Evolutionary Patterns and Coevolutionary Consequences of MIRNA Genes and MicroRNA Targets Triggered by Multiple Mechanisms of Genomic Duplications in Soybean

Abstract

The evolutionary dynamics of duplicated protein-encoding genes (PEGs) is well documented. However, the evolutionary patterns and consequences of duplicated MIRNAs and the potential influence on the evolution of their PEG targets are poorly understood. Here, we demonstrate the evolution of plant MIRNAs subsequent to a recent whole-genome duplication. Overall, the retention of MIRNA duplicates was correlated to the retention of adjacent PEG duplicates, and the retained MIRNA duplicates exhibited a higher level of interspecific preservation of orthologs than singletons, suggesting that the retention of MIRNA duplicates is related to their functional constraints and local genomic stability. Nevertheless, duplication status, rather than local genic collinearity, was the primary determinant of levels of nucleotide divergence of MIRNAs. In addition, the retention of duplicated MIRNAs appears to be associated with the retention of their corresponding duplicated PEG targets. Furthermore, we characterized the evolutionary novelty of a legume-specific microRNA (miRNA) family, which resulted from rounds of genomic duplication, and consequent dynamic evolution of its NB-LRR targets, an important gene family with primary roles in plant-pathogen interactions. Together, these observations depict evolutionary patterns and novelty of MIRNAs in the context of genomic duplication and evolutionary interplay between MIRNAs and their PEG targets mediated by miRNAs.

Plasticity and innovation of regulatory mechanisms underlying seed oil content mediated by duplicated genes in the palaeopolyploid soybean

“…Only a single LEC2 homolog in soybean ( GmLEC2 ) and a single LEC2 homolog in common bean ( PvLEC2 ) were found to be closely related to LEC2 (Figure c), but they were not identified as syntelogs either. According to previous analyses of duplicated genes in soybean (Schmutz et al ., ; Du et al ., ; Zhao et al ., ), GmWRI1a / GmWRI1b and GmLEC1a / GmLEC1b are considered to be two homoeologous pairs formed by the ~13‐mya WGD event (Figure S2), which are likely to be the orthologs of the Arabidopsis WRI1 and LEC1 , respectively.…”

“…As the LEC2 syntelogs were not found in either soybean or common bean, four additional genes (dubbed GmFUS3a , GmFUS3b , GmABI3a , and GmABI3b ) in soybean and two additional genes in common bean (dubbed PvFUS3 and PvABI3 ), which share high degrees of homology with LEC2 , were identified and analyzed (Figure c). According to our previous analyses (Schmutz et al ., ; Du et al ., ; Zhao et al ., ), GmFUS3a / GmFUS3b and GmABI3a / GmABI3b are two homoeologous pairs formed by the ~13‐mya WGD event (Figure S2). GmFUS3a / GmFUS3b and PvFUS3 , and GmABI3a / GmABI3b and PvABI3 are two groups of syntelogs (Figure S1b,c), which are most closely related to the Arabidopsis FUS3 and ABI3 , and are possibly, the FUS3 and ABI3 orthologs, respectively.…”

Landscape of fluid sets of hairpin-derived 21-/24-nt-long small RNAs at seed set uncovers special epigenetic features in Picea glauca

“…Similar to protein-coding genes, the evolution of MIR genes is affected by genomic features (Maher et al. 2006; Axtell and Bowman 2008; Zhao et al. 2015) and correlated with the utility of certain paralogs of DCL s resulting in specific size classes of sRNAs (Vazquez et al.…”

New Insights on Coffea miRNAs: Features and Evolutionary Conservation

“…In addition to model plants, miRNAs have been identified in the crop species cultivated for food [62], textiles [59], and biofuel [16]. Some efforts have been performed to describe miRNAs in coffee.…”