Time points used for this study: 7 and 10 days after inoculation (dai). For each time point, final libraries composed of transcripts with no size selection were sequenced on six SMRT cells. The raw reads generated from six SMRT cells were pooled together for each time point and processed following the RS_IsoSeq protocol 
(https://www.pacb.com/support/software-downloads) available in SMRT analysis package v2.3.0.  Each time point contains two fasta files: 
(1) The error-corrected transcriptome of P. pachyrhizi (7DAI-assembly.fsa.gz and 10DAI-assembly.fsa.gz). The error-corrected transcripts were used for CSEP prediction. 
(2) High quality and low quality consensus transcripts before error correction (7DAI-final.consensus.fasta and 10DAI-final.consensus.fasta). These files were used for error correction using Illumina short-reads as reference. The non-soybean Illumina short read error correction was performed using three error correction algorithms (LoRDEC; HALC; Hercules). The dataset uploaded contains the error-corrected transcripts for each time point generated for the manuscript titled "Transcriptome Analysis of Phakopsora pachyrhizi Uncovers Putative Effector Repertoire During Infection."