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Li W, Dong X, Zhang X, Cao J, Liu M, Zhou X, Long H, Cao H, Lin H, Zhang L. Genome assembly and resequencing shed light on evolution, population selection, and sex identification in Vernicia montana. HORTICULTURE RESEARCH 2024; 11:uhae141. [PMID: 38988615 PMCID: PMC11233859 DOI: 10.1093/hr/uhae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024]
Abstract
Vernicia montana is a dioecious plant widely cultivated for high-quality tung oil production and ornamental purposes in the Euphorbiaceae family. The lack of genomic information has severely hindered molecular breeding for genetic improvement and early sex identification in V. montana. Here, we present a chromosome-level reference genome of a male V. montana with a total size of 1.29 Gb and a contig N50 of 3.69 Mb. Genome analysis revealed that different repeat lineages drove the expansion of genome size. The model of chromosome evolution in the Euphorbiaceae family suggests that polyploidization-induced genomic structural variation reshaped the chromosome structure, giving rise to the diverse modern chromosomes. Based on whole-genome resequencing data and analyses of selective sweep and genetic diversity, several genes associated with stress resistance and flavonoid synthesis such as CYP450 genes and members of the LRR-RLK family, were identified and presumed to have been selected during the evolutionary process. Genome-wide association studies were conducted and a putative sex-linked insertion and deletion (InDel) (Chr 2: 102 799 917-102 799 933 bp) was identified and developed as a polymorphic molecular marker capable of effectively detecting the gender of V. montana. This InDel is located in the second intron of VmBASS4, suggesting a possible role of VmBASS4 in sex determination in V. montana. This study sheds light on the genome evolution and sex identification of V. montana, which will facilitate research on the development of agronomically important traits and genomics-assisted breeding.
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Affiliation(s)
- Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
- College of Biology and Agricultural Resources, Huanggang Normal University, No.146 Xingang 2nd Road, Huangzhou District, Huanggang, Hubei 438000, China
| | - Xiang Dong
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No.7 Pengfei Road, Dapeng New District, Shenzhen 518120, China
| | - Jie Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Xu Zhou
- College of Landscape Architecture, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Hongxu Long
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Heping Cao
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, 1100 Allen Toussaint Blvd, New Orleans, LA 70124-4305, USA
| | - Hai Lin
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
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Umar AW, Ahmad N, Xu M. Reviving Natural Rubber Synthesis via Native/Large Nanodiscs. Polymers (Basel) 2024; 16:1468. [PMID: 38891415 PMCID: PMC11174458 DOI: 10.3390/polym16111468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/28/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Natural rubber (NR) is utilized in more than 40,000 products, and the demand for NR is projected to reach $68.5 billion by 2026. The primary commercial source of NR is the latex of Hevea brasiliensis. NR is produced by the sequential cis-condensation of isopentenyl diphosphate (IPP) through a complex known as the rubber transferase (RTase) complex. This complex is associated with rubber particles, specialized organelles for NR synthesis. Despite numerous attempts to isolate, characterize, and study the RTase complex, definitive results have not yet been achieved. This review proposes an innovative approach to overcome this longstanding challenge. The suggested method involves isolating the RTase complex without using detergents, instead utilizing the native membrane lipids, referred to as "natural nanodiscs", and subsequently reconstituting the complex on liposomes. Additionally, we recommend the adaptation of large nanodiscs for the incorporation and reconstitution of the RTase complex, whether it is in vitro transcribed or present within the natural nanodiscs. These techniques show promise as a viable solution to the current obstacles. Based on our experimental experience and insights from published literature, we believe these refined methodologies can significantly enhance our understanding of the RTase complex and its role in in vitro NR synthesis.
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Affiliation(s)
- Abdul Wakeel Umar
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai 519087, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Ming Xu
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai 519087, China
- Guangdong-Hong Kong Joint Laboratory for Carbon Neutrality, Jiangmen Laboratory of Carbon Science and Technology, Jiangmen 529199, China
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Pathirana R, Carimi F. Plant Biotechnology-An Indispensable Tool for Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2024; 13:1133. [PMID: 38674542 PMCID: PMC11054891 DOI: 10.3390/plants13081133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Traditional plant breeding has helped to increase food production dramatically over the past five decades, and many countries have managed to produce enough food for the growing population, particularly in the developing world [...].
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Affiliation(s)
- Ranjith Pathirana
- School of Agriculture, Food and Wine, Waite Campus, University of Adelaide, Urrbra, SA 5064, Australia
| | - Francesco Carimi
- Istituto di Bioscienze e BioRisorse (IBBR), Consiglio Nazionale delle Ricerche, Via Ugo la Malfa, 153, 90146 Palermo, Italy;
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Zhang YY, Li HK, Huang X, Yuan YJ, Zhang XF, Gao XS, Wang XJ, Wei MM, Huang HS, Li W. Heterozygosity analysis of spontaneous 2n female gametes and centromere mapping of the diploid Hevea brasiliensis based on full-sib triploid populations. PLANT REPRODUCTION 2024; 37:47-56. [PMID: 37758937 DOI: 10.1007/s00497-023-00481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
KEY MESSAGE Unreduced megagametophytes via second-division restitution were confirmed through heterozygosity analysis, and four candidate physical centromeres of rubber were located for the first time. The evaluation of maternal heterozygosity restitution (MHR) is vital in identifying the mechanism of 2n gametogenesis and assessing the utilization value of 2n gametes. In this study, three full-sib triploid populations were employed to evaluate the MHR of 2n female gametes of rubber tree clone GT1 and to confirm their genetic derivation. The 2n female gametes of GT1 were derived from second-division restitution (SDR) and transmitted more than half of the parental heterozygosity. In addition, low recombination frequency markers were developed, and four candidate physical centromeres of rubber tree were located for the first time. The confirmation that 2n female gametes of rubber tree clone GT1 are derived from SDR provides insights into the molecular mechanisms of 2n gametogenesis. In addition, the identified centromere location will aid in the development of centromeric markers for the rapid identification of the 2n gametogenesis mechanism.
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Affiliation(s)
- Yuan-Yuan Zhang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Hong-Kun Li
- Dehong Institute of Tropical Agricultural Sciences of Yunnan Province, Ruili, 678600, Yunnan, China
| | - Xiao Huang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yu-Jiao Yuan
- College of Tropical Crops, Yunnan Agricultural University, Puer, 665099, Yunnan, China
| | - Xiao-Fei Zhang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Xin-Sheng Gao
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Xiang-Jun Wang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Ming-Ming Wei
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Hua-Sun Huang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Weiguo Li
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
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5
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Tan Y, Cao J, Tang C, Liu K. Advances in Genome Sequencing and Natural Rubber Biosynthesis in Rubber-Producing Plants. Curr Issues Mol Biol 2023; 45:9342-9353. [PMID: 38132431 PMCID: PMC10741621 DOI: 10.3390/cimb45120585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Natural rubber (cis-1,4-polyisoprene, NR) is an important raw material utilized widely in the manufacturing of medical, agricultural, and industrial products. Rubber tree (Hevea brasiliensis) and several alternative rubber-producing plants (Taraxacum kok-saghyz, Lactuca sativa, and Parthenium argentatum) have the capability to produce high-quality NR. With the progress of genome sequencing, similar rubber biosynthesis pathways have been discovered among different rubber-producing plant species. NR is synthesized and stored in rubber particles, which are specialized organelles comprising a hydrophobic NR core surrounded by a lipid monolayer and membrane-bound proteins. The rubber transferase complex is considered to be the pivotal enzyme involved in catalyzing NR biosynthesis. However, the exact compositions of the RT complex in rubber-producing plants remain elusive and poorly understood. Here, we review the progress of genome sequencing, natural rubber biosynthesis, and the components of the RT complex in rubber-producing plants. We emphasize that identifying the detailed components of the RT complex holds great significance for exploring the mechanism of NR biosynthesis and accelerating molecular breeding in rubber-producing plants.
