Time points used for this study: 3, 7, 10, and 14 days after inoculation (dai). Strand-specific cDNA libraries were prepared from ribosomal depleted RNA using the NEBNext Ultra II RNA library prep kit according to the manufacturer’s instructions. Paired-end short-read Illumina sequencing was performed on the dual indexed cDNA libraries using HiSeq3000 (150bp from each end; Illumina, San Diego, CA) and MiSeq (300bp from each end; Illumina, San Diego, CA). The raw reads obtained from Illumina short-read sequencing were quality assessed using FastQC v.0.11.2. Paired-end read trimming was conducted by Trimmomatic 0.36 using sliding window 4:15 and excluding read below a minimal length of 36. Trimmed paired-end RNA-Seq reads from 3, 7, 10, and 14 dai were mapped against the soybean genome v2.1 (https://plants.ensembl.org/Glycine_max) using STAR 2.5.3a aligner to remove soybean reads. The non-soybean short reads were de novo assembled using Trinity v2.6.6. BLASTN (Basic Local Alignment Search Tool) search was performed on non-soybean transcripts using Blastplus v2.6.0 (NCBI: National Center for Biotechnology Information) to remove any plant transcripts with a query coverage greater than 80% and identity greater than 95%. The final de novo transcriptome containing non-plant, non-soybean transcripts for each time point was used for prediction of candidate effectors. This dataset contains four fasta files as follows: 3-dai-assembly.fasta.gz 7-dai-assembly.fasta.gz 10-dai-assembly.fasta.gz 14-dai-assembly.fasta.gz Each file contains non-plant, non-soybean transcripts that was used for prediction of candidate effectors. The dataset uploaded contains the de novo transcriptome for each time point generated for the manuscript titled "Transcriptome Analysis of Phakopsora pachyrhizi Uncovers Putative Effector Repertoire During Infection."