Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula

Aux/IAA and auxin response transcription factor (ARF) genes are key regulators of auxin responses in plants. A total of 25 MtIAA and 40 MtARF genes were identified based on the latest updated Medicago truncatula reference genome sequence. They were clustered into 10 and 8 major groups, respectively. The homologs among M. truncatula, soybean, and Arabidopsis thaliana shared close relationships based on phylogenetic analysis. Gene structure analysis revealed that MtIAA and MtARF genes contained one to four concern motifs and they are localized to eight chromosomes, except chromosome 6 without MtARFs. In addition, some MtIAA and MtARF genes were expressed in all tissues, while others were specifically expressed in specific tissues. Analysis of cis-acting elements in promoter region and expression profiles revealed the potential response of MtIAA and MtARF genes to hormones and abiotic stresses. The prediction protein–protein interaction network showed that some ARF proteins could interact with multiple Aux/IAA proteins, and the reverse is also true. The investigation provides valuable, basic information for further studies on the biological functions of MtIAA and MtARF genes in the regulation of auxin-related pathways in M. truncatula.

Genome-Wide Identification Analysis of The Auxin Response Factor Gene Family (ARF) in Zizania Latifolia and its Role in Swelling Stem Formation After Ustilago Esculenta Infection

Background: Auxin signalling plays a crucial role in plant growth and development. Although the auxin response factor (ARF) gene family has been studied in some plant species, its structural features, molecular evolution, and expression profile in Zizania latifolia (Z. latifolia) are still not clear.Results: Our study identified 33 putative YSL genes from the whole Z. latifolia genome. Furthermore, a comprehensive overview of the ZlARFs was undertaken, including phylogenetic relationship, gene structures, conserved domains, synteny, Ka/Ks, motifs, and subcellular locations of the gene product. Synteny analyses and the calculation of Ka/Ks values suggested that all 57 orthologous/paralogous gene pairs between Z. latifolia and Z. latifolia, Z. latifolia and Oryza sativa have experienced strong purifying selection. The phylogenetic analysis of ARFs indicated that the ZlARFs can be divided into 6 classes and that most ZlARFs from Z. latifolia have closer relationships with Oryza sativa than with Arabidopsis. RNA-Seq data and qRT-PCR analyses showed that ZlARF genes were expressed in TDF treatment and U. esculenta infection, while some ZlARFs exhibited high expression levels only in U. esculenta infection. Meanwhile, the interaction networks and gene ontology (GO) term of the ZlARF genes were constructed and 23 ZlARF co-expressed genes were identified, most of which were down-regulated involve auxin-activated signalling pathway in after swelling stem formation. Transcriptome analysis results verified the relevant functions of ARF genes, and most ZlARF genes regulated physiological processes in response to differential cell expansion. Conclusion: Comprehensive bioinformation analysis of the auxin response factor gene family (ARF) in Z. latifolia and its association with swelling stem formation after U. esculenta infection. The bioinformatic and RNA-Seq analyses provided valuable information for further study on the regulation of the growth and development of swelling stem formation by ZlARFs in Z. latifolia.