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Affiliation(s)
- Yingchao Tan
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China; (Y.T.); (J.C.); (C.T.)
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of P.R. China, Hainan University, Haikou 570228, China
| | - Jie Cao
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China; (Y.T.); (J.C.); (C.T.)
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of P.R. China, Hainan University, Haikou 570228, China
| | - Chaorong Tang
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China; (Y.T.); (J.C.); (C.T.)
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of P.R. China, Hainan University, Haikou 570228, China
- Yunnan Institute of Tropical Crops, Xishuangbanna 666100, China
| | - Kaiye Liu
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China; (Y.T.); (J.C.); (C.T.)
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of P.R. China, Hainan University, Haikou 570228, China
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6
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Chao J, Wu S, Shi M, Xu X, Gao Q, Du H, Gao B, Guo D, Yang S, Zhang S, Li Y, Fan X, Hai C, Kou L, Zhang J, Wang Z, Li Y, Xue W, Xu J, Deng X, Huang X, Gao X, Zhang X, Hu Y, Zeng X, Li W, Zhang L, Peng S, Wu J, Hao B, Wang X, Yu H, Li J, Liang C, Tian WM. Genomic insight into domestication of rubber tree. Nat Commun 2023; 14:4651. [PMID: 37532727 PMCID: PMC10397287 DOI: 10.1038/s41467-023-40304-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
Understanding the genetic basis of rubber tree (Hevea brasiliensis) domestication is crucial for further improving natural rubber production to meet its increasing demand worldwide. Here we provide a high-quality H. brasiliensis genome assembly (1.58 Gb, contig N50 of 11.21 megabases), present a map of genome variations by resequencing 335 accessions and reveal domestication-related molecular signals and a major domestication trait, the higher number of laticifer rings. We further show that HbPSK5, encoding the small-peptide hormone phytosulfokine (PSK), is a key domestication gene and closely correlated with the major domestication trait. The transcriptional activation of HbPSK5 by myelocytomatosis (MYC) members links PSK signaling to jasmonates in regulating the laticifer differentiation in rubber tree. Heterologous overexpression of HbPSK5 in Russian dandelion (Taraxacum kok-saghyz) can increase rubber content by promoting laticifer formation. Our results provide an insight into target genes for improving rubber tree and accelerating the domestication of other rubber-producing plants.
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Affiliation(s)
- Jinquan Chao
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shaohua Wu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Minjing Shi
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xia Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiang Gao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Qi Biodesign, Life Science Park, Beijing, 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dong Guo
- Ministry of Agriculture and Rural Affairs Key Laboratory of Tropical Crop Biotechnology, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shuguang Yang
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shixin Zhang
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yan Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xiuli Fan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Hai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiao Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhiwei Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yan Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Wenbo Xue
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaomin Deng
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xiao Huang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xinsheng Gao
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xiaofei Zhang
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yanshi Hu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xia Zeng
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Weiguo Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiqing Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Tropical Crop Biotechnology, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Jilin Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Bingzhong Hao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xuchu Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China.
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Wei-Min Tian
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572024, China.
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
- State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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7
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Cheng H, Song X, Hu Y, Wu T, Yang Q, An Z, Feng S, Deng Z, Wu W, Zeng X, Tu M, Wang X, Huang H. Chromosome-level wild Hevea brasiliensis genome provides new tools for genomic-assisted breeding and valuable loci to elevate rubber yield. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1058-1072. [PMID: 36710373 PMCID: PMC10106855 DOI: 10.1111/pbi.14018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 05/04/2023]
Abstract
The rubber tree (Hevea brasiliensis) is grown in tropical regions and is the major source of natural rubber. Using traditional breeding approaches, the latex yield has increased by sixfold in the last century. However, the underlying genetic basis of rubber yield improvement is largely unknown. Here, we present a high-quality, chromosome-level genome sequence of the wild rubber tree, the first report on selection signatures and a genome-wide association study (GWAS) of its yield traits. Population genomic analysis revealed a moderate population divergence between the Wickham clones and wild accessions. Interestingly, it is suggestive that H. brasiliensis and six relatives of the Hevea genus might belong to the same species. The selective sweep analysis found 361 obvious signatures in the domesticated clones associated with 245 genes. In a 15-year field trial, GWAS identified 155 marker-trait associations with latex yield, in which 326 candidate genes were found. Notably, six genes related to sugar transport and metabolism, and four genes related to ethylene biosynthesis and signalling are associated with latex yield. The homozygote frequencies of the causal nonsynonymous SNPs have been greatly increased under selection, which may have contributed to the fast latex yield improvement during the short domestication history. Our study provides insights into the genetic basis of the latex yield trait and has implications for genomic-assisted breeding by offering valuable resources in this new domesticated crop.
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Affiliation(s)
- Han Cheng
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Xiaoming Song
- School of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yanshi Hu
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Tingkai Wu
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Qihang Yang
- School of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Zewei An
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Shuyan Feng
- School of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Zhi Deng
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Wenguan Wu
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Xia Zeng
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Min Tu
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Xiyin Wang
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
| | - Huasun Huang
- Rubber Research InstituteChinese Academy of Tropical Agricultural ScienceHaikouHainanChina
- Key Laboratory of Biology and Genetic Resources of Rubber TreeMinistry of Agriculture and Rural AffairsHaikouChina
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8
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dos Santos LB, Aono AH, Francisco FR, da Silva CC, Souza LM, de Souza AP. The rubber tree kinome: Genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1068202. [PMID: 36824205 PMCID: PMC9941580 DOI: 10.3389/fpls.2023.1068202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, with the aim of providing novel inferences about the mechanisms associated with the stress response developed by PKs and retained throughout evolution, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species Manihot esculenta and Ricinus communis. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.
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Affiliation(s)
- Lucas Borges dos Santos
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
| | - Felipe Roberto Francisco
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
| | - Livia Moura Souza
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
- São Francisco University (USF), Itatiba, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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9
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A divide-and-conquer approach for genomic prediction in rubber tree using machine learning. Sci Rep 2022; 12:18023. [PMID: 36289298 PMCID: PMC9605989 DOI: 10.1038/s41598-022-20416-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/13/2022] [Indexed: 01/20/2023] Open
Abstract
Rubber tree (Hevea brasiliensis) is the main feedstock for commercial rubber; however, its long vegetative cycle has hindered the development of more productive varieties via breeding programs. With the availability of H. brasiliensis genomic data, several linkage maps with associated quantitative trait loci have been constructed and suggested as a tool for marker-assisted selection. Nonetheless, novel genomic strategies are still needed, and genomic selection (GS) may facilitate rubber tree breeding programs aimed at reducing the required cycles for performance assessment. Even though such a methodology has already been shown to be a promising tool for rubber tree breeding, increased model predictive capabilities and practical application are still needed. Here, we developed a novel machine learning-based approach for predicting rubber tree stem circumference based on molecular markers. Through a divide-and-conquer strategy, we propose a neural network prediction system with two stages: (1) subpopulation prediction and (2) phenotype estimation. This approach yielded higher accuracies than traditional statistical models in a single-environment scenario. By delivering large accuracy improvements, our methodology represents a powerful tool for use in Hevea GS strategies. Therefore, the incorporation of machine learning techniques into rubber tree GS represents an opportunity to build more robust models and optimize Hevea breeding programs.
