Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects

Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.

Plants, with an estimated 300,000 species, provide crucial primary production and ecosystem structure. To date, our quantitative understanding of diversity gradients of megadiverse clades such as plants has been hampered by the paucity of distribution data. Here, we investigate the global-scale species-richness pattern of vascular plants and examine its environmental and potential historical determinants. Across 1,032 geographic regions worldwide, potential evapotranspiration, the number of wet days per year, and measurements of topographical and habitat heterogeneity emerge as core predictors of species richness. After accounting for environmental effects, the residual differences across the major floristic kingdoms are minor, with the exception of the uniquely diverse Cape Region, highlighting the important role of historical contingencies. Notably, the South African Cape region contains more than twice as many species as expected by the global environmental model, confirming its uniquely evolved flora. A combined multipredictor model explains approximately 70% of the global variation in species richness and fully accounts for the enigmatic latitudinal gradient in species richness. The models illustrate the geographic interplay of different environmental predictors of species richness. Our findings highlight that different hypotheses about the causes of diversity gradients are not mutually exclusive, but likely act synergistically with water-energy dynamics playing a dominant role. The presented geostatistical approach is likely to prove instrumental for identifying richness patterns of the many other taxa without single-species distribution data that still escape our understanding.

Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.