Decoding a Multigenomic Symphony: Divergent Evolutionary Tempos Across the Four Genomic Compartments of Teleaulax Cryptophytes

作者：Beiying Wu, Youliang Pan, Agnes Monica Sanjani Harefa, Hao Zhou, Jiawei Li, Ying Wang, Per Juel Hansen, Nina Lundholm, Andreas Altenburger, Qiye Li · 发表于：Molecular Ecology · 年份：2026 · DOI：10.1111/mec.70441 · 研究领域：Protist diversity and phylogeny、Genomics and Phylogenetic Studies、Algal biology and biofuel production

Secondary endosymbiosis drives eukaryotic diversification by integrating genetic compartments from disparate lineages, yet how the host and endosymbiont genomes co-evolve over deep time remains poorly understood. Cryptophytes provide a compelling model to dissect this integration, as they uniquely retain four distinct genomes within a single cell: the host nucleus and mitochondrion, alongside a red algal-derived plastid and its relict nucleus (nucleomorph). Here, we investigate the evolutionary and regulatory dynamics of these four coexisting genomes in two ecologically important cryptophytes, Teleaulax amphioxeia and Teleaulax acuta. We reveal a striking decoupling of evolutionary tempos across these genomic compartments. Plastid genomes exhibit structural and functional stasis, while mitochondrial genomes, despite also maintaining high synteny, show faster sequence evolution and mobile element invasion. Nucleomorph genomes evolves even more rapidly, but their gene expression is rigid, with regulatory flexibility limited to a small, conserved set of plastid-supporting genes. Intriguingly, Teleaulax host nuclear genomes have undergone massive expansion, likely driven by ancient whole-genome duplication that might explain their greatest divergence among the four genomic compartments. This divergence is further characterised by differential expansion of gene families (e.g., PHYB-like photoreceptors and motor-related proteins) potentially linked to ecological adaptation. Diel tr...