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10
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Hu YS, Huang HS, Liu J. Characterization of the complete chloroplast genome of Hevea pauciflora (Euphorbiaceae), an important wild relative of the rubber tree. Mitochondrial DNA B Resour 2022; 7:1589-1593. [PMID: 36106188 PMCID: PMC9467626 DOI: 10.1080/23802359.2022.2115321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Hevea pauciflora belongs to the Euphorbiaceae family, an important wild relative of the rubber tree. This study sequenced, assembled, and annotated the complete chloroplast genome of H. pauciflora. The complete chloroplast genome is 161,123 bp with a canonical quadripartite structure containing a large single-copy (LSC) region (89,109 bp), a small single-copy (SSC) region (18,376 bp), and two inverted repeat regions (IRa and IRb) (26,819 bp, each). A total of 134 genes were annotated, including 86 protein-coding genes, four pseudogenes, 36 tRNA genes, and eight rRNA genes. The 134 genes include four major groups: ‘self-replication’, ‘photosynthesis’, ‘unknown function’, and ‘others’. A phylogenetic analysis clustered H. pauciflora, H. brasiliensis, H. camargoana, and H. benthamiana into one clade, consistent with traditional taxonomy. This study provides useful data for further studies of Hevea genus and the phylogenetic relationships of Euphorbiaceae species.
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Affiliation(s)
- Yan-Shi Hu
- Rubber Research Institute, Chinese Academy of Tropical Agriculture Science, Danzhou, China
| | - Hua-Sun Huang
- Rubber Research Institute, Chinese Academy of Tropical Agriculture Science, Danzhou, China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
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11
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Ugbogu EA, Schweizer LM, Schweizer M. Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. Cells 2022; 11:1909. [PMID: 35741038 PMCID: PMC9221600 DOI: 10.3390/cells11121909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphoribosyl pyrophosphate synthetase (PRS EC 2.7.6.1) is a rate-limiting enzyme that irreversibly catalyzes the formation of phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate and adenosine triphosphate (ATP). This key metabolite is required for the synthesis of purine and pyrimidine nucleotides, the two aromatic amino acids histidine and tryptophan, the cofactors nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), all of which are essential for various life processes. Despite its ubiquity and essential nature across the plant and animal kingdoms, PRPP synthetase displays species-specific characteristics regarding the number of gene copies and architecture permitting interaction with other areas of cellular metabolism. The impact of mutated PRS genes in the model eukaryote Saccharomyces cerevisiae on cell signalling and metabolism may be relevant to the human neuropathies associated with PRPS mutations. Human PRPS1 and PRPS2 gene products are implicated in drug resistance associated with recurrent acute lymphoblastic leukaemia and progression of colorectal cancer and hepatocellular carcinoma. The investigation of PRPP metabolism in accepted model organisms, e.g., yeast and zebrafish, has the potential to reveal novel drug targets for treating at least some of the diseases, often characterized by overlapping symptoms, such as Arts syndrome and respiratory infections, and uncover the significance and relevance of human PRPS in disease diagnosis, management, and treatment.
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Affiliation(s)
- Eziuche A. Ugbogu
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Lilian M. Schweizer
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Michael Schweizer
- Institute of Biological Chemistry, Biophysics & Engineering (IB3), School of Engineering &Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
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12
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Yu N, Sun H, Yang J, Li R. The Diesel Tree Sindora glabra Genome Provides Insights Into the Evolution of Oleoresin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 12:794830. [PMID: 35058955 PMCID: PMC8764381 DOI: 10.3389/fpls.2021.794830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Sindora glabra is an economically important tree that produces abundant oleoresin in the trunk. Here, we present a high-quality chromosome-scale assembly of S. glabra genome by combining Illumina HiSeq, Pacific Biosciences sequencing, and Hi-C technologies. The size of S. glabra genome was 1.11 Gb, with a contig N50 of 1.27 Mb and 31,944 predicted genes. This is the first sequenced genome of the subfamily Caesalpinioideae. As a sister taxon to Papilionoideae, S. glabra underwent an ancient genome triplication shared by core eudicots and further whole-genome duplication shared by early-legume in the last 73.3 million years. S. glabra harbors specific genes and expanded genes largely involved in stress responses and biosynthesis of secondary metabolites. Moreover, 59 terpene backbone biosynthesis genes and 64 terpene synthase genes were identified, which together with co-expressed transcription factors could contribute to the diversity and specificity of terpene compounds and high terpene content in S. glabra stem. In addition, 63 disease resistance NBS-LRR genes were found to be unique in S. glabra genome and their expression levels were correlated with the accumulation of terpene profiles, suggesting potential defense function of terpenes in S. glabra. These together provide new resources for understanding genome evolution and oleoresin production.
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Affiliation(s)
- Niu Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Haixi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinchang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Rongsheng Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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13
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Chen X, Deng Z, Yu D, Zhang X, An Z, Wu W, Liang Q, Huang X, Huang H, Cheng H. Genome-Wide Identification and Analysis of Small Nucleolar RNAs and Their Roles in Regulating Latex Regeneration in the Rubber Tree ( Hevea brasiliensis). FRONTIERS IN PLANT SCIENCE 2021; 12:731484. [PMID: 34764965 PMCID: PMC8575768 DOI: 10.3389/fpls.2021.731484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are a class of conserved nuclear RNAs that play important roles in the modification of ribosomal RNAs (rRNAs) in plants. In rubber trees, rRNAs are run off with latex flow during tapping and need to be regenerated for maintaining the functions of the laticifer cells. SnoRNAs are expected to play essential roles in the regeneration of rRNAs. However, snoRNAs in the rubber tree have not been sufficiently characterized thus far. In this study, we performed nuclear RNA sequencing (RNA-seq) to identify snoRNAs globally and investigate their roles in latex regeneration. We identified a total of 3,626 snoRNAs by computational prediction with nuclear RNA-seq data. Among these snoRNAs, 50 were highly expressed in latex; furthermore, the results of reverse transcription polymerase chain reaction (RT-PCR) showed the abundant expression of 31 of these snoRNAs in latex. The correlation between snoRNA expression and adjusted total solid content (TSC/C) identified 13 positively yield-correlated snoRNAs. To improve the understanding of latex regeneration in rubber trees, we developed a novel insulated tapping system (ITS), which only measures the latex regenerated in specific laticifers. Using this system, a laticifer-abundant snoRNA, HbsnoR28, was found to be highly correlated with latex regeneration. To the best of our knowledge, this is the first report to globally identify snoRNAs that might be involved in latex regeneration regulation and provide new clues for unraveling the mechanisms underlying the regulation of latex regeneration.
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14
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Dai L, Yang H, Zhao X, Wang L. Identification of cis conformation natural rubber and proteins in Ficus altissima Blume latex. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:376-384. [PMID: 34404008 DOI: 10.1016/j.plaphy.2021.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Ficus altissima Blume, a horticultural plant in tropical and warm subtropical regions, can produce natural rubber with comparable molecular weight to the Hevea brasiliensis rubber. The F. altissima latex has an acidic pH (about 4.89). The rubber particle size distribution is a unimodal profile, and the peak frequency is at a size of 4.5 μm. The natural rubber of F. altissima was determined to be a cis conformation via 13C NMR. The Mp (molecular weight of the peak maxima) of the deproteinized F. altissima rubber was 9.34 × 105 Da. LC-MS was used to identify the proteins of rubber particles and serum. The most abundant protein of the creamy rubber particle layer is an acid phosphatase, while the most abundant proteins of serum were an (R)-mandelonitrilelyase and a polygalacturonase inhibitor. Pharmaceutical proteins (ficins) or enzymes related to the biosynthesis of natural medicines (a cannabidiolic acid synthase and two lupeol synthase) were identified in F. altissima latex. The data of this study may be helpful for research on the functions of latex in latex-borne plants and the biosynthesis mechanism of natural rubber.
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Affiliation(s)
- Longjun Dai
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, PR China; State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan, PR China.
| | - Hong Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, PR China; State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan, PR China.
| | - Xizhu Zhao
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, PR China; State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan, PR China.
| | - Lifeng Wang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, PR China; State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Haikou, Hainan, PR China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan, PR China.
