Can Repeated Reductive Genome Evolution Across Archaeplastida Explain Volatility in Traits?

ABSTRACT

Genome sequencing efforts have covered phylodiverse Archaeplastida, the lineage of plants and algae that bears primary plastids. In these efforts, gene gains and novelties are a major focus of comparative genomic analyses. Yet, ancestral reconstructions increasingly infer extensive gene loss in major lineages, challenging narratives that emphasize continual gains in complexity. In this perspective, we examine evidence for recurrent genome contraction across photosynthetic eukaryotes, focusing on red algae, the ancestry of land plants, and subsequent diversification within embryophytes. Recent studies suggest that ancestors of modern lineages often possessed larger and more complex gene repertoires than their descendants. We argue that repeated cycles of genome expansion and reduction have generated substantial trait volatility, making gene loss a central driver of eukaryotic evolutionary innovation and diversification.