Transcriptome analysis of Pará rubber tree (H. brasiliensis) seedlings under ethylene stimulation

Insights from natural rubber biosynthesis evolution for pathway engineering

Natural rubber (NR), valued for its elasticity and impact resistance, is essential for numerous industrial and medical applications, with global demand continuously rising. While approximately 2500 plant species from more than 40 families can produce rubber, the majority is sourced from Hevea brasiliensis grown in tropical regions. Alternative rubber-producing plants, such as Parthenium argentatum and Taraxacum kok-saghyz, offer enhanced environmental adaptability and species diversity, making them promising candidates for rubber production. Recent genome sequencing has shed light on rubber biosynthesis pathways, although the mechanisms involved in producing different forms of polyisoprene across species remain unclear. We explore the evolution of rubber biosynthesis and discuss synthetic biological strategies for enhancing NR-production in subtropical plants and a broader range of plant materials (e.g., Manilkara zapota).

Analysis of regulatory networks provides new insights into the mechanism of rubber synthesis in Lactuca serriola

The rubber tree currently serves as the sole source of natural rubber (NR). However, its limited cultivation range and the increasing global NR demand necessitate the development of an alternative crop for NR production. This study reports that Lactuca serriola can produce high-quality NR suitable for industrial rubber demand. The rubber molecular weight of L. serriola exceeds 750 kg/mol, with NR production occurring throughout the entire plant. Furthermore, treatments with ethylene, methyl jasmonate (MeJA), and salicylic acid (SA) significantly increased rubber content in L. serriola. Transcriptome analysis revealed that ethylene and MeJA treatments affected gene expression associated with isopentenyl pyrophosphate (IPP) synthesis, while ethylene and SA treatments influenced gene expression involved in sucrose transportation and metabolism. Through Pearson correlation coefficient (PCC) analysis and virus-induced gene silencing, several transcription factors and LsCPTs/LsCPTL were identified as key regulators of rubber synthesis in L. serriola. Yeast two-hybrid and co-expression assays suggested that LsCPTL anchors LsCPT1 and LsCPT2 to the endoplasmic reticulum, forming a protein complex that regulates rubber synthesis. This study provides a preliminary analysis of the mechanism by which plant hormones regulate rubber synthesis in L. serriola, revealing its significant potential as an alternative to the rubber tree for NR production.

Genomic diversity of Capillovirus uniheveae (Betaflexiviridae) infecting Hevea brasiliensis Muell. Arg. in Hainan, China

BACKGROUND

Rubber tree (Hevea brasiliensis Muell. Arg.) is a significant commercial crop in tropical areas worldwide, with rubber production threatened by Tapping Panel Dryness (TPD). Rubber tree virus 1 (Capillovirus uniheveae; RTV1) was identified in rubber tree samples with TPD symptoms through RNA-seq. However, its genetic diversity may have hindered the detection of RTV1 via RT-PCR, complicating the further identification of RTV1 as the causative agent of TPD. To assess RTV1 prevalence and genomic diversity, rubber tree bark samples with TPD syndrome were collected from various sites in Hainan, China, for RNA-seq and RTV1 genome determination.

RESULTS

Twenty complete RTV1 genomes were determined from 22 samples with TPD syndrome via RNA-seq and RT-PCR. Using degenerate primers based on conserved sequences in the 3'- and 5'-UTR, 20 complete RTV1 genomes were identified directly from 48 trees affected by TPD via RT-PCR. The 40 RTV1 genome sequences showed significant variations, particularly in the RdRp domain. Phylogenetic analysis of full-genome nucleotide sequences divided RTV1 isolates into three phylogroups (A, B, and C), with phylogroup A being the most prevalent (67.5%). Similar results were observed based on RdRp and CP phylogenetic analysis. Additionally, mixed infections with different genotypes were identified in the same tree. Notably, no genetic recombination was observed among different phylogroups, while ten recombination events were identified within phylogroup A.

CONCLUSIONS

RTV1 was identified in approximately 50% of samples with TPD syndrome collected in Hainan, China, with phylogroup A being the most prevalent. Considerable variations were observed in RTV1 nucleotide sequences among different phylogroups. These findings lay a foundation for accurate diagnostics, etiological characterization, and elucidation of the evolutionary relationships of RTV1 populations, providing a strong guarantee for obtaining virus-free rubber tree seedlings, and promoting the healthy and sustainable development of rubber tree plantations.