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15
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Nakano Y, Mitsuda N, Ide K, Mori T, Mira FR, Rosmalawati S, Watanabe N, Suzuki K. Transcriptome analysis of Pará rubber tree (H. brasiliensis) seedlings under ethylene stimulation. BMC PLANT BIOLOGY 2021; 21:420. [PMID: 34517831 PMCID: PMC8436496 DOI: 10.1186/s12870-021-03196-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
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.
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Affiliation(s)
- Yoshimi Nakano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Kohei Ide
- Bridgestone Corporation, Kodaira, Tokyo, 187-8531, Japan
| | - Teppei Mori
- Bridgestone Corporation, Kodaira, Tokyo, 187-8531, Japan
| | - Farida Rosana Mira
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology, Build. 630, Puspiptek area, Serpong, Tangerang, Selatan, 15314, Indonesia
| | - Syofi Rosmalawati
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology, Build. 630, Puspiptek area, Serpong, Tangerang, Selatan, 15314, Indonesia
| | - Norie Watanabe
- Bridgestone Corporation, Kodaira, Tokyo, 187-8531, Japan
| | - Kaoru Suzuki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 169-8555, Japan.
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16
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Yang Y, Huang L, Xu C, Qi L, Wu Z, Li J, Chen H, Wu Y, Fu T, Zhu H, Saand MA, Li J, Liu L, Fan H, Zhou H, Qin W. Chromosome-scale genome assembly of areca palm (Areca catechu). Mol Ecol Resour 2021; 21:2504-2519. [PMID: 34133844 DOI: 10.1111/1755-0998.13446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
Areca palm (Areca catechu L.; family Arecaceae) is an important tropical medicinal crop and is also used for masticatory and religious purposes in Asia. Improvements to areca properties made by traditional breeding tools have been very slow, and further advances in its cultivation and practical use require genomic information, which is still unavailable. Here, we present a chromosome-scale reference genome assembly for areca by combining Illumina and PacBio data with Hi-C mapping technologies, covering the predicted A. catechu genome length (2.59 Gb, variety "Reyan#1") to an estimated 240× read depth. The assembly was 2.51 Gb in length with a scaffold N50 of 1.7Mb. The scaffolds were then further assembled into 16 pseudochromosomes, with an N50 of 172 Mb. Transposable elements comprised 80.37% of the areca genome, and 68.68% of them were long-terminal repeat retrotransposon elements. The areca palm genome was predicted to harbour 31,571 protein-coding genes and overall, 92.92% of genes were functionally annotated, including enriched and expanded families of genes responsible for biosynthesis of flavonoid, anthocyanin, monoterpenoid and their derivatives. Comparative analyses indicated that A. catechu probably diverged from its close relatives Elaeis guineensis and Cocos nucifera approximately 50.3 million years ago (Ma). Two whole genome duplication events in areca palm were found to be shared by palms and monocots, respectively. This genome assembly and associated resources represents an important addition to the palm genomics community and will be a valuable resource that will facilitate areca palm breeding and improve our understanding of areca palm biology and evolution.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Chunyan Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lan Qi
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Jia Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Tao Fu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hui Zhu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Liyun Liu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Haikou Fan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Huanqi Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Weiquan Qin
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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17
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Leaf isoprene emission as a trait that mediates the growth-defense tradeoff in the face of climate stress. Oecologia 2021; 197:885-902. [PMID: 33420520 DOI: 10.1007/s00442-020-04813-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/01/2020] [Indexed: 12/27/2022]
Abstract
Plant isoprene emissions are known to contribute to abiotic stress tolerance, especially during episodes of high temperature and drought, and during cellular oxidative stress. Recent studies have shown that genetic transformations to add or remove isoprene emissions cause a cascade of cellular modifications that include known signaling pathways, and interact to remodel adaptive growth-defense tradeoffs. The most compelling evidence for isoprene signaling is found in the shikimate and phenylpropanoid pathways, which produce salicylic acid, alkaloids, tannins, anthocyanins, flavonols and other flavonoids; all of which have roles in stress tolerance and plant defense. Isoprene also influences key gene expression patterns in the terpenoid biosynthetic pathways, and the jasmonic acid, gibberellic acid and cytokinin signaling networks that have important roles in controlling inducible defense responses and influencing plant growth and development, particularly following defoliation. In this synthesis paper, using past studies of transgenic poplar, tobacco and Arabidopsis, we present the evidence for isoprene acting as a metabolite that coordinates aspects of cellular signaling, resulting in enhanced chemical defense during periods of climate stress, while minimizing costs to growth. This perspective represents a major shift in our thinking away from direct effects of isoprene, for example, by changing membrane properties or quenching ROS, to indirect effects, through changes in gene expression and protein abundances. Recognition of isoprene's role in the growth-defense tradeoff provides new perspectives on evolution of the trait, its contribution to plant adaptation and resilience, and the ecological niches in which it is most effective.
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Bhardwaj E, Lal M, Anand S, Das S. Independent recurrent evolution of MICRORNA genes converging onto similar non-canonical organisation across green plant lineages is driven by local and segmental duplication events in species, family and lineages. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110661. [PMID: 33218629 DOI: 10.1016/j.plantsci.2020.110661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
The relationship between evolutionary history, organisation and transcriptional regulation of genes are intrinsically linked. These have been well studied in canonically organised protein-coding genes but not of MIRNAs. In the present study, we investigated the non-canonical arrangement of MIRNAs across taxonomic boundaries from algae to angiosperms employing a combination of genome organization, phylogeny and synteny. We retrieved the complete dataset of MIRNA from twenty-five species to identify and classify based on organisational patterns. The median size of cluster was between 2-5 kb and between 1-20 % of all MIRNAs are organized in head-to-head (with bidirectional promoter), head-to-tail (tandem), and overlapping manner. Although majority of the clusters are composed of MIRNA homologs, 25% of all clusters comprises of non-homologous genes with a potential of generating functional and regulatory complexity. A comparison of phylogeny and organizational patterns revealed that multiple independent events, some of which are species-specific, and some ancient, in different lineages, are responsible for non-canonical organization. Detailed investigation of MIR395 family across the plants revealed a complex origin of non-canonical arrangement through ancient and recent, segmental and local duplications; analysis of MIR399 family revealed major expansion occurred prior to monocot-dicot split, with few lineage-specific events. Evolution of "convergent" organization pattern of non-canonical arrangement originating from independent loci through recurrent event highlights our poor understanding of evolutionary process of MIRNA genes. The present investigation thus paves way for comparative functional genomics to understand the role of non-canonical organization on transcriptional regulation and regulatory diversity in MIRNA gene families.
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Affiliation(s)
- Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - S Anand
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110 007, India.
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Abu Bakar MF, Kamerkar U, Abdul Rahman SN, Muhd Sakaff MKL, Othman AS. Transcriptome dataset from bark and latex tissues of three Hevea brasiliensis clones. Data Brief 2020; 32:106188. [PMID: 32904357 PMCID: PMC7452566 DOI: 10.1016/j.dib.2020.106188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/13/2020] [Accepted: 08/11/2020] [Indexed: 11/29/2022] Open
Abstract
Hevea brasiliensis is exploited for its latex production, and it is the only viable source of natural rubber worldwide. The demand for natural rubber remains high due its high-quality properties, which synthetic rubber cannot compete with. In this paper, we present transcriptomic data and analysis of three H. brasiliensis clones using tissue from latex and bark tissues collected from 10-year-old plant. The combined, assembled transcripts were mapped onto an H. brasiliensis draft genome. Gene ontology analysis showed that the most abundant transcripts related to molecular functions, followed by biological processes and cellular components. Simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were also identified, and these can be useful for selection of parental and new clones in a breeding program. Data generated by RNA sequencing were deposited in the NCBI public repository under accession number PRJNA629890.
