The melanose diseases is one the most widespread and economically important fungal diseases of citrus worldwide. The causative agent is filamentous fungus Diaporthe citri Wolf (syn. Phomopsis citri H.S. Fawc.). Here, we report genome assemblies of three strains of D. citri, namely strains ZJUD2, ZJUD14 and Q7, generated using a combination of PacBio Sequel long-read and Illumina paired-end sequencing data. The assembled genomes of D. citri ranged 53.97 Mb to 63.64 Mb in genome size, containing 15,977 ~ 16,622 protein-coding genes. In addition, we sequenced and annotated the genome sequences of two Citrus related Diaporthe species, including D. citriasiana and D. citrichinensis. The described genome sequences and annotations can provide a useful resource in the study of fungal biology, pathogen-host interaction, molecular diagnostic marker development, and population genomic analyses of Citrus-related Diaporthe species.

All the data of Diaporthe species reported here have been deposited at NCBI under the BioProject accession number PRJNA660209. The assembled Diaporthe citri genomes has been deposited in GenBank under the accession number JADAZQ000000000 for strain ZJUD2, JADAZP000000000 for strain ZJUD14, JADAZO000000000 for strain Q7. The assembled genome of Diaporthe citriasiana strain ZJUD30 has been deposited in GenBank under the accession number JADAZS000000000. The assembled genome of Diaporthe citrichinensis strain ZJUD34 has been deposited in GenBank under the accession number JADAZR000000000. The Illumina Hiseq raw reads have been deposited in NCBI SRA database under the accession number SRR12578329 for ZJUD2, SRR12578328 for ZJUD14, and SRR12578327 for Q7. All the annotation data generated in this study have been deposited on the Citrus-Related Diaporthe Database at https: http://www.zjudata.com/blast/diaporthe.php.