title: Identification and Network-Enabled Characterization of Auxin Response Factor Genes inMedicago truncatula.
abstract: The Auxin Response Factor (ARF) family of transcription factors is an important regulator of environmental response and symbiotic nodulation in the legumeMedicago truncatula. While previous studies have identified members of this family, a recent spurt in gene expression data coupled with genome update and reannotation calls for a reassessment of the prevalence of ARF genes and their interaction networks inM. truncatula. We performed a comprehensive analysis of theM. truncatulagenome and transcriptome that entailed search for novel ARF genes and the co-expression networks. Our investigation revealed 8 novelM. truncatulaARF (MtARF) genes, of the total 22 identified, and uncovered novel gene co-expression networks as well. Furthermore, the topological clustering and single enrichment analysis of several network models revealed the roles of individual members of the MtARF family in nitrogen regulation, nodule initiation, and post-embryonic development through a specialized protein packaging and secretory pathway. In summary, this study not just shines new light on an important gene family, but also provides a guideline for identification of new members of gene families and their functional characterization through network analyses.
authors.affiliation: Department of Biological Sciences, University of North Texas Denton, TX, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Burks
authors.affiliation: Department of Biological Sciences, University of North TexasDenton, TX, USA; Department of Mathematics, University of North TexasDenton, TX, USA.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Azad
keywords: Medicago truncatula; auxin response factor; co-expression networks; indole-3-acetic acid; legumes; nodulation