Chromosome-scale Genome Sequence of Alternaria alternata causing Alternaria Brown Spot on Citrus

Althernaria brown spot (ABS) caused by Alternaria alternata is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, our group have assembled a draft genome of A. alternata Z7, which contains 165 contigs. In this study, we report a gapless genome assembly of strain Z7 of A. alternata tangerine pathotype, generated using a combination of Oxford nanopore technologies and Illumina paired-end sequencing data. The genome size of A. alternata Z7 is 34.36 Mb, with a GC content of 50.99%, and it contains 11,810 protein-coding genes, 34 rRNA, and 107 tRNA. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes (ECs) and 2 conditionally dispensable chromosomes (CDCs), which is consistent with the experimental evidences of pulsed-field gel electrophoresis (PFGE). To our knowledge, this is the first chromosome-level genome assembly of A. alternata, which is an important necrotroph worldwide. The described genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata.