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 ).