Genome-wide analysis of long noncoding RNAs affecting rubber biosynthesis in Hevea brasiliensis in response to drought stress

Drought is a major abiotic stress that has detrimental effects on the growth of Hevea brasiliensis. Previous studies mainly focused on the molecular mechanisms of structural genes and transcription factors in response to drought stress. The versatile role of long noncoding RNAs (lncRNAs) in response to abiotic stresses has been established, but a systematic identification and analysis of lncRNAs in rubber trees under drought stress has not been reported. In this study, we analyzed the transcriptomes of bark under drought treatment at three stages using RNA deep sequencing. A total of 17,511 novel lncRNAs were identified. Among these, 762, 502, and 497 lncRNAs were differentially expressed in CK vs D12, CK vs D36, and D12 vs D36, respectively. LncRNA target prediction identified 310 cis -regulated and 1203 trans -regulated differentially expressed lncRNAs (DELncs). Functional enrichment analysis revealed that the target genes of DELncs were associated with latex biosynthetic processes. In the trend analysis, 306 lncRNAs were found to be enriched in 'cluster 1 '. Additionally, the messenger RNA (mRNA) associated with lncRNAs in latex biosynthesis was strongly correlated with transcription factors, such as HD -Zip, bHLH, NAC, Dof, AP2/ERF, NAC, MYB, and GRAS. Furthermore, the majority of differentially expressed genes (DEGs) were significantly downregulated in rubber biosynthesis pathways. Moreover, 54 DELncs were found to directly regulate the expression of nine structural DEGs. Importantly, the key structural gene involved in rubber elongation under drought stress, CPT12, was positively cis -regulated by MSTRG.37159.1 and transregulated by MSTRG.48908.2, MSTRG.50362.1, and MSTRG.6564.1. Our findings provide systematic identification of lncRNAs under drought stress and establish a solid foundation for understanding the regulatory mechanisms of rubber synthesis.