RNA raw reads assembly and analysis for NRRL23338 and E3
RNA sequencing raw reads were uploaded into the software Geneious Prime. After trimming and filtering using the built-in function in Geneious Prime, all the raw reads were mapped into their respective reference genome of NRRL23338 or E3. Expression levels of each CDS were then calculated by Geneious Prime. DEseq2 method was used for differentially expression analysis.
Clusters of orthologous group were identified by NCBI batch entrez (https://www.ncbi.nlm.nih.gov/sites/batchentrez ) and EggNOG database (Huerta-Cepas et al., 2016). iPATH helped visualize the distribution of DEGs over different metabolic pathways (Darzi, Letunic, Bork, & Yamada, 2018). Gene set analysis and reporter metabolites analysis were conducted by R package Piano (Varemo, Nielsen, & Nookaew, 2013) based on a genome-scale metabolic model (11). Hierarchical clustering of DEGs was carried out by a web-based tool, Morpheus (https://software.broadinstitute.org/GENE-E ).