Phylogenetic analysis, lineage-specific expansion and functional divergence of seed dormancy 4-like genes in plants

Abstract

The rice gene <i>seed dormancy 4</i> (<i>OsSdr4</i>) functions in seed dormancy and is a major factor associated with pre-harvest sprouting (PHS). Although previous studies of this protein family were reported for rice and other species, knowledge of the evolution of genes homologous to <i>OsSdr4</i> in plants remains inadequate. Fifty four <i>Sdr4-</i>like (hereafter designated <i>Sdr4L</i>) genes were identified in nine plant lineages including 36 species. Phylogenetic analysis placed these genes in eight subfamilies (I-VIII). Genes from the same lineage clustered together, supported by analysis of conserved motifs and exon-intron patterns. Segmental duplications were present in both dicot and monocot clusters, while tandemly duplicated genes occurred only in monocot clusters indicating that both tandem and segmental duplications contributed to expansion of the grass I and II subfamilies. Estimation of the approximate ages of the duplication events indicated that ancestral <i>Sdr4</i> genes evolved from a common angiosperm ancestor, about 160 million years ago (MYA). Moreover, diversification of <i>Sdr4</i><i>L</i> genes in mono and dicot plants was mainly associated with genome-wide duplication and speciation events. Functional divergence was observed in all subfamily pairs, except IV/VIIIa. Further analysis indicated that functional constraints between subfamily pairs I/II, I/VIIIb, II/VI, II/VIIIb, II/IV, and VI/VIIIb were statistically significant. Site and branch-site model analyses of positive selection suggested that these genes were under strong adaptive selection pressure. Critical amino acids detected for both functional divergence and positive selection were mostly located in the loops, pointing to functional importance of these regions in this protein family. In addition, differential expression studies by transcriptome atlas of 11 <i>Sdr4</i><i>L</i> genes showed that the duplicated genes may have undergone divergence in expression between plant species. Our findings showed that <i>Sdr4</i><i>L</i> genes are functionally divergent and positively selected. These may contribute to further functional analysis and molecular evolution of <i>Sdr4L</i> gene families in land plants