Evolutionary patterns and structural divergence of CENH3 in legumes: Implications for haploid induction breeding

Abstract

Background: The centromeric histone variant CENH3 is crucial for chromosome segregation and haploid induction in plants, yet its evolutionary patterns in legumes remain poorly characterized.

Methods: We investigated CENH3 phylogeny and molecular evolution across legumes, focusing on Vicia using phylogenetic reconstruction, sequence alignment, and evolutionary selection analyses.

Results: Our phylogenetic reconstruction delineated legume species into two major clades (A and B) and revealed a profound contrast between the hypervariable N-terminal tail and the highly conserved histone fold domain (HFD). Within the HFD, the CENP-A targeting domain (CATD) exhibited absolute functional constraint, while the N-terminus demonstrated remarkable evolutionary plasticity. In the genus Vicia, although the exon-intron structure was entirely conserved, substantial sequence polymorphism was identified. Comparative analysis between Vicia sativa L. and Vicia villosa Roth. highlighted species-specific epitope divergence alongside conserved centromere localization. Evolutionary analyses revealed that CENH3 is predominantly under purifying selection, with localized positive selection in specific lineages, whereas canonical H3 exhibited a binary selection pattern dependent on phylogenetic distance.

Conclusions: Our findings elucidate the evolutionary dynamics of CENH3 in legumes and identify the highly conserved yet functionally distinct CATD as a promising, specific target for developing efficient haploid induction systems through genome editing.

Keywords

CENH3 / centromere / genome editing / haploid induction / legumes / molecular evolution / phylogeny

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