Melanose disease is one the most widely distributed and economically important fungal diseases of citrus worldwide. The causative agent is the filamentous fungus Diaporthe citri Wolf (syn. Phomopsis citri H.S. Fawc.). Here, we report the genome assemblies of three strains of D. citri, namely strains ZJUD2, ZJUD14 and Q7, which were generated using a combination of PacBio Sequel long-read and Illumina paired-end sequencing data. The assembled genomes of D. citri ranged from 52.06 Mb to 63.61 Mb in genome size, containing 15,977 ~ 16,622 protein-coding genes. We also sequenced and annotated the genome sequences of two Citrus-related Diaporthe species, D. citriasiana and D. citrichinensis. In addition, a database for citrus-related Diaporthe genomes was established to provide a public platform to access genome sequences, genome annotation and comparative genomics data of these Diaporthe species. The described genome sequences and the citrus-related Diaporthe genomes database provide a useful resource for the study of fungal biology, pathogen-host interaction, molecular diagnostic marker development, and population genomic analyses of Diaporthe species. The database will be updated regularly when the genomes of newly isolated Diaporthe species are sequenced. The citrus-related Diaporthe genomes database is freely available for non-profit use at http://www.zjudata.com/blast/diaporthe.php.
