Thalalassiosirales, which are abundant in the plankton of oceans, lakes, reservoirs, and rivers worldwide. We targeted three species that cover the breadth of phylogenetic diversity in the cyclostephanoid clade of Thalassiosirales: Cyclostephanos tholiformis (JALLPB020000000), Discostella pseudostelligera (JALLBG020000000), and Praestephanos triporus (JALLAZ020000000). The reference genome for D. pseudostelligera was considerably smaller (39 Mb) than those of both P. triporus (73 Mb) and C. tholiformis (177 Mb). Long-read sequencing allowed for the assembly of scaffold-level genomes, including regions rich in repetitive DNA. Compared to short-read assemblies, long-read assemblies increased the contig N50 length as much as 37-fold and reduced the number of contigs by more than 88%. Transcriptome-guided annotation of the protein-coding genes identified between 10,000 and 12,000 genes. This work provides further demonstration of the value of long-read sequencing and provides novel genomic resources for understanding the ecology and evolution of freshwater diatoms.