Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis)

Integrated physiology, transcriptome and proteome analyses highlight the potential roles of multiple hormone-mediated signaling pathways involved in tapping panel dryness in rubber tree

Currently, one of the most serious threats to rubber tree is the tapping panel dryness (TPD) that greatly restricts natural rubber production. Over-tapping or excessive ethephon stimulation is regarded as the main cause of TPD occurrence. Although extensive studies have been carried out, the molecular mechanism underlying TPD remains puzzled. An attempt was made to compare the levels of endogenous hormones and the profiles of transcriptome and proteome between healthy and TPD trees. Results showed that most of endogenous hormones such as jasmonic acid (JA), 1-aminocyclopropanecarboxylic acid (ACC), indole-3-acetic acid (IAA), trans-zeatin (tZ) and salicylic acid (SA) in the barks were significantly altered in TPD-affected rubber trees. Accordingly, multiple hormone-mediated signaling pathways were changed. In total, 731 differentially expressed genes (DEGs) and 671 differentially expressed proteins (DEPs) were identified, of which 80 DEGs were identified as putative transcription factors (TFs). Further analysis revealed that 12 DEGs and five DEPs regulated plant hormone synthesis, and that 16 DEGs and six DEPs were involved in plant hormone signal transduction pathway. Nine DEGs and four DEPs participated in rubber biosynthesis and most DEGs and all the four DEPs were repressed in TPD trees. All these results highlight the potential roles of endogenous hormones, signaling pathways mediated by these hormones and rubber biosynthesis pathway in the defense response of rubber trees to TPD. The present study extends our understanding of the nature and mechanism underlying TPD and provides some candidate genes and proteins related to TPD for further research in the future.

Bark transcriptome analyses reveals molecular mechanisms involved in tapping panel dryness occurrence and development in rubber tree (Hevea brasiliensis)

Tapping panel dryness (TPD) has become the mostimportant limiting factor for increasing natural rubber yield, whereas illuminating the molecular mechanisms underlying TPD is the prerequisite for solving the problem of TPD. However, molecular mechanisms underlying TPD are largely unknown. In this study, healthy and different stages of TPD-affected rubber trees were utilized to analyze TPD for the first time. We found that the changing tendencies of key latex physiological parameters were closely related to TPD occurrence and development. To reveal the molecular mechanisms underlying TPD, we sequenced and compared bark transcriptomes among healthy rubber tree, and TPD-affected ones at initial and advanced stages. In total, 8607 genes were identified as TPD-related genes in contrast to healthy rubber tree. According to gene expression profiles, the five samples were divided into three groups including healthy rubber tree, and TPD-affected rubber tree in the initial and advanced stages, which was consistent with the stages of TPD occurrence and development. Interestingly, only asmall proportionof the TPD-related genes were constantly down- or up-regulated with TPD occurrence and development. The TPD-related genes in KEGG pathways significantly enriched were closely associated with protein metabolism, cell division and differentiation, PCD, stress responses, terpene biosynthesis, and various metabolism processes. Moreover, overexpression of HbAPX2 identified as a TPD-related gene enhanced oxidative stress tolerance in S. cerevisiae. The typical symptoms of TPD, partial or complete dry zone (no latex flow) on tapping panel, might attribute to lower IPP available for rubber biosynthesis, and downregulation of the genes in post-IPP steps of rubber biosynthesis and the genes involved in latex flow. Our results not only provide new insights into molecular mechanisms underlying TPD occurrence and development but also contribute to developing effective measures to control TPD in rubber trees.

Downregulation of HbFPS1 affects rubber biosynthesis of Hevea brasiliensis suffering from tapping panel dryness

