Genome sequence of the potato pathogenic fungus Alternaria solani HWC-168 reveals clues for its conidiation and virulence

Abstract

Background: Alternaria solani is a known air-born deuteromycete fungus with a polycyclic life cycle and is the causal agent of early blight that causes significant yield losses of potato worldwide. However, the molecular mechanisms underlying the conidiation and pathogenicity remain largely unknown.

Results: We produced a high-quality genome assembly of A. solani HWC-168 that was isolated from a major potato-producing region of Northern China, which facilitated a comprehensive gene annotation, the accurate prediction of genes encoding secreted proteins and identification of conidiation-related genes. The assembled genome of A. solani HWC-168 has a genome size 32.8 Mb and encodes 10,358 predicted genes that are highly similar with related Alternaria species including Alternaria arborescens and Alternaria brassicicola. We identified conidiation-related genes in the genome of A. solani HWC-168 by searching for sporulation-related homologues identified from Aspergillus nidulans. A total of 975 secreted protein-encoding genes, which might act as virulence factors, were identified in the genome of A. solani HWC-168. The predicted secretome of A. solani HWC-168 possesses 261 carbohydrate-active enzymes (CAZy), 119 proteins containing RxLx[EDQ] motif and 27 secreted proteins unique to A. solani.

Conclusions: Our findings will facilitate the identification of conidiation- and virulence-related genes in the genome of A. solani. This will permit new insights into understanding the molecular mechanisms underlying the A. solani-potato pathosystem and will add value to the global fungal genome database.

Keywords: Alternaria solani; Conidiation; Genome sequence; Secretome; Virulence.

Fig. 1

Distribution of intergenic distances of all predicted genes present in the genome of A. solani HWC-168 compared with A. arborescens EGS 39–128 and A. brassicicola ATCC 96836. Scatterplot representing 5′ and 3′ intergenic distances for all genes present in the genome. Red circles indicate the predicted genes

Fig. 2

Gene Ontology (GO) classification of genes predicted from the genome of A. solani HWC-168, A. arborescens EGS 39–128 and A. brassicicola ATCC 96836. Predicted genes are assigned to 24 categories in the GO classification. The x-axis legend shows a description of the 24 functional categories and the y-axis indicates the number of genes in a specific function cluster. Among the 24 categories, the cluster of ‘general function prediction’ has the highest number of genes, followed by amino acid transport and metabolism and carbohydrate transport and metabolism

Fig. 3

Gene Ontology (GO) classification of core and species-specific genes identified from comparison of A. solani HWC-168, A. arborescens EGS 39–128 and A. brassicicola ATCC 96836 genomes. Predicted core and species-specific genes are assigned to 24 categories in the GO classification. The x-axis legend shows a description of the 24 functional categories and the y-axis indicates the number of genes in a specific function cluster. Among the 24 categories, the cluster of ‘general function prediction’ contains the highest number of core and species-specific genes, followed by translation, ribosomal structure and biogenesis

Fig. 4

Graphical representation of predicted carbohydrate-active enzymes encoding genes in the genome of A. solani HWC-168. Total 261 predicted CAZymes are identified and they are divided into six sub-groups including 65 auxiliary activity (AA), 17 polysaccharide lyase (PL), 9 glycosyl transferase (GT), 94 glucoside hydrolase (GH), 33 carbohydrate esterases (CE) and 17 carbohydrate-binding molecules (CBM). Glucoside hydrolase is predominant in all predicted CAZymes

Fig. 5

Schematic representation of amino acid sequences alignment of 12 RxLx-motif containing effector candidates. a. Sequence logo derived from 12 predicted secreted effector candidates carrying the RxLx[EDQ] motif located within the region of 120 amino acids downstream of the N-terminal signal peptide. b. the conserved amino acids in the RxLx[EDQ] motif are highlighted and the downstream EDQ amino acids are marked with a red rectangle

Fig. 6

Schematic representation of a proposed model illustrating the regulatory pathway of asexual sporulation in A. solani