Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns

Abstract

Rapid alkalinization factors (RALFs) are plant small peptides that could induce a rapid pH increase in the medium of plant cell suspension culture and play a critical role in plant development. The evolutionary process of the RALF gene family remains unclear. To obtain details of the phylogeny of these genes, this study characterized RALF genes in Arabidopsis, rice, poplar and maize. Phylogenetic trees, evolutionary patterns and molecular evolutionary rates were used to elucidate the evolutionary process of this gene family. In addition, the different signatures of selection, expression patterns, and subcellular localization of RALFs were also analyzed. We found that the RALF gene family had a rapid birth process after the separation of the eudicot and monocot species about 145 million years ago, that tandem duplication played a dominant role in the expansion of Arabidopsis and rice RALF gene family, and that RALFs were under purifying selection according to estimations of the substitution rates of these genes. We also identified a diverse expression pattern of RALF genes and predominant extracellular localization feature of RALF proteins. Our findings shed light on several key differences in RALF gene family evolution among the plant species, which may provide a scaffold for future functional analysis of this family.

Keywords: RALF; evolution; selection; tandem duplication.

Figure 1

Evolutionary change in the number of RALF genes in Arabidopsis, poplar, rice and maize. Notes: The numbers in squares and ellipses represent the maximum numbers of genes in ancestral and extant species (At, Arabidopsis; Pt, poplar; Os, rice; Zm, maize), respectively. The numbers with plus and minus indicate the gene gains and losses, respectively, for each branch. N0, lower land plant ancestor; N1, angiosperm ancestor; N2, eudicot ancestor; N3, monocot ancestor.

Figure 2

Evolution of the one subgroup of Arabidopsis RALF genes. (A) Phylogenetic relationships. (B) Hypothetical origins of seven Arabidopsis RALF genes by tandem duplication, segmental duplication and retroposition. Notes: The letters S, R and T on the nodes of the phylogenetic tree indicate the positions where segmental duplication, retroposition and tandem duplication have occurred, respectively.

Figure 3

Chromosomal locations of Arabidopsis RALF genes. Notes: Approximate positions of RALFs are displayed on the respective chromosome. Letters denote evolutionary classification. s, stable; ss, superstable; u, unstable.

Figure 4

Divergence levels of RALFs (A. thaliana versus A. lyrata). Notes: Mean K_a/K_s ratios of stable (n = 15), unstable (n = 4) and superstable (n = 2) are shown. A. thaliana genes with a single A. lyrata ortholog are included in Figure S6.

Figure 5

Expression profiles of the Arabidopsis RALF genes. Notes: The dynamic expression profiles were extracted from Genevestigator., Green, yellow and red evolutionary branches denote stable, unstable and superstable RALFs in Arabidopsis, respectively.