Purpose This study aimed to systematically characterize the phylogenetic relationships, macro-genomic conservation, and structural architecture of the NPF family in the genus Oryza, and to identify dominant lineages, inter-species collinearity, key functional segments, and adaptive loci, providing a theoretical basis for subsequent genetic resource mining and molecular breeding.
Methods Integrating multi-species genomic data, a systematic was conducted through phylogenetic analysis, 3D structural space dimensionality reduction, multi species collinearity comparison, conserved motif framework analysis, and selection pressure assessment.
Results In the genus Oryza, the NPF family exhibited a well-defined phylogenetic framework, with a few dominant clusters constituting the bulk of the family. The overall copy number of NPF family remained stable, and their distribution across orthologous chromosomes (enriched on chromosomes 1 and 10) displayed a high spatial symmetry. Throughout the domestication and habitat adaptation of Oryza, NPF members showed strong collinearity, and while their protein structures were generally conserved, localized variations in certain domains were also present. The transmembrane core module was largely conserved, albeit with notable local substitutions and lineage-specific differences in its surrounding regions. Evolutionarily, this family was predominantly subject to purifying selection, while a small number of loci had undergone adaptive concerted changes.
Conclusion The evolution of the NPF family in the genus Oryza is characterized by stable major lineages and a generally conserved overall structure, whereas functional divergence in local domains and co-evolution among specific sites drive functional specialization in certain members.
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