ALBERT

Description: The Arabidopsis DA1 genes appear to have multiple functions in regulating organ size and abiotic stress response, but the biological roles of its closely related genes remain unknown. Evolutionary analyses might provide some clues to aid in an understanding of their functional diversification. In this work, we characterized the molecular evolution and expressional diversification of DA1 -like genes. Surveying 354 sequenced genomes revealed 142 DA1 -like genes only in plants, indicating plant-specificity of these genes. The DA1-like protein modular structure was composed of two UIMs (ubiquitin interaction motifs), one LIM-domain (from lin-11 , isl-1 , and mec-3 ), and a conserved C-terminal, and was distinguishable from the already defined three groups of LIM-domain proteins. We further found that the DA1 -like genes diverged into Classes I and II at the ancestor of seed plants and acquired 13 clade-specific residues during their evolutionary history. Moreover, diverse intron size evolution was noted following the transition from size-expandable introns to minimal ones, accompanying the emergence and diversification of angiosperms. Functional diversification as it relates to gene expression was further investigated in soybean. Glycine max DA1 genes showed diverse tissues expression patterns during development and had substantially varied abiotic stress response expression. Thus, variations in the coding regions, intron size, and gene expression contributed to the functional diversification of this gene family. Our data suggest that the evolution of the DA1 -like genes facilitated the development of diverse molecular and functional diversification patterns to accompany the successful radiation of plants into diverse environments during evolution.

Description: Gene loss is the driving force for changes in genome and morphology; however, this particular evolutionary event has been poorly investigated in leguminous plants. Legumes (Fabaceae) have some lineage-specific and diagnostic characteristics that are distinct from other angiosperms. To understand the potential role of gene loss in the evolution of legumes, we compared six genome-sequenced legume species of Papilionoideae, the largest representative clade of Fabaceae, such as Glycine max , with 34 nonlegume plant species, such as Arabidopsis thaliana . The results showed that the putative orthologs of the 34 Arabidopsis genes belonging to 29 gene families were absent in these legume species but these were conserved in the sequenced nonlegume angiosperm lineages. Further evolutionary analyses indicated that the orthologs of these genes were almost completely lost in the Papillionoideae ancestors, thus designated as the legume lost genes (LLGs), and these underwent purifying selection in nonlegume plants. Most LLGs were functionally unknown. In Arabidopsis , two LLGs were well-known genes that played a role in plant immunity such as HARMLESS TO OZONE LAYER 1 and HOPZ-ACTIVATED RESISTANCE 1 , and 16 additional LLGs were predicted to participate in plant–pathogen interactions in in silico expression and protein–protein interaction network analyses. Most of these LLGs’ orthologs in various plants were also found to be associated with biotic stress response, indicating the conserved role of these genes in plant defense. The evolutionary implication of LLGs during the development of the ability of symbiotic nitrogen fixation involving plant and bacterial interactions, which is a well-known characteristic of most legumes, is also discussed. Our work sheds light on the evolutionary implication of gene loss events in Papilionoideae evolution, as well as provides new insights into crop design to improve nitrogen fixation capacity.