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Affiliation(s)
- Mohd Fahmi Abu Bakar
- Faculty of Bioresources & Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200 Besut, Terengganu, Malaysia
| | - Urwashi Kamerkar
- School of Biological Sciences, Universiti Sains Malaysia, 11700 Minden, Pulau Pinang, Malaysia
| | | | | | - Ahmad Sofiman Othman
- School of Biological Sciences, Universiti Sains Malaysia, 11700 Minden, Pulau Pinang, Malaysia
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Feng LY, Liu J, Gao CW, Wu HB, Li GH, Gao LZ. Higher Genomic Variation in Wild Than Cultivated Rubber Trees, Hevea brasiliensis, Revealed by Comparative Analyses of Chloroplast Genomes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis. Int J Mol Sci 2020; 21:ijms21124220. [PMID: 32545790 PMCID: PMC7353026 DOI: 10.3390/ijms21124220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
The natural rubber biosynthetic pathway is well described in Hevea, although the final stages of rubber elongation are still poorly understood. Small Rubber Particle Proteins and Rubber Elongation Factors (SRPPs and REFs) are proteins with major function in rubber particle formation and stabilization. Their corresponding genes are clustered on a scaffold1222 of the reference genomic sequence of the Hevea brasiliensis genome. Apart from gene expression by transcriptomic analyses, to date, no deep analyses have been carried out for the genomic environment of SRPPs and REFs loci. By integrative analyses on transposable element annotation, small RNAs production and gene expression, we analysed their role in the control of the transcription of rubber biosynthetic genes. The first in-depth annotation of TEs (Transposable Elements) and their capacity to produce TE-derived siRNAs (small interfering RNAs) is presented, only possible in the Hevea brasiliensis clone PB 260 for which all data are available. We observed that 11% of genes are located near TEs and their presence may interfere in their transcription at both genetic and epigenetic level. We hypothesized that the genomic environment of rubber biosynthesis genes has been shaped by TE and TE-derived siRNAs with possible transcriptional interference on their gene expression. We discussed possible functionalization of TEs as enhancers and as donors of alternative transcription start sites in promoter sequences, possibly through the modelling of genetic and epigenetic landscapes.
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Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis. PLANTS 2020; 9:plants9060674. [PMID: 32466493 PMCID: PMC7355734 DOI: 10.3390/plants9060674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/23/2020] [Indexed: 11/17/2022]
Abstract
Natural rubber is the main component of latex obtained from laticifer cells of Hevea brasiliensis. For improving rubber yield, it is essential to understand the genetic molecular mechanisms responsible for laticifer differentiation and rubber biosynthesis. Jasmonate enhances both secondary laticifer differentiation and rubber biosynthesis. Here, we carried out time-course RNA-seq analysis in suspension-cultured cells treated with methyljasmonic acid (MeJA) to characterize the gene expression profile. Gene Ontology (GO) analysis showed that the term "cell differentiation" was enriched in upregulated genes at 24 hours after treatment, but inversely, the term was enriched in downregulated genes at 5 days, indicating that MeJA could induce cell differentiation at an early stage of the response. Jasmonate signaling is activated by MYC2, a basic helix-loop-helix (bHLH)-type transcription factor (TF). The aim of this work was to find any links between transcriptomic changes after MeJA application and regulation by TFs. Using an in vitro binding assay, we traced candidate genes throughout the whole genome that were targeted by four bHLH TFs: Hb_MYC2-1, Hb_MYC2-2, Hb_bHLH1, and Hb_bHLH2. The latter two are highly expressed in laticifer cells. Their physical binding sites were found in the promoter regions of a variety of other TF genes, which are differentially expressed upon MeJA exposure, and rubber biogenesis-related genes including SRPP1 and REF3. These studies suggest the possibilities that Hb_MYC2-1 and Hb_MYC2-2 regulate cell differentiation and that Hb_bHLH1 and Hb_bHLH2 promote rubber biosynthesis. We expect that our findings will help to increase natural rubber yield through genetic control in the future.
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Niu YF, Hu YS, Liu ZY, Zheng C, Liu J. Complete chloroplast genome of Hevea benthamiana, a SALB-resistant relative wild species of rubber tree. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2062-2064. [PMID: 33457743 PMCID: PMC7781926 DOI: 10.1080/23802359.2020.1763868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Hevea benthamiana is a SALB-resistant wild species of H. brasiliensis, the only source of mass production of high quality natural rubber. This study sequenced and analyzed the chloroplast genome of H. benthamiana. The chloroplast genome of H. benthamiana contains 161,124 bp and consists of 51,495 bp of A (31.96%), 52,022 bp of T (32.29%), 28,915 bp of G (17.95%), and 28,692 bp of C (17.81%). The ring-shaped genome includes four regions: a large single-copy region (LSC, 89,110 bp), a small single copy (SSC, 18,376 bp) region, and two inverted repeat regions (IRs, 26,819 bp). A total of 134 genes were annotated, of which 86 encode proteins; four are pseudogenes; 36 are tRNA genes, and eight are rRNA genes. Phylogenetic analyses showed that H. benthamiana is very closely related to H. Brasiliensis, this result indicates that H. benthamiana is highly valuable for the breeding of SALB-resistant varieties of rubber trees.
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Affiliation(s)
- Ying-Feng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Yan-Shi Hu
- Rubber Research Institute, Chinese Academy of Tropical Agriculture Science, Danzhou, China
| | - Zi-Yan Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Jin Liu
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Liu J, Shi C, Shi CC, Li W, Zhang QJ, Zhang Y, Li K, Lu HF, Shi C, Zhu ST, Xiao ZY, Nan H, Yue Y, Zhu XG, Wu Y, Hong XN, Fan GY, Tong Y, Zhang D, Mao CL, Liu YL, Hao SJ, Liu WQ, Lv MQ, Zhang HB, Liu Y, Hu-Tang GR, Wang JP, Wang JH, Sun YH, Ni SB, Chen WB, Zhang XC, Jiao YN, Eichler EE, Li GH, Liu X, Gao LZ. The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis. MOLECULAR PLANT 2020; 13:336-350. [PMID: 31838037 DOI: 10.1016/j.molp.2019.10.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/16/2019] [Accepted: 10/30/2019] [Indexed: 05/23/2023]
Abstract
The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ∼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by ∼65.88% (∼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains ∼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.
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Affiliation(s)
- Jin Liu
- Yunnan Institute of Tropical Crops, Jinghong 666100, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Cong Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Qun-Jie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Yun Zhang
- Asia-Pacific Tropical Forestry Germplasm Institution, Southwest China Forestry University, Kunming 650224, China
| | - Kui Li
- School of Life Sciences, Nanjing University, Nanjing 210023, China; Novogene Bioinformatics Institute, Beijing 100083, China
| | | | - Chao Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | | | - Zai-Yun Xiao
- Yunnan Institute of Tropical Crops, Jinghong 666100, China
| | - Hong Nan
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Yue
- BGI-Qingdao, Qingdao 266555, China
| | - Xun-Ge Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Wu
- Yunnan Institute of Tropical Crops, Jinghong 666100, China
| | | | - Guang-Yi Fan
- BGI-Qingdao, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Chang-Li Mao
- Yunnan Institute of Tropical Crops, Jinghong 666100, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | | | | | | | - Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Yuan Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Ge-Ran Hu-Tang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Peng Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | | | | | - Shu-Bang Ni
- Yunnan Institute of Tropical Crops, Jinghong 666100, China
| | | | - Xing-Cai Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Evan E Eichler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Guo-Hua Li
- Yunnan Institute of Tropical Crops, Jinghong 666100, China
| | - Xin Liu
- BGI-Qingdao, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China.