Integrative analysis of transcriptome and metabolome reveals how ethylene increases natural rubber yield in Hevea brasiliensis

Hevea brasiliensis is an important cash crop with the product named natural rubber (NR) for markets. Ethylene (ET) is the most effective yield stimulant in NR production but the molecular mechanism remains incomplete. Here, latex properties analysis, transcriptome analysis, and metabolic profiling were performed to investigate the mechanism of NR yield increase in four consecutive tappings after ET stimulation. The results revealed that sucrose and inorganic phosphate content correlated positively with dry-rubber yield and were induced upon ET stimulation. Stimulation with ET also led to significant changes in gene expression and metabolite content. Genes involved in phytohormone biosynthesis and general signal transduction as well as 51 transcription factors potentially involved in the ET response were also identified. Additionally, KEGG annotation of differentially accumulated metabolites suggested that metabolites involved in secondary metabolites, amino-acid biosynthesis, ABC transporters, and galactose metabolism were accumulated in response to ET. Integrative analysis of the data collected by transcriptomics and metabolomics identified those differentially expressed genes and differentially accumulated metabolites are mainly involved in amino-acid biosynthesis and carbohydrate metabolism. Correlation analysis of genes and metabolites showed a strong correlation between amino-acid biosynthesis during ET stimulation. These findings provide new insights into the molecular mechanism underlying the ET-induced increase in rubber yield and further our understanding of the regulatory mechanism of ethylene signaling in rubber biosynthesis.

Cloning, Expression Characteristics of Farnesyl Pyrophosphate Synthase Gene from Platycodon grandiflorus and Functional Identification in Triterpenoid Synthesis

Platycodon grandiflorus is a medicinal plant whose main component is platycodins, which have a variety of pharmacological effects and nutritional values. The farnesyl pyrophosphate synthase (FPS) is a key enzyme in the isoprenoid biosynthesis pathway, which catalyzes the synthesis of farnesyl diphosphate (FPP). In this study, we cloned the FPS gene from P. grandiflorus (PgFPS) with an ORF of 1260 bp, encoding 419 amino acids with a deduced molecular weight and theoretical pI of 46,200.98 Da and 6.52, respectively. The squalene content of overexpressed PgFPS in tobacco leaves and yeast cells extract was 1.88-fold and 1.21-fold higher than that of the control group, respectively, and the total saponin content was also increased by 1.15 times in yeast cells extract, which verified the biological function of PgFPS in terpenoid synthesis. After 48 h of MeJA treatment and 6 h of ethephon treatment, the expression of the PgFPS gene in roots and stems reached its peak, showing a 3.125-fold and 3.236-fold increase compared to the untreated group, respectively. Interestingly, the expression of the PgFPS gene in leaves showed a decreasing trend after exogenous elicitors treatment. The discovery of this enzyme will provide a novel perspective for enhancing the efficient synthesis of platycodins.

Advancing image segmentation with DBO-Otsu: Addressing rubber tree diseases through enhanced threshold techniques

Addressing the profound impact of Tapping Panel Dryness (TPD) on yield and quality in the global rubber industry, this study introduces a cutting-edge Otsu threshold segmentation technique, enhanced by Dung Beetle Optimization (DBO-Otsu). This innovative approach optimizes the segmentation threshold combination by accelerating convergence and diversifying search methodologies. Following initial segmentation, TPD severity levels are meticulously assessed using morphological characteristics, enabling precise determination of optimal thresholds for final segmentation. The efficacy of DBO-Otsu is rigorously evaluated against mainstream benchmarks like Peak Signal-to-Noise Ratio (PSNR), Structural Similarity Index (SSIM), and Feature Similarity Index (FSIM), and compared with six contemporary swarm intelligence algorithms. The findings reveal that DBO-Otsu substantially surpasses its counterparts in image segmentation quality and processing speed. Further empirical analysis on a dataset comprising TPD cases from level 1 to 5 underscores the algorithm's practical utility, achieving an impressive 80% accuracy in severity level identification and underscoring its potential for TPD image segmentation and recognition tasks.

