*4.8. Data Availability*

The partial gene sequences isolated in this study were deposited in the GenBank under accession IDs: MK790145 to MK790156. The *Rhizoctonia solani* was sequenced to identify the specific anastomosis group and was deposited under GenBank accession ID: MK801228.

#### **5. Conclusions**

During the invasion process, an invasive species from a small founding population may face difficulties due to adverse abiotic and biotic stresses, impacting its survival and reproduction. Invasive species can undergo genetic changes to overcome these natural barriers. Our findings are consistent with previous studies, which identified that many stress induced genes are differentially expressed between invasive and native plant species [29–31]. Our study advances our current understanding of hormone resistance to a widespread pathogen in an invasive species compared to its native congener. In addition, our findings provide insights into the significance of invasive plant defense pathway genes that may have evolved during the invasion process. The manipulation of host defense hormones in favor of pathogen colonization in native plant species may be a mechanism where invasive species gain an advantage over co-occurring native congeners, and this should be the focus of future research. Further studies are required to identify the currently unknown virulence factors (i.e., pathogen effectors or toxins that mimic plant hormone coronatine from *R. solani* and other pathogens) that may affect the signaling pathways differentially between invasive and native species [56]. More specifically, research is needed on resistance (*R*) genes, such as the non-expresser of PR genes 1 (NPR1) of hormone SA, which is a major transcriptional activator that activates antagonism to JA or ET during disease development [117].

**Supplementary Materials:** All supplementary material from this study is available online at http://www.mdpi. com/1422-0067/20/19/4916/s1, including Figure S1: Endogenous hormone salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) contents in both *Alternanthera philoxiroides* and *A. sessilis* after *Rhizoctonia solani* inoculations. Figure S2: Comparative phylogenetic analysis of the selected hormone genes in both the invasive and native species, as well as other closely related species. Figure S3: Identification of conserved motifs in selected genes from both invasive and native species. Figure S4: Identification and alignment of the conserved domain in each of the selected genes from both invasive and native species. Figure S5: Multiple sequence alignments of predicted amino acid sequences of both *Alternanthera philoxeroides* and *A. sessilis* along with other closely related plants. Figure S6: Endogenous hormone Salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) contents in *Alternanthera philoxiroides* after infected with *Rhizoctonia solani*. Figure S7: Sampling site of invasive *Alternanthera philoxeroides* and native *A*. *sessilis*. Table S1: Fold-change ratio of defense hormones and their responsive genes under different treatment conditions in invasive *Alternanthera philoxeroides* compared to native *A. sessilis*. Table S2: Primers used for quantitative RT-qPCR. Table S3: List of putative defense hormones and responsive genes isolated in both *Alternanthera philoxeroides* and *A. sessilis*. Table S4: Sequence information of six defense hormones and responsive

genes isolated from *Alternanthera philoxeroides* and *A. sessilis*. Table S5: Functional analysis of three hormone genes in both *Alternanthera philoxeroides* and *A. sessilis*. Table S6: Screening and isolation of defense hormones and responsive gene sequences from both invasive *Alternanthera philoxeroides* and native *A*. *sessilis*.

**Author Contributions:** Z.C.D., S.S.Q., D.L.D. and B.M. designed the research; Q.C., Q.L., Y.H.Y. and J.L. performed plant growth, sample collection and pathogenicity tests; B.M. and V.D. performed gene isolation and bioinformatic analyses; B.M., V.D., S.R., J.S.H.W. and S.J. analyzed the data; B.M. performed the research and wrote the manuscript; Z.C.D., S.S.Q., S.R., J.S.H.W. and S.J. reviewed the manuscript.

**Funding:** This study was funded by the State Key Research Development Program of China (2017YFC1200100), the National Natural Science Foundation of China (31700342, 31600326, 31770446, 31570414), the Natural Science Foundation of Jiangsu (BK20150503), and the China Postdoctoral Science Foundation (2017T100329). Part of the funding for this research was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), the Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, and the Study Abroad Scholarship of Jiangsu Province and Jiangsu University.

**Acknowledgments:** We thank the Jiangsu University postdoctoral fellowship program.

**Conflicts of Interest:** The authors declare that they have no conflict of interest.
