Three reference genomes for freshwater diatom ecology and evolution.

Area of Science:

• * Microbial Ecology
• * Genomics
• * Evolutionary Biology

Background:

• * Diatoms are vital freshwater and marine ecosystem components, yet genomic resources predominantly exist for marine species.
• * Freshwater diatom genomes are essential for understanding their ecological roles and evolutionary adaptations, especially amid environmental changes.
• * The order Thalassiosirales, including freshwater species, is globally abundant in planktonic communities.

Purpose of the Study:

• * To generate high-quality reference genomes for three freshwater diatom species within the Thalassiosirales order.
• * To explore the phylogenetic diversity within the cyclostephanoid clade using genomic data.
• * To demonstrate the utility of long-read sequencing for assembling diatom genomes.

Main Methods:

• * Utilized both long- and short-read sequencing technologies for genome assembly.
• * Focused on three species: *Cyclostephanos tholiformis*, *Discostella pseudostelligera*, and *Praestephanos triporus*.
• * Employed transcriptome-guided annotation to identify protein-coding genes.

Main Results:

• * Successfully assembled scaffold-level genomes, capturing repetitive DNA regions.
• * Long-read assemblies significantly improved contig N50 length (up to 37-fold) and reduced contig count (>88%) compared to short-read assemblies.
• * Identified 10,000–12,000 protein-coding genes per species, with *D. pseudostelligera* having a smaller genome (39 Mb) than *P. triporus* (73 Mb) and *C. tholiformis* (177 Mb).

Conclusions:

• * Long-read sequencing is highly effective for assembling complex freshwater diatom genomes.
• * The generated genomic resources will advance research into the ecology and evolution of freshwater diatoms.
• * This study expands genomic representation for key freshwater microbial groups.