Tapping panel dryness (TPD) is a century-old problem that has plagued the natural rubber production of Hevea brasiliensis. TPD may result from self-protective mechanisms of H. brasiliensis in response to stresses such as excessive hormone stimulation and mechanical wounding (bark tapping). It has been hypothesized that TPD impairs rubber biosynthesis; however, the underlying mechanisms remain poorly understood. In the present study, we firstly verified that TPD-affected rubber trees exhibited lower rubber biosynthesis activity and greater rubber molecular weight compared to healthy rubber trees. We then demonstrated that HbFPS1, a key gene of rubber biosynthesis, and its expression products were downregulated in the latex of TPD-affected rubber trees, as revealed by transcriptome sequencing and iTRAQ-based proteome analysis. We further discovered that the farnesyl diphosphate synthase HbFPS1 could be recruited to small rubber particles by HbSRPP1 through protein-protein interactions to catalyze farnesyl diphosphate (FPP) synthesis and facilitate rubber biosynthesis initiation. FPP content in the latex of TPD-affected rubber trees was significantly decreased with the downregulation of HbFPS1, ultimately resulting in abnormal development of rubber particles, decreased rubber biosynthesis activity, and increased rubber molecular weight. Upstream regulator assays indicated that a novel regulator, MYB2-like, may be an important regulator of downregulation of HbFPS1 in the latex of TPD-affected rubber trees. Our findings not only provide new directions for studying the molecular events involved in rubber biosynthesis and TPD syndrome and contribute to rubber management strategies, but also broaden our knowledge of plant isoprenoid metabolism and its regulatory networks.

Dynamic analysis of Tapping Panel Dryness in Hevea brasiliensis reveals new insights on this physiological syndrome affecting latex production

Tapping Panel Dryness (TPD) is a physiological disorder affecting natural rubber production in Hevea brasiliensis. TPD is associated with clonal susceptibility and overexploitation of rubber trees. Most studies are based on a binary point view of the absence or presence of TPD. This study sets out to characterize the dynamic of the TPD onset through the monthly monitoring of the dry cut length. This reveals the presence of dry spots on the tapped panel of any trees. The frequency of these dry spots increases dramatically in trees developing high level of TPD. Brown bast is an irreversible form of TPD. Brown bast is correlated to a high level of dry cut length. Application of an intensive harvesting system induces early TPD occurrence, which facilitates the study of TPD. Among latex diagnosis parameters, only sucrose content is significantly associated with TPD. Other parameters are more prone to environmental effects and are not reliable as physiological markers. These findings explain the contradictory conclusions of some papers. This study suggests to use intensive harvesting system and monitor the dry cut length for genetic analysis of TPD.

Genome-wide identification of lncRNAs, miRNAs, mRNAs and their regulatory networks involved in tapping panel dryness in rubber tree (Hevea brasiliensis)

Noncoding RNAs (ncRNAs) play pivotal roles in various biological processes in plants. However, the role of ncRNAs in tapping panel dryness (TPD) of rubber tree (Hevea brasiliensis Muell. Arg.) is largely unknown. Here, the whole transcriptome analyses of bark tissues from healthy and TPD trees were performed to identify differentially expressed long ncRNAs (DELs), microRNAs/miRNAs (DEMs), genes (DEGs) and their regulatory networks involved in TPD. A total of 263 DELs, 174 DEMs and 1574 DEGs were identified in the bark of TPD tree compared with that of healthy tree. Kyoto Encyclopedia of Genes and Genomes analysis revealed that most of the DEGs and targets of DELs and DEMs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Additionally, the majority of DEGs and DELs related to rubber biosynthesis were downregulated in TPD trees. Furthermore, 98 DEGs and 44 DELs were targeted by 54 DEMs, 190 DEGs were identified as putative targets of 56 DELs, and 2 and 44 DELs were predicted as precursors and endogenous target mimics of 2 and 6 DEMs, respectively. Based on these, the DEL-DEM-DEG regulatory network involved in TPD was constructed, and 13 hub DELs, 3 hub DEMs and 2 hub DEGs were identified. The results provide novel insights into the regulatory roles of ncRNAs underlying TPD and lay a foundation for future functional characterization of long ncRNAs, miRNAs and genes involved in TPD in rubber tree.

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

BACKGROUND

Natural rubber (cis-1,4-polyioprene, NR) is an indispensable industrial raw material obtained from the Pará rubber tree (H. brasiliensis). Natural rubber cannot be replaced by synthetic rubber compounds because of the superior resilience, elasticity, abrasion resistance, efficient heat dispersion, and impact resistance of NR. In NR production, latex is harvested by periodical tapping of the trunk bark. Ethylene enhances and prolongs latex flow and latex regeneration. Ethephon, which is an ethylene-releasing compound, applied to the trunk before tapping usually results in a 1.5- to 2-fold increase in latex yield. However, intense mechanical damage to bark tissues by excessive tapping and/or over-stimulation with ethephon induces severe oxidative stress in laticifer cells, which often causes tapping panel dryness (TPD) syndrome. To enhance NR production without causing TPD, an improved understanding of the molecular mechanism of the ethylene response in the Pará rubber tree is required. Therefore, we investigated gene expression in response to ethephon treatment using Pará rubber tree seedlings as a model system.

