Identification of long non-coding RNAs in Verticillium dahliae following inoculation of cotton

Authors: LI, RAN - CHINESE ACADEMY OF AGRICULTURAL SCIENCES; XUE, HUI-SHAN - CHINESE ACADEMY OF AGRICULTURAL SCIENCES; ZHANG, DAN-DAN - CHINESE ACADEMY OF AGRICULTURAL SCIENCES; WANG, DAN - CHINESE ACADEMY OF AGRICULTURAL SCIENCES; SONG, JIAN - CHINESE ACADEMY OF AGRICULTURAL SCIENCES; SUBBARAO, KRISHNA - UNIVERSITY OF CALIFORNIA; Klosterman, Steven; CHEN, JIE-YIN - CHINESE ACADEMY OF AGRICULTURAL SCIENCES; DAI, XIAO-FENG - CHINESE ACADEMY OF AGRICULTURAL SCIENCES

Submitted to: Microbiology Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/4/2022
Publication Date: 1/6/2022
Citation: Li, R., Xue, H.S., Zhang, D.D., Wang, D., Song, J., Subbarao, K.V., Klosterman, S.J., Chen, J.Y., Dai, X.F. 2022. Identification of long non-coding RNAs in Verticillium dahliae following inoculation of cotton. Microbiology Research. 257. Article 126962. https://doi.org/10.1016/j.micres.2022.126962.
DOI: https://doi.org/10.1016/j.micres.2022.126962

Interpretive Summary: The soilborne fungus Verticillium dahliae causes Verticillium wilt disease on numerous crop species, worldwide. The genomic DNA of various strains of V. dahliae have been sequenced, providing valuable information on sequences corresponding to race and other features. In this study, 352 RNA sequences that do not code for proteins were examined for their expression patterns and their locations within the eight chromosomes of V. dahliae. Since the expression of these types of RNAs can influence the regulation of neighboring genes, we further characterized all neighboring genes, revealing that some of the neighboring genes encode virulence factors. The discovery and identity of novel RNAs and their association with virulence may be new targets for developing different disease control measures.

Technical Abstract: Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, these functions have not been assessed in Verticillium dahliae, a soil-borne fungal pathogen that causes devastating wilt diseases in many crops. The discovery and identity of novel lncRNAs and their association with virulence may contribute to an increased understanding of the regulation of virulence in V. dahliae. Here, we identified a total of 352 lncRNAs in V. dahliae. The lncRNAs were transcribed from all V. dahliae chromosomes, typically with shorter open reading frames, lower GC content, and fewer exons than protein-coding genes. In addition, 308 protein-coding genes located within 10 kb upstream and 10 kb downstream of lncRNAs were identified as neighboring genes, and which were considered as potential targets of lncRNA. These neighboring genes encode products involved in development, stress responses, and pathogenicity of V. dahliae, such as transcription factors (TF), kinase, and members of the secretome. Furthermore, 47 lncRNAs were significantly differentially expressed in V. dahliae following inoculation of susceptible cotton (Gossyoiumhisutum) cultivar Junmian No.1, suggesting that lncRNAs may be involved in the regulation of virulence in V. dahliae. Moreover, correlations in expression patterns between lncRNA and their neighboring genes were detected. Expression of lncRNA012077 and its neighboring gene was up-regulated 6 h following inoculation of cotton, while the expression of lncRNA007722 was down-regulated at 6 h but up-regulated at 24 h, in a pattern opposite to that of its neighboring gene. Overexpression of lncRNA012077 in wild-type strain (Vd991) enhanced its virulence on cotton while overexpression of lncRNA009491 reduced virulence. Identification of novel lncRNAs and their association with virulence may provide new targets for disease control.