Genome-wide identification of rubber tree pathogenesis-related 10 (PR-10) proteins with biological relevance to plant defense

Pathogenesis-related 10 (PR-10) is a group of small intracellular proteins that is one of 17 subclasses of pathogenesis-related proteins in plants. The PR-10 proteins have been studied extensively and are well-recognized for their contribution to host defense against phytopathogens in several plant species. Interestingly, the accumulation of PR-10 proteins in the rubber tree, one of the most economically important crops worldwide, after being infected by pathogenic organisms has only recently been reported. In this study, the homologous proteins of the PR-10 family were systemically identified from the recently available rubber tree genomes in the NCBI database. The sequence compositions, structural characteristics, protein physical properties, and phylogenetic relationships of identified PR-10 proteins in rubber trees support their classification into subgroups, which mainly consist of Pru ar 1-like major allergens and major latex-like (MLP) proteins. The rubber tree PR10-encoding genes were majorly clustered on chromosome 15. The potential roles of rubber tree PR-10 proteins are discussed based on previous reports. The homologous proteins in the PR-10 family were identified in the recent genomes of rubber trees and were shown to be crucial in host responses to biotic challenges. The genome-wide identification conducted here will accelerate the future study of rubber tree PR-10 proteins. A better understanding of these defense-related proteins may contribute to alternative ways of developing rubber tree clones with desirable traits in the future.

Brassinosteroids Regulate the Water Deficit and Latex Yield of Rubber Trees

Brassinolide (BR) is an important plant hormone that regulates the growth and development of plants and the formation of yield. The yield and quality of latex from Hevea brasiliensis are regulated by phytohormones. The understanding of gene network regulation mechanism of latex formation in rubber trees is still very limited. In this research, the rubber tree variety CATAS73397 was selected to analyze the relationship between BR, water deficit resistance, and latex yield. The results showed that BR improves the vitality of rubber trees under water deficit by increasing the rate of photosynthesis, reducing the seepage of osmotic regulatory substances, increasing the synthesis of energy substances, and improving the antioxidant system. Furthermore, BR increased the yield and quality of latex by reducing the plugging index and elevating the lutoid bursting index without decreasing mercaptan, sucrose, and inorganic phosphorus. This was confirmed by an increased expression of genes related to latex flow. RNA-seq analysis further indicated that DEG encoded proteins were enriched in the MAPK signaling pathway, plant hormone signal transduction and sucrose metabolism. Phytohormone content displayed significant differences, in that trans-Zeatin, ethylene, salicylic acid, kinetin, and cytokinin were induced by BR, whereas auxin, abscisic acid, and gibberellin were not. In summary, the current research lays a foundation for comprehending the molecular mechanism of latex formation in rubber trees and explores the potential candidate genes involved in natural rubber biosynthesis to provide useful information for further research in relevant areas.

Genome-Wide Identification, Evolution and Expression Analysis of the Glutathione S-Transferase Supergene Family in Euphorbiaceae

Euphorbiaceae, a family of plants mainly grown in the tropics and subtropics, is also widely distributed all over the world and is well known for being rich in rubber, oil, medicinal materials, starch, wood and other economically important plant products. Glutathione S-transferases (GSTs) constitute a family of proteins encoded by a large supergene family and are widely expressed in animals, bacteria, fungi and plants, but with few reports of them in Euphorbiaceae plants. These proteins participate in and regulate the detoxification and oxidative stress response of heterogeneous organisms, resistance to stress, growth and development, signal transduction and other related processes. In this study, we identified and analyzed the whole genomes of four species of Euphorbiaceae, namely Ricinus communis, Jatropha curcas, Hevea brasiliensis, and Manihot esculenta, which have high economic and practical value. A total of 244 GST genes were identified. Based on their sequence characteristics and conserved domain types, the GST supergene family in Euphorbiaceae was classified into 10 subfamilies. The GST supergene families of Euphorbiaceae and Arabidopsis have been found to be highly conserved in evolution, and tandem repeats and translocations in these genes have made the greatest contributions to gene amplification here and have experienced strong purification selection. An evolutionary analysis showed that Euphorbiaceae GST genes have also evolved into new subtribes (GSTO, EF1BG, MAPEG), which may play a specific role in Euphorbiaceae. An analysis of expression patterns of the GST supergene family in Euphorbiaceae revealed the functions of these GSTs in different tissues, including resistance to stress and participation in herbicide detoxification. In addition, an interaction analysis was performed to determine the GST gene regulatory mechanism. The results of this study have laid a foundation for further analysis of the functions of the GST supergene family in Euphorbiaceae, especially in stress and herbicide detoxification. The results have also provided new ideas for the study of the regulatory mechanism of the GST supergene family, and have provided a reference for follow-up genetics and breeding work.