RESULTS

After ethephon treatment, 3270 genes showed significant differences in expression compared with the mock treatment. Genes associated with carotenoids, flavonoids, and abscisic acid biosynthesis were significantly upregulated by ethephon treatment, which might contribute to an increase in latex flow. Genes associated with secondary cell wall formation were downregulated, which might be because of the reduced sugar supply. Given that sucrose is an important molecule for NR production, a trade-off may arise between NR production and cell wall formation for plant growth and for wound healing at the tapping panel.

CONCLUSIONS

Dynamic changes in gene expression occur specifically in response to ethephon treatment. Certain genes identified may potentially contribute to latex production or TPD suppression. These data provide valuable information to understand the mechanism of ethylene stimulation, and will contribute to improved management practices and/or molecular breeding to attain higher yields of latex from Pará rubber trees.

HbWRKY82, a novel IIc WRKY transcription factor from Hevea brasiliensis associated with abiotic stress tolerance and leaf senescence in Arabidopsis

WRKY group transcription factors of model plants and major crops are confirmed to play essential roles in stress responses, senescence, secondary metabolism processes and hormone signal transduction. Previous studies have identified 81 HbWRKY genes from Hevea brasiliensis (the Pará rubber tree), but the functions of HbWRKYs in response to abiotic stresses and leaf senescence are unclear. In this study, one novel group IIc WRKY transcription factor named HbWRKY82 was identified and characterized as a stress-associated WRKY in rubber tree. Transient expression and transcriptional activation analyses indicated that HbWRKY82 encoded a nuclear protein and functioned as a transcription activator. The transcription levels of HbWRKY82 were induced by exogenous Ethrel (ET) (ethylene releaser) and abscisic acid (ABA) stimulations, down-regulated in tapping panel dryness rubber trees, and also exhibits significant decrease during the progression of leaf senescence. Overexpression of HbWRKY82 in Arabidopsis improved the tolerance to dehydration and salinity, and decreased the sensitivity to exogenous ABA. Moreover, real-time quantitative PCR analysis demonstrated that HbWRKY82 regulated the transcriptional expression of several stress-responsive genes (DREB1A, ERD10, HKT1, P5CS, RD22, RD29B, SKOR), leaf senescence marker genes (EIN3, WRKY53, NAP), ROS-related genes (RbohD, CSD1, CSD2, FSD3) and hormone signaling genes (EIN3, ABF3, ABF4). Collectively, our findings suggested that HbWRKY82 might function as an important transcriptional regulator in ET- and ABA-mediated leaf senescence and abiotic stress responses, and also be involved in tapping panel dryness, latex flow and regeneration processes of rubber trees via participating in the ET and reactive oxygen species signaling pathways.

Reference gene validation in Eotetranychus sexmaculatus (Acari: Tetranychidae) feeding on mite-susceptible and mite-resistant rubber tree germplasms

Reliable reference genes are quite important in calculating gene transcript levels by using real-time quantitative reverse transcription-PCR (RT-qPCR). Eotetranychus sexmaculatus is known as a dangerous mite causing significant yield reduction of rubber tree latex; however, selection of appropriate reference genes for validation of target gene expression in E. sexmaculatus has not been conducted yet. In the present study, nine candidate reference genes were analyzed for their expression stability in different life stages of E. sexmaculatus by using common algorithms including comparative ΔCq method, geNorm, NormFinder and BestKeeper. In addition, a comprehensive analysis software (RefFinder) was used to assign an overall final rank for each candidate gene. The results showed that β-actin and β-TUB were the best two reference genes and were subjected to evaluate expression of two protective enzyme genes (EsCu/ZnSOD and EsCAT1) in E. sexmaculatus. We found that the expression of EsCu/ZnSOD and EsCAT1 in E. sexmaculatus feeding on mite-resistant rubber tree germplasm was significantly lower compared with those feeding on mite-susceptible germplasm. These results will facilitate research in revealing molecular mechanisms underlying rubber tree resistance to the spider mite.

