Genomic signatures of polyploid origin and diploidization in Campanula americana.

Abstract

Cycles of whole-genome duplication (WGD) followed by return to diploidy have played a major role in plant evolution, yet genome evolution during intermediate stages of diploidization in autopolyploids remains less well characterized than in allopolyploids. We present a chromosome-scale genome assembly of Campanula americana to reconstruct its polyploid history and examine post-WGD diploidization. Our analyses revealed three WGDs, the most recent occurring approximately 10.4 million years ago. Multiple lines of evidence support an autopolyploid origin for C. americana, with none showing the chromosome-scale differentiation expected under allopolyploidy. At the structural level, duplicated homologous regions show extensive inversions and translocations, and the current chromosome number is reduced relative to the ancestral base number. These patterns are consistent with substantial cytological diploidization. In contrast, genic diploidization appears more gradual and balanced. Gene retention is broadly symmetric between homologous regions, and losses occur primarily as dispersed single-gene events rather than block-scale deletions, with no evidence for subgenome dominance. This pattern is consistent with limited inherited asymmetries between duplicated regions and differs from allopolyploids that show subgenome-biased fractionation. Phylogenetic and cytological evidence further suggest that the most recent WGD is shared across a small North American clade. Together, our results characterize C. americana as a polyploid in an intermediate diploidization stage (i.e. mesopolyploid), in which chromosome-level reorganization appears more advanced than gene fractionation. This genome establishes a foundation for comparative studies of genome evolution following WGD across the North American Campanulaceae, and more broadly for understanding how polyploid genomes return to a diploid-like state.