An integrative transcriptomic and genomic analysis reveals novel insights into the hub genes and regulatory networks associated with rubber synthesis in H. brasiliensis

Abstract

Rubber tree (Hevea brasiliensis) is an important tropical plant that produces natural rubber; however, the hub genes and regulatory networks associated with rubber synthesis remain largely unclear. In this work, 129 publically available RNA-seq datasets were collected to perform gene co-expression network analysis in rubber tree. In total, 25 co-expressed gene modules (M1-M25) were identified, and the molecular functions and hub genes of each module were systematically analyzed. Associations between modules and tissues/stresses revealed that modules were significantly associated with stresses in the tissues where the modules were specifically highly expressed. Notably, module M7 was highly expressed in latex and dramatically responsive to ethylene, jasmonate, and tapping panel dryness treatments. Besides, the genes from M7 were significantly enriched in isoprenoid metabolism, indicating a great contribution of this module to rubber biosynthesis. The co-expression network of rubber biosynthesis genes from M7 revealed that small rubber particle protein 1 (SRPP1), cis-prenyltransferase 2 (CPT2), and rubber elongation factor 1 (REF1) were the most connected hub genes participating in rubber biosynthesis. Two candidate cis-regulatory motifs and three transcription factors that might regulate rubber biosynthesis were further identified. Genomic evolutionary analysis suggested that the expansion of two independently evolved REF/SRPP clusters, II (containing SRPP1) and V (containing REF1), was critical for rubber synthesis. Together, this integrative transcriptomic and genomic analysis provides novel insights into the hub genes and regulatory networks underlying rubber synthesis in H. brasiliensis.