Deep expression analysis reveals distinct cold-response strategies in rubber tree (Hevea brasiliensis)

Background

Natural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. The rubber tree species Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg., which is native the Amazon rainforest, is the major producer of latex worldwide. Rubber tree breeding is time consuming, expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. In this work, transcriptome sequencing was used to identify a full set of transcripts and to evaluate the gene expression involved in the different cold-response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes.

Results

We built a comprehensive transcriptome using multiple database sources, which resulted in 104,738 transcripts clustered in 49,304 genes. The RNA-seq data from the leaf tissues sampled at four different times for each genotype were used to perform a gene-level expression analysis. Differentially expressed genes (DEGs) were identified through pairwise comparisons between the two genotypes for each time series of cold treatments.

DEG annotation revealed that RRIM600 and GT1 exhibit different chilling tolerance strategies. To cope with cold stress, the RRIM600 clone upregulates genes promoting stomata closure, photosynthesis inhibition and a more efficient reactive oxygen species (ROS) scavenging system. The transcriptome was also searched for putative molecular markers (single nucleotide polymorphisms (SNPs) and microsatellites) in each genotype. and a total of 27,111 microsatellites and 202,949 (GT1) and 156,395 (RRIM600) SNPs were identified in GT1 and RRIM600. Furthermore, a search for alternative splicing (AS) events identified a total of 20,279 events.

Conclusions

The elucidation of genes involved in different chilling tolerance strategies associated with molecular markers and information regarding AS events provides a powerful tool for further genetic and genomic analyses of rubber tree breeding.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5852-5) contains supplementary material, which is available to authorized users.

A Rubber-Tapping Robot Forest Navigation and Information Collection System Based on 2D LiDAR and a Gyroscope

Natural rubber is widely used in human life because of its excellent quality. At present, manual tapping is still the main way to obtain natural rubber. There is a sore need for intelligent tapping devices in the tapping industry, and the autonomous navigation technique is of great importance to make rubber-tapping devices intelligent. To realize the autonomous navigation of the intelligent rubber-tapping platform and to collect information on a rubber forest, the sparse point cloud data of tree trunks are extracted by the low-cost LiDAR and a gyroscope through the clustering method. The point cloud is fitted into circles by the Gauss–Newton method to obtain the center point of each tree. Then, these center points are threaded through the Least Squares method to obtain the straight line, which is regarded as the navigation path of the robot in this forest. Moreover, the Extended Kalman Filter (EKF) algorithm is adopted to obtain the robot’s position. In a forest with different row spacings and plant spacings, the heading error and lateral error of this robot are analyzed and a Fuzzy Controller is applied for the following activities: walking along one row with a fixed lateral distance, stopping at fixed points, turning from one row into another, and collecting information on plant spacing, row spacing, and trees’ diameters. Then, according to the collected information, each tree’s position is calculated, and the geometric feature map is constructed. In a forest with different row spacings and plant spacings, three repeated tests have been carried out at an initial speed of 0.3 m/s. The results show that the Root Mean Square (RMS) lateral errors are less than 10.32 cm, which shows that the proposed navigation method provides great path tracking. The fixed-point stopping range of the robot can meet the requirements for automatic rubber tapping of the mechanical arm, and the average stopping error is 12.08 cm. In the geometric feature map constructed by collecting information, the RMS radius errors are less than 0.66 cm, and the RMS plant spacing errors are less than 11.31 cm. These results show that the method for collecting information and constructing a map recursively in the process of navigation proposed in the paper provides a solution for forest information collection. The method provides a low-cost, real-time, and stable solution for forest navigation of automatic rubber tapping equipment, and the collected information not only assists the automatic tapping equipment to plan the tapping path, but also provides a basis for the informationization and precise management of a rubber plantation.