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
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Niu YF, Hu YS, Zheng C, Liu ZY, Liu J. The complete chloroplast genome of Hevea camargoana. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:607-608. [PMID: 33366668 PMCID: PMC7748615 DOI: 10.1080/23802359.2019.1710605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hevea camargoana is a natural latex producing tropical plant and a close relative of H. brasiliensis, the primary commercial source of natural rubber. This study sequenced and analyzed the chloroplast genome of H. camargoana. The circular chloroplast genome of H. camargoana contains 161,291 bp with a GC content of 35.72%. This region contains two inverted repeat regions (26,819 bp), a large single-copy region (89,281 bp), and a small single-copy (18,372 bp) region in the complete chloroplast genome. A total of 134 genes were annotated, including 86 protein-coding genes, 36 transfer RNA genes, 8 ribosomal RNA genes, and 4 pseudogenes. The results showed that H. camargoana and H. brasiliensis were closely related, suggesting that H. camargoana may be used for the future variety improvement of rubber trees.
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Affiliation(s)
- Ying-Feng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Yan-Shi Hu
- Rubber Research Institute, Chinese Academy of Tropical Agriculture Science, Danzhou, China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Zi-Yan Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Jin Liu
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Li J, Gao X, Sang S, Liu C. Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae. BMC Genomics 2019; 20:912. [PMID: 31874634 PMCID: PMC6929338 DOI: 10.1186/s12864-019-6319-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/21/2019] [Indexed: 01/19/2023] Open
Abstract
Background Euphorbiaceae is one of the largest families of flowering plants. Due to its exceptional growth form diversity and near-cosmopolitan distribution, it has attracted much interest since ancient times. SBP-box (SBP) genes encode plant-specific transcription factors that play critical roles in numerous biological processes, especially flower development. We performed genome-wide identification and characterization of SBP genes from four economically important Euphorbiaceae species. Results In total, 77 SBP genes were identified in four Euphorbiaceae genomes. The SBP proteins were divided into three length ranges and 10 groups. Group-6 was absent in Arabidopsis thaliana but conserved in Euphorbiaceae. Segmental duplication played the most important role in the expansion processes of Euphorbiaceae SBP genes, and all the duplicated genes were subjected to purify selection. In addition, about two-thirds of the Euphorbiaceae SBP genes are potential targets of miR156, and some miR-regulated SBP genes exhibited high intensity expression and differential expression in different tissues. The expression profiles related to different stress treatments demonstrated broad involvement of Euphorbiaceae SBP genes in response to various abiotic factors and hormonal treatments. Conclusions In this study, 77 SBP genes were identified in four Euphorbiaceae species, and their phylogenetic relationships, protein physicochemical characteristics, duplication, tissue and stress response expression, and potential roles in Euphorbiaceae development were studied. This study lays a foundation for further studies of Euphorbiaceae SBP genes, providing valuable information for future functional exploration of Euphorbiaceae SBP genes.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyang Gao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shiye Sang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China. .,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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Genome-Wide Identification and Characterization of Heat-Shock Transcription Factors in Rubber Tree. FORESTS 2019. [DOI: 10.3390/f10121157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Heat-shock transcription factors (Hsfs) play a pivotal role in the response of plants to various stresses. The present study aimed to characterize the Hsf genes in the rubber tree, a primary global source of natural rubber. In this study, 30 Hsf genes were identified in the rubber tree using genome-wide analysis. They possessed a structurally conserved DNA-binding domain and an oligomerization domain. On the basis of the length of the insert region between HR-A and HR-B in the oligomerization domain, the 30 members were clustered into three classes, Classes A (18), B (10), and C (2). Members within the same class shared highly conserved gene structures and protein motifs. The background expression levels of 11 genes in cold-tolerant rubber-tree clone 93-14 were significantly higher than those in cold-sensitive rubber-tree clone Reken501, while four genes exhibited inverse expression patterns. Upon cold stress, 20 genes were significantly upregulated in 93-114. Of the upregulated genes, HbHsfA2b, HbHsfA3a, and HbHsfA7a were also significantly upregulated in three other cold-tolerant rubber-tree clones at one or more time intervals upon cold stress. Their nuclear localization was verified, and the protein–protein interaction network was predicted. This study provides a basis for dissecting Hsf function in the enhanced cold tolerance of the rubber tree.
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Single-nucleotide polymorphism markers within MVA and MEP pathways among Hevea brasiliensis clones through transcriptomic analysis. 3 Biotech 2019; 9:388. [PMID: 31656726 DOI: 10.1007/s13205-019-1921-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022] Open
Abstract
In this study, RNA sequencing of several Hevea brasiliensis clones grown in Malaysia with different annual rubber production yields and disease resistance was performed on the Illumina platform. A total of 29,862,548 reads were generated, resulting in 101,269 assembled transcripts that were used as the reference transcripts. A similarity search against the non-redundant (nr) protein databases presented 83,771 (83%) positive BLASTx hits. The transcriptome was annotated using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Pfam database. A search for putative molecular markers was performed to identify single-nucleotide polymorphisms (SNPs). Overall, 3,210,629 SNPs were detected and a total of 1314 SNPs associated with the genes involved in MVA and MEP pathways were identified. A total of 176 SNP primer pairs were designed from sequences that were related to the MVA and MEP pathways. The transcriptome of RRIM 3001 and RRIM 712 were subjected to pairwise comparison and the results revealed that there were 1262 significantly differentially expressed genes unique to RRIM 3001, 1499 significantly differentially expressed genes unique to RRIM 712 and several genes related to the MVA and MEP pathways such as AACT, HMGS, PMK, MVD, DXS and HDS were included. The results will facilitate the characterization of H. brasiliensis transcriptomes and the development of a new set of molecular markers in the form of SNPs from transcriptome assembly for the genotype identification of various rubber varieties with superior traits in Malaysia.
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Cherian S, Ryu SB, Cornish K. Natural rubber biosynthesis in plants, the rubber transferase complex, and metabolic engineering progress and prospects. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2041-2061. [PMID: 31150158 PMCID: PMC6790360 DOI: 10.1111/pbi.13181] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/24/2019] [Accepted: 05/29/2019] [Indexed: 05/26/2023]
Abstract
Natural rubber (NR) is a nonfungible and valuable biopolymer, used to manufacture ~50 000 rubber products, including tires and medical gloves. Current production of NR is derived entirely from the para rubber tree (Hevea brasiliensis). The increasing demand for NR, coupled with limitations and vulnerability of H. brasiliensis production systems, has induced increasing interest among scientists and companies in potential alternative NR crops. Genetic/metabolic pathway engineering approaches, to generate NR-enriched genotypes of alternative NR plants, are of great importance. However, although our knowledge of rubber biochemistry has significantly advanced, our current understanding of NR biosynthesis, the biosynthetic machinery and the molecular mechanisms involved remains incomplete. Two spatially separated metabolic pathways provide precursors for NR biosynthesis in plants and their genes and enzymes/complexes are quite well understood. In contrast, understanding of the proteins and genes involved in the final step(s)-the synthesis of the high molecular weight rubber polymer itself-is only now beginning to emerge. In this review, we provide a critical evaluation of recent research developments in NR biosynthesis, in vitro reconstitution, and the genetic and metabolic pathway engineering advances intended to improve NR content in plants, including H. brasiliensis, two other prospective alternative rubber crops, namely the rubber dandelion and guayule, and model species, such as lettuce. We describe a new model of the rubber transferase complex, which integrates these developments. In addition, we highlight the current challenges in NR biosynthesis research and future perspectives on metabolic pathway engineering of NR to speed alternative rubber crop commercial development.
