Genomic and transcriptomic basis of morphological and life cycle diversity in the prasinophyte alga Pseudoscourfieldia marina

The prasinophyte green alga Pseudoscourfieldia marina exhibits striking morphological diversity, with coccoid and flagellated forms now recognized as a single species. To investigate the basis of this divergence, we compare here the genomes and transcriptomes of two morphotypes: CCMP1203 (coccoid, non-flagellated) and UIO007 (scaly, flagellated). Although their genome architecture is largely conserved, the strains differ in ploidy and repeat content, and harbor divergent outlier chromosomes enriched in transposable elements and carbohydrate metabolism genes, suggesting roles in antiviral defense. CCMP1203 is predominantly diploid, whereas UIO007 is haploid and strongly upregulates genes for flagellar assembly and scale formation, including those encoding the complete biosynthetic pathway for the 2-keto sugar 3-deoxy-D-manno-octulosonate, a major carbohydrate component of prasinophyte scales. The presence of meiosis-specific and life-cycle genes in P. marina supports a heteromorphic haplodiplontic life cycle, with the flagellated, scaly UIO007 strain representing the haploid phase and the coccoid CCMP1203 strain the diploid phase. Comparative genomics of two Pseudoscourfieldia marina morphotypes reveals ploidy differences and coordinated expression of scale and flagellar genes, supporting a heteromorphic haplodiplontic life cycle.