Whole-genome resequencing datasets of four Alternaria isolates obtained from carrot seeds

Carrot (Daucus carota) is a widely cultivated vegetable crop with high nutritional value. Alternaria is one of the most damaging fungal pathogens to carrots, responsible for diseases such as leaf blight and root rot. However, public genomic resources for carrot-associated Alternaria remain limited, and no genomic data have been reported for seed-transmitted pathogens of this genus to date. This Data Note presents resequencing datasets of four Alternaria isolates obtained from carrot seeds, which will support future research on pathogen diversity and population genetics. We isolated > 20 Alternaria-like isolates from carrot seeds collected from commercial seed production fields in Suzhou District of Jiuquan City and Jinta County of Jiayuguan City, Gansu Province, China (2023–2025; ~7–8 per year), delineated four species based on phenotypic characterization and multilocus sequencing of the ITS rDNA region (primers ITS1/ITS4) and the EF-1α gene (primers EF1-F/EF1-R), and resequenced one representative per species—A. tenuissima (AtD1), A. dauci (AdD3), A. carotiincultae (AcD3), and A. alternata (AaD2)—using paired-end 150-bp sequencing on an Illumina HiSeq/NovaSeq platform. Datasets are available in the NCBI SRA under BioProject PRJNA1344466 (https://identifiers.org/ncbi/bioproject:PRJNA1344466) as four SRA Runs: SRR35781711, SRR35781712, SRR35781713, and SRR35781714.