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Affiliation(s)
- Sam Cherian
- Plant Systems Engineering Research CentreKorea Research Institute of Bioscience and Biotechnology (KRIBB)Yuseong‐guDaejeonKorea
- Research & Development CenterDRB Holding Co. LTDBusanKorea
| | - Stephen Beungtae Ryu
- Plant Systems Engineering Research CentreKorea Research Institute of Bioscience and Biotechnology (KRIBB)Yuseong‐guDaejeonKorea
- Department of Biosystems and BioengineeringKRIBB School of BiotechnologyKorea University of Science and Technology (UST)DaejeonKorea
| | - Katrina Cornish
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOHUSA
- Department of Food, Agricultural and Biological EngineeringThe Ohio State UniversityWoosterOHUSA
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Chow KS, Khoo JS, Mohd.-Zainuddin Z, Ng SM, Hoh CC. Utility of PacBio Iso-Seq for transcript and gene discovery in Hevea latex. J RUBBER RES 2019. [DOI: 10.1007/s42464-019-00026-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Proteomic Landscape Has Revealed Small Rubber Particles Are Crucial Rubber Biosynthetic Machines for Ethylene-Stimulation in Natural Rubber Production. Int J Mol Sci 2019; 20:ijms20205082. [PMID: 31614967 PMCID: PMC6829444 DOI: 10.3390/ijms20205082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
Rubber particles are a specific organelle for natural rubber biosynthesis (NRB) and storage. Ethylene can significantly improve rubber latex production by increasing the generation of small rubber particles (SRPs), regulating protein accumulation, and activating many enzyme activities. We conducted a quantitative proteomics study of different SRPs upon ethylene stimulation by differential in-gel electrophoresis (DIGE) and using isobaric tags for relative and absolute quantification (iTRAQ) methods. In DIGE, 79 differentially accumulated proteins (DAPs) were determined as ethylene responsive proteins. Our results show that the abundance of many NRB-related proteins has been sharply induced upon ethylene stimulation. Among them, 23 proteins were identified as rubber elongation factor (REF) and small rubber particle protein (SRPP) family members, including 16 REF and 7 SRPP isoforms. Then, 138 unique phosphorylated peptides, containing 129 phosphorylated amino acids from the 64 REF/SRPP family members, were identified, and most serine and threonine were phosphorylated. Furthermore, we identified 226 DAPs from more than 2000 SRP proteins by iTRAQ. Integrative analysis revealed that almost all NRB-related proteins can be detected in SRPs, and many proteins are positively responsive to ethylene stimulation. These results indicate that ethylene may stimulate latex production by regulating the accumulation of some key proteins. The phosphorylation modification of REF and SRPP isoforms might be crucial for NRB, and SRP may act as a complex natural rubber biosynthetic machine.
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Loh SC, Othman AS, Veera Singham G. Identification and characterization of jasmonic acid- and linolenic acid-mediated transcriptional regulation of secondary laticifer differentiation in Hevea brasiliensis. Sci Rep 2019; 9:14296. [PMID: 31586098 PMCID: PMC6778104 DOI: 10.1038/s41598-019-50800-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/17/2019] [Indexed: 11/30/2022] Open
Abstract
Hevea brasiliensis remains the primary crop commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. Here, we described the transcriptional events related to jasmonic acid (JA)- and linolenic acid (LA)-induced secondary laticifer differentiation (SLD) in H. brasiliensis clone RRIM 600 based on RNA-seq approach. Histochemical approach proved that JA- and LA-treated samples resulted in SLD in H. brasiliensis when compared to ethephon and untreated control. RNA-seq data resulted in 86,614 unigenes, of which 2,664 genes were differentially expressed in JA and LA-induced secondary laticifer harvested from H. brasiliensis bark samples. Among these, 450 genes were unique to JA and LA as they were not differentially expressed in ethephon-treated samples compared with the untreated samples. Most transcription factors from the JA- and LA-specific dataset were classified under MYB, APETALA2/ethylene response factor (AP2/ERF), and basic-helix-loop-helix (bHLH) gene families that were involved in tissue developmental pathways, and we proposed that Bel5-GA2 oxidase 1-KNOTTED-like homeobox complex are likely involved in JA- and LA-induced SLD in H. brasiliensis. We also discovered alternative spliced transcripts, putative novel transcripts, and cis-natural antisense transcript pairs related to SLD event. This study has advanced understanding on the transcriptional regulatory network of SLD in H. brasiliensis.
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Affiliation(s)
- Swee Cheng Loh
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - G Veera Singham
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
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Abstract
The commercial production of high quality natural rubber (NR) solely depends on Hevea brasiliensis Muell. Arg, (Para rubber tree) and accounts for >98% of total production worldwide. NR with its unique properties is an essential commodity for the automobile industry and its synthetic counterparts are in no way substitute to it. The rubber tree genome is very complex and plays an important role in delivering the unique properties of Hevea. But a lack of knowledge on the molecular mechanisms of rubber biosynthesis, disease resistance, etc., in elite clones of rubber still persists. Marker-assisted selection and transgenic techniques were proved to be advantageous in improving the breeding efficiency for latex yield, disease resistance, etc. The suppression subtractive hybridization (SSH), in the form of subtracted cDNA libraries and microarrays, can assist in searching the functions of expressed genes (candidate gene approach). Expressed sequence tags (ESTs) related to various metabolic aspects are well utilized to create EST banks that broadly represent the genes expressed in one tissue, such as latex cells, that assists in the study of gene function and regulation. Transcriptome analysis and gene mapping have been accomplished in Hevea at various stages. However, a selection criterion to delineate high yielding genotypes at the juvenile stage has not been accomplished so far. This is the main pit fall for rubber breeding apart from stock-scion interactions leading to yield differences among a clonally multiplied population. At least four draft genome sequences have been published on Hevea rubber, and all give different genome size and contig lengths-a comprehensive and acceptable genomic map remains unfulfilled. The progress made in molecular markers, latex biosynthesis genes, transcriptome analysis, chloroplast and mitochondrial DNA diversity, paternity identification through Breeding without Breeding (BwB), stimulated latex production and its molecular intricacies, molecular biology of tapping panel dryness, genomics for changed climates and genome mapping are discussed in this review. These information can be utilized to improvise the molecular breeding programs of Hevea in future.
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Xie Q, Ding G, Zhu L, Yu L, Yuan B, Gao X, Wang D, Sun Y, Liu Y, Li H, Wang X. Proteomic Landscape of the Mature Roots in a Rubber-Producing Grass Taraxacum Kok-saghyz. Int J Mol Sci 2019; 20:ijms20102596. [PMID: 31137823 PMCID: PMC6566844 DOI: 10.3390/ijms20102596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
The rubber grass Taraxacum kok-saghyz (TKS) contains large amounts of natural rubber (cis-1,4-polyisoprene) in its enlarged roots and it is an alternative crop source of natural rubber. Natural rubber biosynthesis (NRB) and storage in the mature roots of TKS is a cascade process involving many genes, proteins and their cofactors. The TKS genome has just been annotated and many NRB-related genes have been determined. However, there is limited knowledge about the protein regulation mechanism for NRB in TKS roots. We identified 371 protein species from the mature roots of TKS by combining two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Meanwhile, a large-scale shotgun analysis of proteins in TKS roots at the enlargement stage was performed, and 3545 individual proteins were determined. Subsequently, all identified proteins from 2-DE gel and shotgun MS in TKS roots were subject to gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and most proteins were involved in carbon metabolic process with catalytic activity in membrane-bounded organelles, followed by proteins with binding ability, transportation and phenylpropanoid biosynthesis activities. Fifty-eight NRB-related proteins, including eight small rubber particle protein (SRPP) and two rubber elongation factor(REF) members, were identified from the TKS roots, and these proteins were involved in both mevalonate acid (MVA) and methylerythritol phosphate (MEP) pathways. To our best knowledge, it is the first high-resolution draft proteome map of the mature TKS roots. Our proteomics of TKS roots revealed both MVA and MEP pathways are important for NRB, and SRPP might be more important than REF for NRB in TKS roots. These findings would not only deepen our understanding of the TKS root proteome, but also provide new evidence on the roles of these NRB-related proteins in the mature TKS roots.