Involvement of HbMC1-mediated cell death in tapping panel dryness of rubber tree (Hevea brasiliensis)

Tapping panel dryness (TPD) causes a significant reduction in the latex yield of rubber tree (Hevea brasiliensis Muell. Arg.). It is reported that TPD is a typical programmed cell death (PCD) process. Although PCD plays a vital role in TPD occurrence, there is a lack of detailed and systematic study. Metacaspases are key regulators of diverse PCD in plants. Based on our previous result that HbMC1 was associated with TPD, we further elucidate the roles of HbMC1 on rubber tree TPD in this study. HbMC1 was up-regulated by TPD-inducing factors including wounding, ethephon and H2O2. Moreover, the expression level of HbMC1 was increased along with TPD severity in rubber tree, suggesting a positive correlation between HbMC1 expression and TPD severity. To investigate its biological function, HbMC1 was overexpressed in yeast (Saccharomyces cerevisiae) and tobacco (Nicotiana benthamiana). Transgenic yeast and tobacco overexpressing HbMC1 showed growth retardation compared with controls under H2O2-induced oxidative stress. In addition, overexpression of HbMC1 in yeast and tobacco reduced cell survival after high-concentration H2O2 treatment and resulted in enhanced H2O2-induced leaf cell death, respectively. A total of 11 proteins, rbcL, TM9SF2-like, COX3, ATP9, DRP, HbREF/Hevb1, MSSP2-like, SRC2, GATL8, CIPK14-like and STK, were identified and confirmed to interact with HbMC1 by yeast two-hybrid screening and co-transformation in yeast. The 11 proteins mentioned above are associated with many biological processes, including rubber biosynthesis, stress response, autophagy, carbohydrate metabolism, signal transduction, etc. Taken together, our results suggest that HbMC1-mediated PCD plays an important role in rubber tree TPD, and the identified HbMC1-interacting proteins provide valuable information for further understanding the molecular mechanism of HbMC1-mediated TPD in rubber tree.

Identification and Analysis of a CPYC-Type Glutaredoxin Associated with Stress Response in Rubber Trees

Glutaredoxins (GRXs) are a class of small oxidoreductases which modulate various biological processes in plants. Here, we isolated a GRX gene from the rubber tree (Hevea brasiliensis Müll. Arg.), named as HbSRGRX1, which encoded 107 amino acid residues with a CPYC active site. Phylogenetic analysis displayed that HbSRGRX1 was more correlated with GRXs from Manihot esculenta Crantz. and Ricinus communis L. HbSRGRX1 was localized in the nuclei of tobacco cells, and its transcripts were preferentially expressed in male flowers and in the high-yield variety Reyan 7-33-97 with strong resistance against cold. The expression levels of HbSRGRX1 significantly decreased in tapping panel dryness (TPD) trees. Furthermore, HbSRGRX1 was regulated by wounding, hydrogen peroxide (H2O2), and multiple hormones. Altogether, these results suggest important roles of HbSRGRX1 in plant development and defense response to TPD and multiple stresses.

Transcriptome analysis in Hevea brasiliensis latex revealed changes in hormone signalling pathways during ethephon stimulation and consequent Tapping Panel Dryness

Tapping Panel Dryness (TPD) affects latex production in Hevea brasiliensis. This physiological syndrome involves the agglutination of rubber particles, which leads to partial or complete cessation of latex flow. Latex harvesting consists in tapping soft bark. Ethephon can be applied to stimulate latex flow and its regeneration in laticifers. Several studies have reported transcriptome changes in bark tissues. This study is the first report on deep RNA sequencing of latex to compare the effect of ethephon stimulation and TPD severity. Trees were carefully selected for paired-end sequencing using an Illumina HiSeq 2000. In all, 43 to 60 million reads were sequenced for each treatment in three biological replicates (slight TPD trees without ethephon stimulation, and slight and severe TPD trees with ethephon treatment). Differentially expressed genes were identified and annotated, giving 8,111 and 728 in response to ethephon in slight TPD trees and in ethephon-induced severe TPD trees, respectively. A biological network of responses to ethephon and TPD highlighted the major influence of metabolic processes and the response to stimulus, especially wounding and jasmonate depression in TPD-affected trees induced by ethephon stimulation.

Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches

BACKGROUND

Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene.

RESULTS

A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily.

CONCLUSION

The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/ .

Transcriptomic analyses reveal molecular mechanisms underlying growth heterosis and weakness of rubber tree seedlings

BACKGROUND

Breeding rubber tree seedling with growth heterosis is vital for natural rubber production. It is the prerequisites for effectively utilizing growth heterosis to elucidate its molecular mechanisms, but the molecular mechanisms remain poorly understood in rubber tree. To elucidate seedling growth heterosis, we conducted comparative transcriptomic analyses between the two hybrids and their parents.

