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Makita Y, Ng KK, Veera Singham G, Kawashima M, Hirakawa H, Sato S, Othman AS, Matsui M. Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. DNA Res 2017; 24:159-167. [PMID: 28431015 PMCID: PMC5397604 DOI: 10.1093/dnares/dsw056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/18/2016] [Indexed: 11/16/2022] Open
Abstract
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer. With these data, we updated around 5,500 gene structures and newly annotated around 9,500 transcription start sites. Second, to elucidate the rubber biosynthetic pathways and their transcriptional regulation, we carried out tissue- and cultivar-specific RNA-Seq analysis. By using our recently published genome sequence, we confirmed the expression patterns of the rubber biosynthetic genes. Our data suggest that the cytoplasmic mevalonate (MVA) pathway is the main route for isoprenoid biosynthesis in latex production. In addition to the well-studied polymerization factors, we suggest that rubber elongation factor 8 (REF8) is a candidate factor in cis-polyisoprene biosynthesis. We have also identified 39 transcription factors that may be key regulators in latex production. Expression profile analysis using two additional cultivars, RRIM 901 and PB 350, via an RNA-Seq approach revealed possible expression differences between a high latex-yielding cultivar and a disease-resistant cultivar.
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan
| | - Kiaw Kiaw Ng
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan.,Molecular Ecology and Evolution Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - G Veera Singham
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan.,Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Pulau Pinang, Malaysia
| | - Mika Kawashima
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu Chiba 292-0818, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu Chiba 292-0818, Japan
| | - Ahmad Sofiman Othman
- Molecular Ecology and Evolution Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia.,Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Pulau Pinang, Malaysia
| | - Minami Matsui
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan
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Neale DB, Martínez-García PJ, De La Torre AR, Montanari S, Wei XX. Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:457-483. [PMID: 28226237 DOI: 10.1146/annurev-arplant-042916-041049] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants. Our review of the published data suggests that, although many gene families are conserved among herbaceous and tree species, some gene families, such as those involved in resistance to biotic and abiotic stresses and in the synthesis and transport of sugars, are often expanded in tree genomes. As the genomes of more tree species are sequenced, comparative genomics will further elucidate the complexity of tree genomes and how this relates to traits unique to trees.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, California 95616;
| | | | - Amanda R De La Torre
- Department of Plant Sciences, University of California, Davis, California 95616;
| | - Sara Montanari
- Department of Plant Sciences, University of California, Davis, California 95616;
| | - Xiao-Xin Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Guo D, Zhou Y, Li HL, Zhu JH, Wang Y, Chen XT, Peng SQ. Identification and characterization of the abscisic acid (ABA) receptor gene family and its expression in response to hormones in the rubber tree. Sci Rep 2017; 7:45157. [PMID: 28332623 PMCID: PMC5362889 DOI: 10.1038/srep45157] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/21/2017] [Indexed: 12/17/2022] Open
Abstract
Abscisic acid (ABA) is an essential phytohormone involved in diverse physiological processes. Although genome-wide analyses of the ABA receptor PYR/PYL/RCAR (PYL) protein/gene family have been performed in certain plant species, little is known about the ABA receptor protein/gene family in the rubber tree (Hevea brasiliensis). In this study, we identified 14 ABA receptor PYL proteins/genes (designated HbPYL1 through HbPYL14) in the most recent rubber tree genome. A phylogenetic tree was constructed, which demonstrated that HbPYLs can be divided into three subfamilies that correlate well with the corresponding Arabidopsis subfamilies. Eight HbPYLs are highly expressed in laticifers. Five of the eight genes are simultaneously regulated by ABA, jasmonic acid (JA) and ethylene (ET). The identification and characterization of HbPYLs should enable us to further understand the role of ABA signal in the rubber tree.
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Affiliation(s)
- Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No. 4 Xueyuan Road, Haikou 571101, China
| | - Ying Zhou
- Life Science and Technology Center, China National Seed Group Co. Ltd., Wuhan 430206, China
| | - Hui-Liang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No. 4 Xueyuan Road, Haikou 571101, China
| | - Jia-Hong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No. 4 Xueyuan Road, Haikou 571101, China
| | - Ying Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No. 4 Xueyuan Road, Haikou 571101, China
| | - Xiong-Ting Chen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No. 4 Xueyuan Road, Haikou 571101, China
| | - Shi-Qing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No. 4 Xueyuan Road, Haikou 571101, China
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De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species. Sci Rep 2017; 7:41457. [PMID: 28150702 PMCID: PMC5288721 DOI: 10.1038/srep41457] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022] Open
Abstract
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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Dai L, Nie Z, Kang G, Li Y, Zeng R. Identification and subcellular localization analysis of two rubber elongation factor isoforms on Hevea brasiliensis rubber particles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 111:97-106. [PMID: 27915177 DOI: 10.1016/j.plaphy.2016.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/01/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
Rubber elongation factor (REF) is the most abundant protein found on the rubber particles or latex from Hevea brasiliensis (the Para rubber tree) and is considered to play important roles in natural rubber (cis-polyisoprene) biosynthesis. 16 BAC (benzyldimethyl-n-hexadecylammonium chloride)/SDS-PAGE separations and mass spectrometric identification had revealed that two REF isoforms shared similar amino acid sequences and common C-terminal sequences. In this study, the gene sequences encoding these two REF isoforms (one is 23.6 kDa in size with 222 amino acid residues and the other is 27.3 kDa in size with 258 amino acid residues) were obtained. Their proteins were relatively enriched by sequential extraction of the rubber particle proteins and separated by 16 BAC/SDS-PAGE. The localization of these isoforms on the surfaces of rubber particles was further verified by western blotting and immunogold electron microscopy, which demonstrated that these two REF isoforms are mainly located on the surfaces of larger rubber particles and that they bind more tightly to rubber particles than the most abundant REF and SRPP (small rubber particle protein).
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Affiliation(s)
- Longjun Dai
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, PR China; State Key Laboratory Incubation Base, Danzhou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, PR China.
| | - Zhiyi Nie
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, PR China; State Key Laboratory Incubation Base, Danzhou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, PR China.
| | - Guijuan Kang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, PR China; State Key Laboratory Incubation Base, Danzhou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, PR China.
| | - Yu Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, PR China; State Key Laboratory Incubation Base, Danzhou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, PR China.
| | - Rizhong Zeng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, PR China; State Key Laboratory Incubation Base, Danzhou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, PR China.
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Transcriptome Analysis of the Signalling Networks in Coronatine-Induced Secondary Laticifer Differentiation from Vascular Cambia in Rubber Trees. Sci Rep 2016; 6:36384. [PMID: 27808245 PMCID: PMC5093416 DOI: 10.1038/srep36384] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/14/2016] [Indexed: 11/09/2022] Open
Abstract
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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