Abstract: Genome integrity is fundamentally linked to histone proteins, which emerged as a key regulator for genomic accessibility, adaptive plasticity and epigenetic regulation. Despite their importance, studies on evolutionary dynamics of histone families across the land plant have remained mostly restricted to angiosperms leaving other plants, especially ferns, understudied. Ferns are particularly interesting because they often possess large genomes, high chromosome numbers and two morphologically distinct life phases (gametophyte and sporophyte). Therefore, ferns provide a powerful system to investigate how genome expansion, duplication, and diploidization shape histone family expansion and functional divergence. Leveraging available fern genomes, we conducted comparative genomic and phase-specific expression analyses of histones to assess how genome size, life-cycle, and lineage shape histone gene diversity in fern and representative land plants. We showed that histone gene family size correlates strongly with genome size in land plants, with ferns and angiosperms exhibiting the strongest correlation suggesting that the plasticity in the number of histone genes may hold the key to explain the large genome adaptability in land plants. Extensive expansion of CENH3-like genes was found exclusively in homosporous ferns, supporting that despite their exceptional conservation, histone gene families can experience rapid evolutionary turnover, likely contributing to genome stability in species with large and structurally complex karyotypes. We showed that distinct subsets of H2A, H2B, H3 and H4 genes are reciprocally up-regulated between gametophyte and sporophyte, indicating the existence of generation-specific functional partitioning and a biphasic chromatin regulatory system that underlies the phenotypic distinction of the two generations.

Key words: centromere, chromosomes, gametophyte, life-cycle, nucleosomes, CENH3, H2A.W