RESULTS

By identifying and comparing differently expressed genes (DEGs), we found that the hybrids (BT 3410 and WC 11) show significantly differential expression profiles from their parents (PR 107 and RRIM 600). In BT 3410-parent triad, 1092 (49.95%) and 1094 (50.05%) DEGs indicated clear underdominance or overdominance, respectively. Whereas in WC 11-parent triad, most DEGs (78.2%, 721) showed low- or high-parent dominance; 160 (17.35%) exhibited expression patterns that are not statistically distinguishable from additivity, and 8 (0.87%) and 33 (3.58%) DEGs exhibited underdominance and overdominance, respectively. Furthermore, some biological processes are differentially regulated between two hybrids. Interestingly, the pathway in response to stimulus is significantly downregulated and metabolic pathways are more highly regulated in BT 3410.

CONCLUSIONS

Taken together, the genotypes, transcriptomes and biological pathways (especially, carbohydrate metabolism) are highly divergent between two hybrids, which may be associated with growth heterosis and weakness. Analyzing gene action models in hybrid-parent triads, we propose that overdominance may play important roles on growth heterosis, whereas dominance on hybrid weakness in rubber tree seedlings. These findings bring new insights into our understanding of growth heterosis of rubber tree seedling.

Papain-like cysteine protease encoding genes in rubber (Hevea brasiliensis): comparative genomics, phylogenetic, and transcriptional profiling analysis

43 HbPLCPs representing nine subfamilies or 20 orthologous groups were found in rubber, where paralogs were resulted from the recent WGD and local duplication. Several senescence-associated genes were also identified. Papain-like cysteine proteases (PLCPs) comprise a large family of proteolytic enzymes involved in plant growth and development, seed germination, organ senescence, immunity, and stress response. Despite their importance and the extensive research in the model plant Arabidopsis thaliana, little information is available on rubber tree (Hevea brasiliensis), a rubber-producing plant of the Euphorbiaceae family. This study performed a genome-wide identification of PLCP family genes in rubber, resulting in a relatively high number of 43 members. The phylogenetic analysis assigned these genes into nine subfamilies, i.e., RD21 (6), CEP (4), XCP (4), XBCP3 (2), THI (1), SAG12 (18), RD19 (4), ALP (2), and CTB (2). Most of them were shown to have orthologs in Arabidopsis; however, several members in SAG12, CEP and XBCP3 subfamilies form new groups as observed in other core eudicots such as Manihot esculenta, Ricinus communis, Populus trichocarpa, and Vitis vinifera. Based on an expert sequence comparison, 20 orthologous groups (OGs) were proposed for core eudicots, and rubber paralogs were shown to be resulted from the recent whole-genome duplication (WGD) as well as local duplication. Transcriptional profiling showed distinct expression pattern of different members across various tissues, e.g., root, leaf, bark, laticifer, flower, and seed. By using the senescence-specific HbSAG12H1 as the indicator, the transcriptome of senescent rubber leaves was deeply sequenced and several senescence-associated PLCP genes were identified. Results obtained from this study provide valuable information for future functional analysis and utilization of PLCP genes in Hevea and other species.

Survey of the rubber tree genome reveals a high number of cysteine protease-encoding genes homologous to Arabidopsis SAG12

Arabidopsis thaliana SAG12, a senescence-specific gene encoding a cysteine protease, is widely used as a molecular marker for the study of leaf senescence. To date, its potential orthologues have been isolated from several plant species such as Brassica napus and Nicotiana tabacum. However, little information is available in rubber tree (Hevea brasiliensis), a rubber-producing plant of the Euphorbiaceae family. This study presents the identification of SAG12-like genes from the rubber tree genome. Results showed that an unexpected high number of 17 rubber orthologues with a single intron were found, contrasting the single copy with two introns in Arabidopsis. The gene expansion was also observed in another two Euphorbiaceae plants, castor bean (Ricinus communis) and physic nut (Jatropha curcas), both of which contain 8 orthologues. In accordance with no occurrence of recent whole-genome duplication (WGD) events, most duplicates in castor and physic nut were resulted from tandem duplications. In contrast, the duplicated HbSAG12H genes were derived from tandem duplications as well as the recent WGD. Expression analysis showed that most HbSAG12H genes were lowly expressed in examined tissues except for root and male flower. Furthermore, HbSAG12H1 exhibits a strictly senescence-associated expression pattern in rubber tree leaves, and thus can be used as a marker gene for the study of senescence mechanism in Hevea.

