Using genome and transcriptome analysis to elucidate biosynthetic pathways

[Display omitted] •Multidimensional and multistaged multi-omics integration becomes popular.•Genome and transcriptome data can be integrated to decipher biological pathways.•Differentially expressed genes in transcriptome can be analyzed and mined.•Pathway gaps can be filled with alternative enzymes revealed from other organisms.•Principle of designing transcriptome comparison experiments was discussed. With the rapid development of sequencing and multi-omics analysis technologies, the elucidation of the biosynthetic pathways become realistic for plant or microbial natural products. The arrangement of omics sample from product producing and non-producing species, tissues or growth phase is essential for obtaining differential expressed genes, which are the candidates for key pathway enzymes. Here, we summarize the process of data analysis, enumerate the grouping of genome and transcriptome samples in recent projects, and discuss the principle of designing omics samples. The challenges of identifying functional enzymes and the potential of machine learning in elucidating biosynthetic pathways are also discussed.