Comparative full-length transcriptome analysis provides novel insights into the regulatory mechanism of natural rubber biosynthesis in Taraxacum kok-saghyz Rodin roots

Taraxacum kok-saghyz Rodin (TKS) is a promising alternative rubber-producing plant due to the high-quality natural rubber (NR) synthesized in its root. Nevertheless, the comprehensive molecular mechanisms of NR biosynthesis in TKS roots remains segmented and elusive. In the current study, to elucidate the regulatory mechanism of NR synthesis at the transcriptional level, high-quality full-length root transcriptomic data of the TKS were generated based on Oxford Nanopore Technology (ONT). The transcripts with alternative splicing events, polyadenylation sites, and simple sequence repeats (SSRs) were screened. Then, comparative transcriptome analysis was conducted between the lines containing high rubber (HR) and low rubber (LR) contents, and a total of 3134 differentially expressed genes (DEGs) were identified. Among the genes, 1157 DEGs were upregulated, and 1977 DEGs were downregulated in the HR lines vs. the LR lines. The genes involved in NR synthesis were upregulated in HR lines. In contrast, the key genes involved in the synthesis of squalene, phenylpropanoid, fatty acids and ketone, which require the same substrates (isopentenyl pyrophosphate or acetyl-CoA) as NR biosynthesis, were downregulated in HR lines. The results indicated that the expression levels of NR synthesis-related genes were proportional to the NR production, and competition between NR and some metabolites synthesis existed when common substrates were used. Hence, this work provides novel insights into the regulatory mechanism of NR biosynthesis in TKS. Furthermore, the genes or pathways related to NR synthesis identified in this study will be important targets for genetic modification and molecular breeding in further.