De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species

Para rubber tree (Hevea brasiliensis) is an important economic species as it is the sole commercial producer of high-quality natural rubber. Here, we report a de novo hybrid assembly of BPM24 accession, which exhibits resistance to major fungal pathogens in Southeast Asia. Deep-coverage 454/Illumina short-read and Pacific Biosciences (PacBio) long-read sequence data were acquired to generate a preliminary draft, which was subsequently scaffolded using a long-range "Chicago" technique to obtain a final assembly of 1.26 Gb (N50 = 96.8 kb). The assembled genome contains 69.2% repetitive sequences and has a GC content of 34.31%. Using a high-density SNP-based genetic map, we were able to anchor 28.9% of the genome assembly (363 Mb) associated with over two thirds of the predicted protein-coding genes into rubber tree's 18 linkage groups. These genetically anchored sequences allowed comparative analyses of the intragenomic homeologous synteny, providing the first concrete evidence to demonstrate the presence of paleotetraploidy in Hevea species. Additionally, the degree of macrosynteny conservation observed between rubber tree and cassava strongly supports the hypothesis that the paleotetraploidization event took place prior to the divergence of the Hevea and Manihot species.

Transcriptome Analysis of the Signalling Networks in Coronatine-Induced Secondary Laticifer Differentiation from Vascular Cambia in Rubber Trees

The secondary laticifer in rubber tree (Hevea brasiliensis Muell. Arg.) is a specific tissue within the secondary phloem. This tissue differentiates from the vascular cambia, and its function is natural rubber biosynthesis and storage. Given that jasmonates play a pivotal role in secondary laticifer differentiation, we established an experimental system with jasmonate (JA) mimic coronatine (COR) for studying the secondary laticifer differentiation: in this system, differentiation occurs within five days of the treatment of epicormic shoots with COR. In the present study, the experimental system was used to perform transcriptome sequencing and gene expression analysis. A total of 67,873 unigenes were assembled, and 50,548 unigenes were mapped at least in one public database. Of these being annotated unigenes, 15,780 unigenes were differentially expressed early after COR treatment, and 19,824 unigenes were differentially expressed late after COR treatment. At the early stage, 8,646 unigenes were up-regulated, while 7,134 unigenes were down-regulated. At the late stage, the numbers of up- and down-regulated unigenes were 7,711 and 12,113, respectively. The annotation data and gene expression analysis of the differentially expressed unigenes suggest that JA-mediated signalling, Ca²⁺ signal transduction and the CLAVATA-MAPK-WOX signalling pathway may be involved in regulating secondary laticifer differentiation in rubber trees.

Expression Profiles, Characterization and Function of HbTCTP in Rubber Tree (Hevea brasiliensis)

As a highly conserved protein, the translationally controlled tumor protein (TCTP) carries out vital roles in various life processes. In rubber tree, two TCTP genes, HbTCTP and HbTCTP1, were cloned, but only HbTCTP1 was studied in details. In this study, cis-acting regulatory elements, expression patterns, subcellular localization, interacting proteins, and antioxidant activity of HbTCTP were systematically analyzed. Besides the common cis-acting regulatory elements, HbTCTP promoter also harbored various known cis-elements that respond to hormone/stresses. Being consistent with the aforementioned results, HbTCTP was regulated by drought, low temperature, high salt, ethylene (ET), wounding, H2O2, and methyl jasmonate (MeJA) treatments. HbTCTP was expressed throughout different tissues and developmental stages of leaves. In addition, HbTCTP was associated with tapping panel dryness (TPD). HbTCTP was localized in the membrane, cytoplasm and the nucleus, and interacted with four proteins rubber elongation factor (REF), 17.5 kDa heat shock family protein, annexin, and REF-like stress related protein 1. Being similar to HbTCTP1, HbTCTP also indicated antioxidant activity in metal-catalyzed oxidation (MCO) system. Our results are useful for further understanding the molecular characterization and expression profiles of HbTCTP, but also lay a solid foundation for elucidating the function of HbTCTP in rubber tree.