Chromosome Numbers and Reproductive Life Cycles in Green Plants: A Genomic Perspective

Green plants, as the primary producers in the biosphere, play a crucial role in both the biosphere and human activities. Despite their importance, many aspects of their evolutionary history remain mysterious. One such mystery is the association between chromosome number and reproductive life cycle. Heterosporous plants, which include all seed plants, generally have smaller chromosome numbers compared to homosporous plants, which typically have larger chromosome numbers.

Previous hypotheses, such as the gametophytic selfing hypothesis, have tried to explain this pattern but have been rejected. Recent studies suggest that heterosporous lineages may have undergone higher rates of genome downsizing via chromosome number reduction, relative to homosporous lineages. However, the exact mechanisms underlying this process remain unclear.

In this study, we investigate the association between chromosome numbers and reproductive life cycles using genomic data from a wide range of green plant lineages. We focus on two main questions: (1) Have any gene families undergone significant expansion or contraction in heterosporous lineages? (2) Have any gene families undergone distinct selection patterns in heterosporous lineages? By exploring these questions, we aim to shed light on the genomic factors associated with the evolution of heterospory and its link to reduced chromosome numbers.

We conducted comparative genomic analyses across a broad sampling of green plant lineages, including 112 species spanning over 500 million years of evolutionary history. Using gene family evolution models and selection analyses, we identified gene families that have undergone significant expansion, contraction, or selection in heterosporous lineages. Our results reveal both shared and lineage-specific genomic changes associated with the evolution of heterospory. We found expansions in gene families related to developmental regulation, signaling pathways, and stress responses across heterosporous groups. Notably, the MATE efflux family showed consistent expansion and evidence of selection in heterosporous lineages, suggesting a potentially conserved role in heterospory evolution. Further research is needed to explore how such genes might be involved in chromosome behavior and spore production.

Meanwhile, these findings highlight novel genomic insights that may underpin the association between heterospory and reduced chromosome numbers.