Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification

PLoS One. 2017 Sep 25;12(9):e0185439. doi: 10.1371/journal.pone.0185439. eCollection 2017.

Abstract

The GRAS gene family is a large plant-specific family of transcription factors that are involved in diverse processes during plant development. Medicago truncatula is an ideal model plant for genetic research in legumes, and specifically for studying nodulation, which is crucial for nitrogen fixation. In this study, 59 MtGRAS genes were identified and classified into eight distinct subgroups based on phylogenetic relationships. Motifs located in the C-termini were conserved across the subgroups, while motifs in the N-termini were subfamily specific. Gene duplication was the main evolutionary force for MtGRAS expansion, especially proliferation of the LISCL subgroup. Seventeen duplicated genes showed strong effects of purifying selection and diverse expression patterns, highlighting their functional importance and diversification after duplication. Thirty MtGRAS genes, including NSP1 and NSP2, were preferentially expressed in nodules, indicating possible roles in the process of nodulation. A transcriptome study, combined with gene expression analysis under different stress conditions, suggested potential functions of MtGRAS genes in various biological pathways and stress responses. Taken together, these comprehensive analyses provide basic information for understanding the potential functions of GRAS genes, and will facilitate further discovery of MtGRAS gene functions.

MeSH terms

  • Amino Acid Sequence
  • Chromosome Mapping
  • Chromosomes, Plant / genetics
  • Evolution, Molecular
  • Gene Duplication
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Genes, Plant*
  • Medicago truncatula / genetics*
  • Medicago truncatula / growth & development
  • Medicago truncatula / physiology
  • Multigene Family
  • Nitrogen Fixation / genetics
  • Phylogeny
  • Plant Proteins / genetics
  • Plant Root Nodulation / genetics
  • Sequence Homology, Amino Acid
  • Stress, Physiological
  • Transcription Factors / genetics

Substances

  • Plant Proteins
  • Transcription Factors

Grants and funding

The work was supported by the “100-Talent Program of the Chinese Academy of Sciences” foundation, the National Science Foundation for Fostering Talents in Basic Research of China (J1210069), Postdoc Youth Elite Project in Helongjiang province (LBH-TZ1209) and the National Natural Science Foundation of Shandong province in China (ZR201702170122). The funders have participated in decision to publish and preparation of the manuscript.