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

The
rice gene seed dormancy 4 (OsSdr4) 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 OsSdr4 in plants remains inadequate. Fifty four Sdr4-like (hereafter designated Sdr4L) 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 Sdr4 genes evolved from a common angiosperm ancestor, about 160 million years ago (MYA). Moreover,
diversification of Sdr4L 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 Sdr4L genes showed that the
duplicated genes may have undergone divergence in expression between plant
species. Our findings showed
that Sdr4L genes are functionally divergent and positively
selected. These may contribute to further functional analysis and molecular
evolution of Sdr4L gene families in land plants.