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Transcription profiling and identification of infection-related genes in Phytophthora cactorum

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Abstract

Phytophthora cactorum, an oomycete pathogen, infects more than 200 plant species within several plant families. To gain insight into the repertoire of the infection-related genes of P. cactorum, Illumina RNA-Seq was used to perform a global transcriptome analysis of three life cycle stages of the pathogen, mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). From over 9.8 million Illumina reads for each library, 18,402, 18,569 and 19,443 distinct genes were identified for MY, ZO and GC libraries, respectively. Furthermore, the transcriptome difference among MY, ZO and GC stages was investigated. Gene ontology (GO) and KEGG pathway enrichment analyses revealed diverse biological functions and processes. Comparative analysis identified a large number of genes that are associated with specific stages and pathogenicity, including 166 effector genes. Of them, most of RXLR and NLP genes showed induction while the majority of CRN genes were down-regulated in GC, the important pre-infection stage, compared to either MY or ZO. And 14 genes encoding small cysteine-rich (SCR) secretory proteins showed differential expression during the developmental stages and in planta. Ectopic expression in the Solanaceae indicated that SCR113 and one elicitin PcINF1 can trigger cell death on Nicotiana benthamiana, tobacco (N. tabacum) and tomato (Solanum lycopersicum) leaves. Neither conserved domain nor homologues of SCR113 in other organisms can be identified. Collectively, our study provides a comprehensive examination of gene expression across three P. cactorum developmental stages and describes pathogenicity-related genes, all of which will help elucidate the pathogenicity mechanism of this destructive pathogen.

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Acknowledgements

Financial support towards this work is from the National Natural Science Foundation of China (Nos. 31671971, 31500209), Natural Science Foundation of Yangzhou City (China) (Nos. YZ2016121, YZ2015106), the Special Fund for Agro-Scientific Research in the Public Interest of China (No. 201303018), Natural Science Foundation of the Higher Education Institutions of Jiangsu Province of China (15KJB210007) and the Yangzhou University 2016 Project for Excellent Young Key Teachers.

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  1. College of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui Eastern Road, Yangzhou, 225009, Jiangsu, China

    Xiao-Ren Chen, Shen-Xin Huang, Ye Zhang, Gui-Lin Sheng, Bo-Yue Zhang, Qi-Yuan Li, Feng Zhu & Jing-You Xu

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  1. Xiao-Ren Chen
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Correspondence to Xiao-Ren Chen.

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This article does not contain any studies with human participants or animals performed by any of the authors.

Data availability

The RNA-Seq reads were deposited at the National Center for Biotechnology Information (NCBI) Sequence Read Archive database through the project accession no. SRP059996. The P. cactorum gene sequences can be accessed using the accession no. GBGX00000000 at the NCBI Transcriptome Shotgun Assembly sequence database. The gene sequences cited in the manuscript have been submitted to NCBI database with accession no. AIY34486, KM068098, MF177883 to MF177887. Other supporting data are accessible in additional files.

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Communicated by S. Hohmann.

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Chen, XR., Huang, SX., Zhang, Y. et al. Transcription profiling and identification of infection-related genes in Phytophthora cactorum . Mol Genet Genomics 293, 541–555 (2018). https://doi.org/10.1007/s00438-017-1400-7

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