Bioinformatics Study of Aux/IAA Family Genes and Their Expression in Response to Different Hormones Treatments during Japanese Apricot Fruit Development and Ripening

Genome-Wide Identification of the Paulownia fortunei Aux/IAA Gene Family and Its Response to Witches' Broom Caused by Phytoplasma

The typical symptom of Paulownia witches' broom (PaWB), caused by phytoplasma infection, is excessive branching, which is mainly triggered by auxin metabolism disorder. Aux/IAA is the early auxin-responsive gene that participates in regulating plant morphogenesis such as apical dominance, stem elongation, lateral branch development, and lateral root formation. However, no studies have investigated the response of the Aux/IAA gene family to phytoplasma infection in Paulownia fortunei. In this study, a total of 62 Aux/IAA genes were found in the genome. Phylogenetic analysis showed that PfAux/IAA genes could be divided into eight subgroups, which were formed by tandem duplication and fragment replication. Most of them had a simple gene structure, and several members lacked one or two conserved domains. By combining the expression of PfAux/IAA genes under phytoplasma stress and SA-treated phytoplasma-infected seedlings, we found that PfAux/IAA13/33/45 may play a vital role in the occurrence of PaWB. Functional analysis based on homologous relationships showed a strong correlation between PfAux/IAA45 and branching. Protein-protein interaction prediction showed that PfARF might be the binding partner of PfAux/IAA, and the yeast two-hybrid assay and bimolecular fluorescent complementary assay confirmed the interaction of PfAux/IAA45 and PfARF13. This study provides a theoretical basis for further understanding the function of the PfAux/IAA gene family and exploring the regulatory mechanism of branching symptoms caused by PaWB.

Auxin-responsive protein MaIAA17-like modulates fruit ripening and ripening disorders induced by cold stress in 'Fenjiao' banana

Cold stress severely affects the banana fruit softening and de-greening, significantly inhibiting the ripening processes. However, the mechanism of ripening disorder caused by chilling injury (CI) in banana fruit remains largely unknown. Herein, MaIAA17-like, an Auxin/Indole-3-Acetic Acid (Aux/IAA) family member, was found to be highly related to the softening and de-greening in 'Fenjiao' banana. Its expression was rapidly increased with fruit ripening and then gradually decreased under normal ripening conditions (22 °C). Notably, cold storage severely repressed MaIAA17-like expression but was rapidly increased following ethephon treatment for ripening in fruits without CI. However, the expression repression was not reverted in fruits with serious CI symptoms after 12 days of storage at 7 °C. AtMaIAA17-like bound and regulated the activities of promoters of chlorophyll (MaNOL and MaSGR1), starch (MaBAM6 and MaBAM8), and cell wall (MaSUR14 and MaPL8) degradation-related genes. MaIAA17-like also interacted with ethylene-insensitive 3-binding F-box protein (MaEBF1), further activating the expression of MaNOL, MaBAM8, MaPL8, and MaSUR14. Generally, the transient overexpression of MaIAA17-like promoted fruit ripening by inducing the expression of softening and de-greening related genes. However, silencing MaIAA17-like inhibited fruit ripening by reducing the expression of softening and de-greening related genes. These results imply that MaIAA17-like modulates fruit ripening by transcriptionally upregulating the key genes related to fruit softening and de-greening.

Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean (Glycine max) Growth and Development

The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Little is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We also revealed their phylogeny, structure, motif analysis, chromosome location, and expression. Based on their evolutionary links, we divided the 111 potential soybean J-proteins into 12 main clades (I-XII). Gene-structure estimation revealed that each clade had an exon-intron structure resembling or comparable to others. Most soybean J-protein genes lacked introns in Clades I, III, and XII. Moreover, transcriptome data obtained from a publicly accessible soybean database and RT-qPCR were used to examine the differential expression of DnaJ genes in various soybean tissues and organs. The expression level of DnaJ genes indicated that, among 14 tissues, at least one tissue expressed the 91 soybean genes. The findings suggest that J-protein genes could be involved in the soybean growth period and offer a baseline for further functional research into J-proteins' role in soybean. One important application is the identification of J-proteins that are highly expressed and responsive during flower and seed development in soybean. These genes likely play crucial roles in these processes, and their identification can contribute to breeding programs to improve soybean yield and quality.

Genome-Wide Identification and Expression Analysis of the Aux/IAA Gene Family of the Drumstick Tree (Moringa oleifera Lam.) Reveals Regulatory Effects on Shoot Regeneration

Auxin plays a critical role in organogenesis in plants. The classical auxin signaling pathway holds that auxin initiates downstream signal transduction by degrading Aux/IAA transcription repressors that interact with ARF transcription factors. In this study, 23 MoIAA genes were identified in the drumstick tree genome. All MoIAA genes were located within five subfamilies based on phylogenetic evolution analysis; the gene characteristics and promoter cis-elements were also analyzed. The protein interaction network between the MoIAAs with MoARFs was complex. The MoIAA gene family responded positively to NAA treatment, exhibiting different patterns and degrees, notably for MoIAA1, MoIAA7 and MoIAA13. The three genes expressed and functioned in the nucleus; only the intact encoding protein of MoIAA13 exhibited transcriptional activation activity. The shoot regeneration capacity in the 35S::MoIAA13-OE transgenic line was considerably lower than in the wild type. These results establish a foundation for further research on MoIAA gene function and provide useful information for improved tissue culture efficiency and molecular breeding of M. oleifera.