Genome-Wide Identification and Expression of the Paulownia fortunei MADS-Box Gene Family in Response to Phytoplasma Infection

Abstract

Paulownia witches’ broom (PaWB), caused by phytoplasmas, is the most devastating infectious disease of Paulownia. Although a few MADS-box transcription factors have been reported to be involved in the formation of PaWB, there has been little investigation into all of the MADS-box gene family in Paulownia. The objective of this study is to identify the MADS-box gene family in Paulownia fortunei on a genome-wide scale and explore their response to PaWB infection. Bioinformatics software were used for identification, characterization, subcellular localization, phylogenetic analysis, the prediction of conserved motifs, gene structures, cis-elements, and protein-protein interaction network construction. The tissue expression profiling of PfMADS-box genes was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Transcriptome data and the protein interaction network prediction were combined to screen the genes associated with PaWB formation. We identified 89 MADS-box genes in the P. fortunei genome and categorized them into 14 subfamilies. The comprehensive analysis showed that segment duplication events had significant effects on the evolution of the PfMADS-box gene family; the motif distribution of proteins in the same subfamily are similar; development-related, phytohormone-responsive, and stress-related cis-elements were enriched in the promoter regions. The tissue expression pattern of PfMADS-box genes suggested that they underwent subfunctional differentiation. Three genes, PfMADS3, PfMADS57, and PfMADS87, might be related to the occurrence of PaWB. These results will provide a valuable resource to explore the potential functions of PfMADS-box genes and lay a solid foundation for understanding the roles of PfMADS-box genes in paulownia–phytoplasma interactions.

Paulownia Witches’ Broom Disease: A Comprehensive Review

“…Combined with metabolome data, a model of the early defense response to PaWB disease was constructed [59]. Mining the paulownia genome data identified some transcription factor (TF) and functional gene families, such as ARF [77], Aux/IAA [78], BTB [79], bZIP [80], CaM/CML [81], GRAS [82], MADS [83], NCED [84], NLR [85], PP2C [86], SERK [87], SPL [88], TCP [89], UBC E2 [90], and WPR [91], that could be affected by phytoplasma colonization. Expression pattern analyses of transcriptome data and using RT-qPCR further showed that some of these gene family members were differentially expressed among healthy, diseased and MMS-treated diseased in vitro paulownia plantlets, indicating that they may be related to the presence of PaWB phytoplasmas (Table 2).…”

Genome-wide identification of thaumatin-like protein family genes in Panax notoginseng and analysis of their responses to Fusarium solani infection

“…The gene structure information was extracted from the P. notoginseng genome data, and a gene structure map was drawn using TBtools (version 1.120) (Deng, Dong, et al, 2023). The conserved motifs of PnTLPs with default parameters were analyzed using MEME (https://meme.Nbcr.net/meme/cgi-bin/meme.cgi), and the maximum discovery number of motifs set to 10 (Li, .…”

Phytoplasma Diseases of Trees: A Comprehensive Review

“…The expression patterns of PfMADS-box genes in different tissues were analyzed using quantitative real-time polymerase chain reaction (qRT-PCR). By integrating transcriptome data and protein interaction network predictions, potential genes associated with PaWB formation were identified.89 MADS-box genes, classified into 14 subfamilies were found in P. fortunei genome by Deng et al [140]. The comprehensive analysis revealed that segment duplication events largely contribute to the evolution of the PfMADS-box gene family; identical motif distribution of proteins in the same subfamily; the promoter regions were highly enriched in cis-elements related to stress and phytohormone-responsive development.The tissue expression pattern of PfMADS-box genes revealed significant subfunctional differentiation they undergo.PfMADS3, PfMADS57, and PfMADS87 are the three genes that might be associated with the presence of PaWB.These investigations led to a useful resource for investigating the possible activities and functions of PfMADS-box genes and establish a strong basis for comprehending the functions of PfMADS-box genes involved in interactions between Paulownia and phytoplasmas.…”