Gene loss in polyploid Actinidia species inferred from the chromosome-level assembly of Clematoclethra scandens

Gene loss plays a key role in shaping the evolutionary trajectories of polyploid genomes. Actinidia (Actinidiaceae) species exhibit a wide range of ploidy levels, yet the fate and functional consequences of duplicated genes remain poorly understood. Here, we assembled a chromosome-level genome of Clematoclethra scandens, a species from the sister genus of Actinidia, and used it as a reference to infer post-polyploid gene loss in 12 Actinidia species. We found that the Ad-α polyploid event occurred before the divergence of Clematoclethra and Actinidia (~17.0-18.9 Ma). Decayed loss is the predominant mode of gene loss; polyploids A. deliciosa and A. arguta exhibit higher loss rates than diploid relatives and show significantly different gene loss rates among haploid genomes, with biases among haploid genomes and hotspots on certain chromosomes. Localized decayed loci differed significantly among homologous chromosomes; within chromosomes, decayed genes were depleted near chromosome ends but enriched in subterminal and intermediate regions. Decayed loss rates were negatively associated with gene expression, but positively associated with gene copy number, indicating functional redundancy may facilitate gene loss during adaptation to environmental stresses. Species-specific gene-loss events were enriched mainly in translation- and mitochondrial-associated functions. These results show that gene loss in Actinidia is structured by genomic context and intrinsic gene properties and may contribute to the adaptive evolution of mixed-ploidy populations under local environmental conditions.