High-quality genome assemblies of Colletotrichum orbiculare, a re-emerging anthracnose pathogen threatening cucurbits in the eastern U.S.

Cucurbit anthracnose, caused by Colletotrichum orbiculare, is a re-emerging disease in the eastern U.S. causing significant yield losses and threatening vegetable production. Preliminary analyses of nine isolates showed differences in QoI fungicide sensitivity, as well as nucleotide sequence differences in the internal transcribed spacer of the rDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and cytochrome B between populations from watermelon and those from cucumber and cantaloupe. High-quality, whole genome assemblies are needed as references for population genomic studies to better understand the biology of C. orbiculare. DNA of isolates obtained from watermelon and cucumber in Georgia was extracted and sequenced using PacBio. Sequencing reads were trimmed, assembled, and scaffolded. The final assemblies resulted in high-quality genomes containing 12 and 14 scaffolds with total lengths of 90.0 and 92.2 Mb, largest scaffold sizes of 22.3 and 26.4 Mb, and N50 values of 18.9 and 13.0 Mb for the watermelon and cucumber isolates, respectively. BUSCO analyses showed completeness scores greater than 98.4% and 96.3% using Sordariomycetes and Glomerellales databases, respectively. Moreover, more than 98.3% and 96.3% of the genes were single copy using the same databases. These genomes provide robust resources for further comparative analyses of C. orbiculare from different hosts. Next, 200 isolates from different cucurbit hosts across the eastern U.S. will be re-sequenced to investigate population structure to enhance disease management programs.