This dataset contains sequences of assembled transcripts from isolates Race 5 and Race 4 of the tomato pathogen Cladosporium fulvum during interaction with its host. transcripts: Assembled transcripts in FASTA and GTF fomats. The GTF files have coordinates of the transcripts in the reference genomes of isolates Race 5 (GCA_020509005.2) and Race 4 (GCA_035196885.1). The other FASTA files include the predicted open reading frames (ORFs) in the transcripts. The nucleotide coding sequence and translated amino acid sequences of the ORFs are in separated FASTA files. In the file names isolate Race 5 is indicated with '*R5*', and isolate Race 4 is indicated with '*R4*'. Description of the files is shown below: representatives_R4_diff_introns.fasta: full-length transcript sequences from isolate Race 4. representatives_R5_diff_introns.fasta: full-length transcript sequences from isolate Race 5. representatives_R4_diff_introns.gtf: coordinates of the transcripts from isolate Race 4 in the genome of Race 4. representatives_R5_diff_introns.gtf: coordinates of the transcripts from isolate Race 5 in the genome of Race 5. representatives_orfs_aa_R4_diff_introns.fasta: predicted protein sequences encoded in the transcripts from isolate Race 4. representatives_orfs_aa_R5_diff_introns.fasta: predicted protein sequences encoded in the transcripts from isolate Race 5. representatives_orfs_cds_R4_diff_introns.fasta: predicted coding sequences in the transcripts from isolate Race 4. representatives_orfs_cds_R5_diff_introns.fasta: predicted coding sequences in the transcripts from isolate Race 5. expression: Contains tab-separated files with the expression values (transcripts per million - TPM) of the transcripts from isolates Race 5 and Race 4 at specific time points (2, 4, 6, 8, 10, 12, and 14 dpi) during interaction with tomato. TPM values were estimated with the alignment-free method Salmon.