Genome-wide identification and analysis of a cotton secretome reveals its role in resistance against Verticillium dahliae

Authors: LI, RAN - Chinese Academy Of Agricultural Sciences; MA, XI-YUE - Chinese Academy Of Agricultural Sciences; ZHANG, YE-JING - Chinese Academy Of Agricultural Sciences; ZHANG, YONG-JUN - Chinese Academy Of Agricultural Sciences; ZHU, HE - Chinese Academy Of Agricultural Sciences; SHAO, SHENG-NAN - Chinese Academy Of Agricultural Sciences; ZHANG, DAN-DAN - Chinese Academy Of Agricultural Sciences; Klosterman, Steven; DAI, XIAO-FENG - Chinese Academy Of Agricultural Sciences; SUBBARAO, KRISHNA - University Of California; CHEN, JIEYIN - Chinese Academy Of Agricultural Sciences

Submitted to: BMC Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/16/2023
Publication Date: 8/4/2023
Citation: Li, R., Ma, X.Y., Zhang, Y.J., Zhang, Y.J., Zhu, H., Shao, S.N., Zhang, D.D., Klosterman, S.J., Dai, X.F., Subbarao, K.V., Chen, J.Y. 2023. Genome-wide identification and analysis of a cotton secretome reveals its role in resistance against Verticillium dahliae. BMC Biology. 21. Article 166. https://doi.org/10.1186/s12915-023-01650-x.
DOI: https://doi.org/10.1186/s12915-023-01650-x

Interpretive Summary: Verticillium dahliae is a soilborne pathogenic fungus that causes disease on over 200 plant species worldwide, including many agriculturally important crops. In some crop systems such as cotton, the available genetic resources allow more in-depth studies to be carried out to identify specific genes and proteins that are up or down-regulated following pathogen treatment. Identification of these genes and their encoded protein products provides insights into how plants defend themselves. In this study, we identified cotton genes encoding predicted secreted proteins from both resistant and susceptible cultivars. Transcriptome analysis revealed differential expression of components of the cotton secretome in response to V. dahliae. Through gene silencing experiments, we further determined that some of these genes are directly involved in cotton defense against V. dahliae. This work is of special interest since it is typically pathogen secretomes that are analyzed, rather than those of the hosts. Moreover, because V. dahliae attacks such a broad range of plants, the work will be useful to guide additional research on resistance mechanisms in multiple plant-pathogen systems.

Technical Abstract: The extracellular space between the cell wall and plasma membrane is a battlefield in plant-pathogen interactions. Within this space the pathogen employs its diverse secretome to attack the hostin a variety of ways, including by immunity manipulation. However, the role of the plant secretome is rarely studied for its role in disease resistance. Here, we examined the secretome of Verticillium wilt resistant Gossypium hirsutum cultivar Zhongzhimian No.2 (ZZM2, encoding 95,327 predicted coding sequences), to determine its role in disease resistance against the pathogen Verticillium dahliae. Bioinformatics-driven analyses showed that ZZM2 encodes 2,085 secreted protein members which display disequilibrium in their distribution among the chromosomes, and which may play important biological function. Protein property analysis showed that the secretome is different in its characteristics (amino acid residue abundance) due to localization in the extracellular space. The secretome of cotton genome revealed conservation for an allotetraploid genome, but nevertheless exhibited variation of orthologs and comparable unique genes between the two sub-genomes. Functional annotation suggested that the secretome is enriched for responses to biological stress as may occur in the extracellular space, such as the defense responses and polysaccharide metabolism. Transcriptome analysis strongly suggested the cotton may employ the secretome to enhance the extracellular stress response (hydrolase activity, oxidoreductase activity and extracellular region, etc.), thus contributing to resistance against the V. dahliae infection. Further, the defense response genes (the immunity marker gene NbHIN1, the salicylic acid marker gene NbPR1, and the jasmonic acid marker gene NbLOX4) were activated in varying degrees when Nicotina benthamiana leaves were agro-infiltrated with 28 randomly selected members, suggesting that the secretome plays important role in the immunity response. Finally, gene silencing assays of 11 members from 13 selected candidates in ZZM2 displayed higher susceptibility to V. dahliae, which directly suggested that the secretome members confer the Verticillium wilt resistance in cotton. In conclusion, our data demonstrate that the cotton secretome plays an important role in Verticillium wilt resistance, which will facilitate development of the resistance gene markers and increase the understanding of their mechanisms in disease resistance.