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

Li, Dejun; Wang, Xuncheng; Zhi, Deng; Liu, Hui; Yang, Hong; He, Guangming

doi:10.1038/srep23540

Cited by 36 publications

(32 citation statements)

References 36 publications

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“…To assess the quality of our de novo assembly, independent sources of publicly available rubber tree DNA and cDNA sequences were aligned to the assembled genome ( Supplementary Table S2 ). These sequences included the first published draft genome assembly 13 , EST reads and transcriptome assembly obtained from 454 and Illumina sequencing 12 13 33 34 and our PacBio Isoform Sequencing (Iso-seq) data. Over 99% of the scaffolds assembled by the Malaysian group could be aligned to our genome assembly.…”

Section: Resultsmentioning

confidence: 99%

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

Pootakham

Sonthirod

Naktang

et al. 2017

Sci Rep

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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.

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Section: Resultsmentioning

confidence: 99%

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

Pootakham

Sonthirod

Naktang

et al. 2017

Sci Rep

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“…Gébelin et al ( 2013 ) found that the target genes of TPD-related microRNAs were associated with RB, ROS-scavenging systems, and PCD. By identifying and analyzing TPD-related genes in rubber tree bark, Li et al ( 2016 ) further reported that the TPD-related genes significantly enriched in eight GO terms and five KEGG pathways were closely associated with ROS metabolism, PCD, and RB. In this study, the HbTCTP transcripts were higher in TPD rubber tree than healthy rubber one.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2016

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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.

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“…In this study, we achieved more than 7 Gb of clean reads from each of the four sets of sequencing samples derived from the cambia-containing materials of rubber tree clone CATAS7-33-97. The sequencing depth of each sample was higher than the reported 0.2–6 Gb sequencing depth of bark in rubber tree3031323334 and equivalent to sequencing depth (7–8 Gb) reported by Mantello et al 35. This high sequencing depth is beneficial for global transcriptome assembly.…”

Section: Discussionmentioning

confidence: 69%

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

Zhang

Chao

et al. 2016

Sci Rep

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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.

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

Cited by 36 publications

References 36 publications

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

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

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

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

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