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

文献类型： 外文期刊

作者： Ding, Zehong 1 ; Fu, Lili 1 ; Tan, Deguan 1 ; Sun, Xuepiao 1 ; Zhang, Jiaming 1 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Hainan Bioenergy Ctr, Inst Trop Biosci & Biotechnol, MOA Key Lab Trop Crops Biol & Genet Resources, Xueyuan Rd 4, Haikou 571101, Hainan, Peoples R China

2.Chinese Acad Trop Agr Sci, Hainan Acad Trop Agr Resource, Xueyuan Rd 4, Haikou 571101, Hainan, Peoples R China

关键词： Hevea brasiliensis; Integrative analysis; Co-expression network; Hub gene; REF/SRPP evolution; Rubber biosynthesis

期刊名称：INDUSTRIAL CROPS AND PRODUCTS （ 影响因子：5.645； 五年影响因子：5.749 ）

ISSN： 0926-6690

年卷期： 2020 年 153 卷

页码：

收录情况： SCI

摘要： 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.

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