Genome-Wide Transcriptome Analysis Reveals the Comprehensive Response of Two Susceptible Poplar Sections to Marssonina brunnea Infection

G C A T T A C G G C A T genes Article Genome-Wide Transcriptome Analysis Reveals the Comprehensive Response of Two Susceptible Poplar Sections to Marssonina brunnea Infection Yanfeng Zhang 1,2 ID , Longyan Tian 2 , Dong-Hui Yan 1, * and Wei He 2, * 1 2 * The Key Open Laboratory of Forest Protection affiliated to State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China; Correspondence: (D.-H.Y.); (W.H.); Tel.: +86-10-6288-9270 (D.-H.Y.); +86-10-6233-8127 (W.H.) Received: 22 January 2018; Accepted: 1 March 2018; Published: 12 March 2018 Abstract: Marssonina leaf spot disease of poplar (MLDP), caused by the hemibiotrophic pathogen Marssonina brunnea, frequently results in damage to many poplar species. In nature, two formae speciales of M. brunnea exist that are susceptible to different poplar subgenera. Marssonina brunnea f. sp. monogermtubi infects poplar hosts from Populus sect. Aigeiros (Aig), while M. brunnea f. sp. multigermtubi always infects poplar hosts from Populus sect. Leuce Duby (Leu). Based on the fungal penetration structures, a comprehensive transcriptomic approach was used to investigate the gene expression patterns of these two poplar subgenera at three crucial infection stages. MLDP significantly altered the expression patterns of many genes involved in mitogen activated protein kinase (MAPKs) and calcium signaling, transcription factors, primary and secondary metabolism, and other processes in both poplar subgenera. However, major differences in gene expression were also observed between the two poplar subgenera. Aig was most responsive at the initial infection stage, while Leu largely interacted with M. brunnea at the necrotrophic phase. Furthermore, the differentially expressed genes (DEGs) involved in pathways related to biotic stress also differed substantially between the two poplar subgenera. Further analysis indicated that the genes involved in cell wall metabolism and phenylpropanoid metabolism were differentially expressed in the progression of the disease. By examining the expression patterns of genes related to the defense against disease, we found that several genes annotated with causing hypersensitive cell death were upregulated at the necrotrophic phase of MLDP, inferring that plant immune response potentially happened at this infection stage. The present research elucidated the potential molecular differences between the two susceptible interaction systems in MLDP and provided novel insight into the temporal regulation of genes during the susceptible response. To the best of our knowledge, this study also constitutes the first to reveal the molecular mechanisms of poplar in response to the transition of hemibiotrophic fungal pathogens from the biotrophic phase to the necrotrophic phase. Keywords: poplar; Marssonina leaf spot fisease of poplar; Marssonina brunnea; transcriptome; differentially expressed genes; response; interaction 1. Introduction Plant–pathogen interaction networks are complex, and long-term co-evolution has resulted in the establishment of two primary means of communication between plants and their pathogens. Plants attempt to recognize pathogens and defend themselves against potential pathogens on their Genes 2018, 9, 154; doi:10.3390/genes9030154 www.mdpi.com/journal/genes Genes 2018, 9, 154 2 of 25 surface, while pathogens, in contrast, endeavor to manipulate the biology of the plant to complete their growth and reproduction [1]. Understanding the molecular mechanisms of plant–pathogen interactions is crucial for elucidating disease development. Many studies have detailed the types of plant molecular defense mechanisms in response to unsusceptible pathogens [2]. However, investigations into the pathogenesis between susceptible plants and pathogens could help develop models of plant disease as well as provide information regarding susceptible genes, which would facilitate the prediction of pathogen and host fitness in varying environments and inform resistance breeding programs [3]. Importantly, the elucidation of disease resistance requires an understanding of susceptibility. Poplars (Populus spp.) are important commercial tree species that are globally distributed and have become the model trees for forests [4]. The genus Populus comprises six sections: Abaso, Leuce, Leucoides, Aigeiros, Turanga, and Tacamahaca [5]. Most poplar species tolerate a variety of diseases throughout their lifespan, and many pathogens can seriously impact wood production and even cause death in poplars. Marssonina leaf disease of poplar (MLDP), which mostly causes early defoliation, is one of the main diseases affecting poplar [6]. The average loss to wood production attributable to MLDP could reach 30% annually [7]. Considering that the area of poplar plantations exceeds 8.5 million ha in China [8], research on this disease has become more necessary. Previous studies of MLDP have described the disease symptomatology [9,10] and the physiological responses of poplars to MLDP have also been reported. As MLDP progresses, the concentration of ozone might accelerate the disease on older leaves and might increase the resistance to Marssonina spp. on the young leaves [11]. Erickson et al. noted declines in leaf photosynthesis as a result of a disruption to photosynthesis, including reduced leaf stomatal conductance [12]. At the molecular level, several secreted proteins, including potential effectors, were identified in Marssonina brunnea [13]. For poplar hosts, the expression of two Populus deltoids lipoxygenase genes (PdLOX1 and PdLOX2), and two extracellular proteins, PdPGIP2 and PdPGIP4, were both upregulated under the penetration of M. brunnea [14,15]. Additionally, PtrWRKY genes contained in the complete WRKY domain in Populus spp. were also induced during MLDP development [16]. Using microarray hybridization, a previous study discovered that 1160 poplar genes involved in categories such as metabolism were found to be induced in MLDP [17]. However, most of these studies were focused on special genes and lacked complete molecular data on this disease. In China, MLDP is mainly caused by M. brunnea, which belongs to the family Dermateaceae [18]. Reports indicate that M. brunnea has two formae speciales: M. brunnea f. sp. monogermtubi and M. brunnea f. sp. multigermtubi [10,18,19]. In nature, M. brunnea f. sp. monogermtubi infects poplar hosts from Populus sect. Aigeiros (Aig), while M. brunnea f. sp. multigermtubi always infects poplar hosts from Populus sect. Leuce Duby (Leu) [10,19]. It is worth emphasizing that the pathogens and hosts in different susceptible pathogenetic systems are normally incompatible [10,18,19]. The specificity of M. brunnea towards Aig and Leu implies complex interactions between plants and pathogens. (...truncated)