Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)

Abstract

Transcription factors (TF) are essential for proper plant growth and development. Several legumes, particularly soybean, are rich sources of protein and oil, with great impact in the economy of several countries. Here we report a phylogenomic analysis of major TF families in legumes and their potential association with important traits such as nitrogen fixation and seed development. We used TF DNA-binding domains to systematically screen the genomes of 15 legume and 5 non-legume species. The percentage of TFs ranged from 3-8% of the gene complements. TF orthologous groups (OG) in extant species were used to estimate OG sizes in ancestor nodes using a gene birth-death model, which allowed us to identify lineage-specific expansions. Together, OG analysis and rate of synonymous substitutions (Ks) between gene pairs show that major TF expansions are strongly associated with known whole-genome duplication (WGD) events in the legume ([~]58 mya) and Glycine ([~]13 mya) lineages, which account for a large fraction of the Ph. vulgaris and Gl. max TF repertoires. Out of the 3407 Gl. max TFs, 1808 and 676 can be traced back to a single homeolog in Ph. vulgaris and Vi vinifera, respectively. We found a trend for TFs expanded in legumes to be preferentially transcribed in roots and nodules, suggesting their recruitment early in the evolution of nodulation in the legume clade. We also found TF expansions in the Glycine WGD that were followed by gene loss in the wild soybean Gl. soja, including genes located within important quantitative trait loci. Together, our findings strongly support the roles of two WGDs in shaping the TF repertoires in the legume and Glycine lineages, which are likely related to important aspects of legume and soybean biology.