Pseudogenes in the G. elata genome were identified by searching against G. elata intergenic regions using D. officinale or P. equestris protein sequences as the seed sequences (TBLASTN, E-value cut-off 1e−5). Before the BLAST search, regions of the 18,969 true genes were masked. The BLAST hits were conjoined by Solar software. GeneWise was used to predict the pseudogene structures with the ‘-pseudo’ parameter. Pseudogenes were then classified by PseudoPipe59. The PseudoPipe program applies a set of sequence identity and completeness cut-off to report a final set of good-quality pseudogene sequences. We used the following cutoffs: amino acid (AA) sequence identity >30% and match length >50 AA to filter out false positives. GeneWise results that fulfilled the cut-off criteria were denoted as high-confidence pseudogenes. High-confidence pseudogenes were then assigned to three categories. (1) Processed/retrotransposed pseudogenes (PSSDs), which formed through retrotransposition. Retrotransposition occurred by reintegration of a cDNA, a reverse transcribed mRNA transcript, into the genome at a new location. (2) Duplicated pseudogenes (DUPs), which formed through gene duplication, following by decay of genes, include frameshifts or premature stop codons. (3) Pseudogenic fragments (FRAGs), which were fragments that have high-sequence similarity to known proteins, but were too decayed to be reliably assessed as processed or duplicated. We used the following criteria to classify PSSDs, DUPs, and FRAGs: (i) PSSDs, exon number = 1, 0.7 < align ratio ≤ 0.95, 0.3 ≤ identity ≤ 0.95; (ii) DUPs, exon number > 1, 0.3 ≤ identity ≤ 0.95, and existing insertion, deletion, termination, or frameshift; (iii) FRAGs, exon number = 1, align ratio < 0.7, 0.3 ≤ identity ≤ 0.95.