A High-Quality Genome Assembly of Chaetoceros muelleri Reveals Extensive Gene Duplication, Functional Diversification, and Unique Lineage-Specific Innovation

Diatoms are major contributors to marine primary production, yet high-quality nuclear genome resources remain scarce for ecologically dominant lineages such as Chaetoceros. Here, we present the first high-quality nuclear genome assembly of Chaetoceros muelleri, generated from living cells resurrected from resting spores preserved in Baltic Sea sediments and sequenced using PacBio HiFi long-read technology. The assembly is compact (43{square}Mb), highly contiguous (N50{square}={square}1.40{square}Mb), and highly complete (93% BUSCO). Comparative analyses across 14 diatom genomes revealed extensive lineage-specific and expanded gene families in C. muelleri, alongside a small, conserved core genome, reflecting rapid evolutionary turnover. Functional enrichment highlighted diversification of polysaccharide biosynthesis, vesicle-mediated trafficking, membrane remodelling, and transcriptional regulation, consistent with adaptations linked to frustule formation and environmental responsiveness. Transposable elements (TEs) strongly shape the genome, accounting for [~]18% of the assembly, with dominant LTR retrotransposons and a large fraction of unclassified repeats suggesting novel or highly diverged TE lineages. Enrichment of DNA replication, recombination, and repair functions further indicates compensatory genome maintenance associated with TE-driven structural dynamics. Direct comparison with C. tenuissimus revealed contrasting patterns of gene family expansion and regulatory innovation, underscoring divergent evolutionary strategies within Chaetoceros. By integrating resurrection ecology with long-read genomics, this study provides a foundational genomic resource for C. muelleri and highlights the role of TE-mediated genome plasticity in diatom evolution.