Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula

Abstract

The Auxin Response Factor (ARF) family of transcription factors is an important regulator of environmental response and symbiotic nodulation in the legume Medicago 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 in M. truncatula. We performed a comprehensive analysis of the M. truncatula genome and transcriptome that entailed search for novel ARF genes and the co-expression networks. Our investigation revealed 8 novel M. truncatula ARF (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.

Comparative Transcriptomic and Physiological Analyses Reveal Key Factors for Interstocks to Improve Grafted Seedling Growth in Tangor

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The Arabidopsis gene co‐expression network

“…Functional coupling, revealed in such networks, could be across tissues or could be specific to a tissue. Of course, tissue‐specific networks may reveal additional information (e.g., Burks & Azad, 2016 ), which can be investigated in follow‐up studies. The modules are an important feature of a co‐expression network and can be visualized at both coarse‐grained and fine‐grained resolutions.…”

Coexpression gene network analysis of cold‐tolerant Solanum commersonii reveals new insights in response to low temperatures

“…It also helped researchers to reveal stress-related genes in rice (Sircar & Parekh, 2015;Zhu et al, 2019) and barrel clover (Medicago truncatula Gaertn.) (Burks & Azad, 2016).…”

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