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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.    Electronic supplementary material  The online version of this article (10.1186/s12866-018-1324-3) contains supplementary material, which is available to authorized users.

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