Collectors, not hoarders: Complex gene structures in Amphidinium carterae revealed through nanopore sequencing

Dinoflagellates are ecologically vital marine microalgae with notoriously large and complex genomes, marked by extensive repetition and unconventional gene structures. Here, we present a near-complete genome assembly for Amphidinium carterae, assembled exclusively using Oxford Nanopore long-read sequencing and comprehensively annotated using a transcriptome-guided approach. The 1.25 Gb nuclear genome spans 2,478 contigs with a coverage of 60X, N50 of 1.1 Mb, and contains 55% repetitive elements. Annotation was challenging due to the prevalence of short exons, long introns, tandem gene duplication, and frequent nesting of genes. Standard BUSCO analysis using AUGUSTUS underestimated completeness; however, super-transcriptome-guided correction revealed over 89.6% of conserved genes, underscoring the importance of tailored annotation approaches for dinoflagellates. For the 68 densely packed tandemly repeated gene sets, with copy numbers ranging from 3 to 52, identification and annotation required a combination of methods including manual curation. Comparison to a recent independent assembly of an alternate A. carterae strain corroborated the results with slight variation in gene copy and nucleotide sequence but overall showed strong conservation of tandem gene sets. Many tandem repeat gene regions displayed high conservation across both coding and non-coding segments, implying DNA-based duplication. Gene expression analyses revealed that tandem gene arrays contributed significantly to transcriptional output, with expression levels positively correlated with copy number (p = 1.7e-15), suggesting a dose-dependent regulatory mechanism. The most highly duplicated gene, Major Basic Nuclear Protein (MBNP), was also one of the most highly expressed gene families and existed in distinct long and short isoforms arranged in alternating tandem patterns. This genome represents a comprehensive assembly with exhaustive annotation of tandem gene sets within a free-living dinoflagellate genome and offers new insights into gene organization, expression regulation, and repeat-driven genome architecture. Our findings challenge the long-held view of dinoflagellates as genomic “hoarders”, instead revealing a strategy of selective gene retention, curation, and amplification related to selection pressures. This work provides a valuable reference for future genomic studies and paves the way for improved annotation of complex, repeat-rich eukaryotic genomes.