GO functional and KEGG pathway enrichment analysis of differentially expressed genes (DEGs)

To compare the differentially expressed genes (DEGs) in the ST and parent plants, the expression value of each gene was calculated using the fragments per kilobase of transcript per million mapped reads (FPKM) method. This method can eliminate the effect of differences in gene length and sequencing on gene expression, and the results can be directly used to compare gene expression differences between different samples. We used false discovery rate (FDR) (the P value after FDR corrected) and log2 (FPKM_ST/FPKM_diploid) to screen for differential genes at FDR < 0.05 and |log2FC| > 1.

To further understand the function of DEGs between the ST and its parent plants, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases were used for functional enrichment classification of these genes. All DEGs were mapped to GO terms in the Gene Ontology database (http://www.geneontology.org/) to calculate the numbers of genes for each term, and significantly enriched GO terms in the DEGs compared to the genome background were defined by a hypergeometric test. The P value [69] is calculated as follows:

where, N is the number of all genes with GO annotation, n is the number of DEGs in N, M is the number of all genes that were annotated to certain GO terms, and m is the number of DEGs in M.

Pathway enrichment analysis was identified by the Kyoto encyclopedia of genes and genomes (KEGG) database. The P value [63] is calculated in the same manner as in the GO term analysis. In this formula, N is the number of all genes with KEGG annotation, n is the number of DEGs in N, M is the number of all genes annotated to specific pathways, and m is the number of DEGs in M.

The raw data of the cassava transcriptome used here have been deposited in the SRA database of the NCBI (accession number SRP151951).