Out of the Water: Origin and Diversification of the LBD Gene Family

Abstract

LBD (lateral organ boundaries domain) genes are essential to the developmental programs of many fundamental plant organs and function in some of the basic metabolic pathways of plants. However, our historical perspective on the roles of LBD genes during plant evolution has, heretofore, been fragmentary. Here, we show that the LBD gene family underwent an initial radiation that established five gene lineages in the ancestral genome of most charophyte algae and land plants. By inference, the LBD gene family originated after the emergence of the green plants (Viridiplantae), but prior to the diversification of most extant streptophytes. After this initial radiation, we find limited instances of gene family diversification in land plants until successive rounds of expansion in the ancestors of seed plants and flowering plants. The most dynamic phases of LBD gene evolution, therefore, trace to the aquatic ancestors of embryophytes followed by relatively recent lineage-specific expansions on land.

Keywords: Charophyte algae; LBD genes; Phylogenomics; Viridiplantae.

Fig. 1.

ML phylogeny of LBD proteins. (A) Phylogram of global relationships among LBD genes shows that a long branch separates Class II proteins from the larger Class I clade. (B) Class I lineage of LBD proteins rooted along the branch separating Classes IA, IB, and IE, from Class IC/ID. Colored taxon names indicate the presence of charophyte algae (green), bryophytes (orange), lycophytes (purple), monilophytes (red), gymnosperms (blue), and angiosperms (teal), in all five of the main sublineages of the gene family.

Fig. 2.

Alignment of Arabidopsis, Selaginella, and Isoetes Class IB LBD proteins. Note that the characteristic motif of the angiosperm Class IB sequences (“CGACKFLRRKC,” residues 1–11) is conserved in the lycophyte species.