Whole-genome resequencing of four seed-borne Alternaria isolates from carrot

We present whole-genome resequencing datasets for four seed-borne Alternaria isolates from carrot (Daucus carota) collected in Jiuquan, Gansu, China during 2023-2025. One representative isolate was sequenced per species: Alternaria tenuissima (AtD1), Alternaria dauci (AdD3), Alternaria carotiincultae (AcD3), and Alternaria alternata (AaD2). Sequencing was performed on an Illumina NovaSeq 6000 platform using paired-end 2x150 bp reads with approximately 300-350 bp insert size. These datasets provide genome-wide variation resources to support studies of diversity, population structure, and pathogenicity of carrot-associated Alternaria.