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Affiliation(s)
- Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Guohua Ding
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Liping Zhu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Li Yu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Boxuan Yuan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Xuan Gao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China.
| | - Yong Sun
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China.
| | - Yang Liu
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
| | - Xuchu Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
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Chao J, Zhao Y, Jin J, Wu S, Deng X, Chen Y, Tian WM. Genome-Wide Identification and Characterization of the JAZ Gene Family in Rubber Tree ( Hevea brasiliensis). Front Genet 2019; 10:372. [PMID: 31118943 PMCID: PMC6504806 DOI: 10.3389/fgene.2019.00372] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/09/2019] [Indexed: 11/13/2022] Open
Abstract
Jasmonate signaling plays a vital role in the regulation of secondary laticifer differentiation and natural rubber biosynthesis in Hevea brasiliensis. Jasmonate ZIM-domain (JAZ) proteins are the master regulators of jasmonate signaling. Although several JAZs have been reported in the laticifer cells of H. brasiliensis, the genome-wide screening of HbJAZ members has not yet been explored. In the present study, 18 HbJAZs were identified based on the recent H. brasiliensis genome. Phylogenetic construction revealed that the HbJAZs were clustered into five subgroups and that members within the same subgroup shared highly conserved gene structures and protein motifs. Cis-element analysis of HbJAZ promoters suggested the presence of hormone, stress and development-related cis-elements. HbJAZ1.0, HbJAZ2.0, and HbJAZ5.0 interacted with CORONATINE INSENSITIVE1 (COI1) in the presence of coronatine (COR, a JA mimic). HbJAZ1.0, HbJAZ2.0, HbJAZ5.0, and HbJAZ12.0 could also interact with each other. Of the 18 HbJAZs, transcripts of 15 HbJAZs were present in the vascular cambium region except for that of HbJAZ7.0, HbJAZ8.0d, and HbJAZ13.0. Fourteen of the 15 HbJAZs were significantly up-regulated upon COR treatment. The transcripts of three genes that were absent from vascular cambium region were also absent from the latex. Among the 15 HbJAZs in the latex, the expression patterns of 13 HbJAZs were different between the tapping and ethrel treatments. Eight of the 14 COR-up-regulated HbJAZs in the vascular cambium region were also activated by tapping in latex. Of the eight tapping-activated HbJAZs, 5 HbJAZs were repressed by ethrel application. Based on the computational analyses and gene expression patterns described in this study, the HbJAZ5.0 and HbJAZ10.0b may be associated with laticifer differentiation while the HbJAZ8.0b is a negative regulator for natural rubber biosynthesis in H. brasiliensis.
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Affiliation(s)
- Jinquan Chao
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yue Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Jin
- Nextomics Biosciences Co., Ltd., Wuhan, China
| | - Shaohua Wu
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaomin Deng
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yueyi Chen
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei-Min Tian
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Yu J, Golicz AA, Lu K, Dossa K, Zhang Y, Chen J, Wang L, You J, Fan D, Edwards D, Zhang X. Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:881-892. [PMID: 30315621 PMCID: PMC6587448 DOI: 10.1111/pbi.13022] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/28/2018] [Accepted: 10/10/2018] [Indexed: 05/08/2023]
Abstract
Sesame (Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces (S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars (S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference-assisted assembly approach to improve the draft assemblies of four of the sesame varieties. We then constructed a sesame pan-genome of 554.05 Mb. The pan-genome contained 26 472 orthologous gene clusters; 15 409 (58.21%) of them were core (present across all five sesame genomes), whereas the remaining 41.79% (11 063) clusters and the 15 890 variety-specific genes were dispensable. Comparisons between varieties suggest that modern cultivars from China and India display significant genomic variation. The gene families unique to the sesame modern cultivars contain genes mainly related to yield and quality, while those unique to the landraces contain genes involved in environmental adaptation. Comparative evolutionary analysis indicates that several genes involved in plant-pathogen interaction and lipid metabolism are under positive selection, which may be associated with sesame environmental adaption and selection for high seed oil content. This study of the sesame pan-genome provides insights into the evolution and genomic characteristics of this important oilseed and constitutes a resource for further sesame crop improvement.
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Affiliation(s)
- Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleMelbourneVicAustralia
| | - Kun Lu
- College of Agronomy and Biotechnology, and Academy of Agricultural SciencesSouthwest UniversityBeibeiChongqingChina
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS)ThièsSenegal
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
| | - Jinfeng Chen
- Department of Plant Pathology & MicrobiologyUniversity of CaliforniaRiversideCAUSA
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
| | | | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
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Uthup TK, Rajamani A, Ravindran M, Saha T. Distinguishing CPT gene family members and vetting the sequence structure of a putative rubber synthesizing variant in Hevea brasiliensis. Gene 2019; 689:183-193. [PMID: 30528269 DOI: 10.1016/j.gene.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/21/2018] [Accepted: 12/01/2018] [Indexed: 11/19/2022]
Abstract
cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze the cis-1,4-polymerization of isoprene units to generate isoprenoids with carbon skeletons varying from C10 (neryl pyrophosphate) to C > 10,000 (natural rubber). Though the previously reported CPTs in Hevea are designated based on sequence variations, their classification was done mostly by phylogenetic analysis using a mixture of partial as well as full length sequences often excluding the UTRs. In this context an attempt was made to reclassify the CPTs strictly based on their sequence similarity and distinguish the members putatively associated with rubber biosynthesis from the others. Extensive computational analysis was carried out on CPT sequences obtained from public resources and whole genome assemblies of Hevea. Based on the results from BLAST analysis, multiple sequence alignments of protein, nucleotide and untranslated regions, open reading frame analysis, gene prediction analysis and sequence length variations, we conclude that there exists mainly three CPTs namely RubCPT1, RubCPT2 and RubCPT3 putatively associated with rubber biosynthesis in Hevea brasiliensis. The rest were categorised as variants of dehydrodolichyl diphosphate synthase (DHDDS) involved in the synthesis of dolichols having short chain isoprenoids. Analysis of the sequence structure of the most highly expressed RubCPT1 in latex revealed the allele richness and diversity of this important variant prevailing in the popular rubber clones. Haplotypes consisting of SNPs with high degree of heterozygosity were also identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor towards the generation of allelic diversity rather than point mutations. Alternatively, gene expression analysis indicated the possibility of association between specific haplotypes and RubCPT1 expression in Hevea clones which may have downstream impact up to the level of rubber production. The conclusions from this study may pave way for the identification and better understanding of CPTs directly involved with natural rubber biosynthesis in Hevea and the SNP data generated may aid in the development of molecular markers putatively associated with yield in rubber.
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Affiliation(s)
- Thomas Kadampanattu Uthup
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India.
| | - Anantharamanan Rajamani
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
| | - Minimol Ravindran
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
| | - Thakurdas Saha
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
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Men X, Wang F, Chen GQ, Zhang HB, Xian M. Biosynthesis of Natural Rubber: Current State and Perspectives. Int J Mol Sci 2018; 20:E50. [PMID: 30583567 PMCID: PMC6337083 DOI: 10.3390/ijms20010050] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Natural rubber is a kind of indispensable biopolymers with great use and strategic importance in human society. However, its production relies almost exclusively on rubber-producing plants Hevea brasiliensis, which have high requirements for growth conditions, and the mechanism of natural rubber biosynthesis remains largely unknown. In the past two decades, details of the rubber chain polymerization and proteins involved in natural rubber biosynthesis have been investigated intensively. Meanwhile, omics and other advanced biotechnologies bring new insight into rubber production and development of new rubber-producing plants. This review summarizes the achievements of the past two decades in understanding the biosynthesis of natural rubber, especially the massive information obtained from the omics analyses. Possibilities of natural rubber biosynthesis in vitro or in genetically engineered microorganisms are also discussed.
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Affiliation(s)
- Xiao Men
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Fan Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guo-Qiang Chen
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Hai-Bo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
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Rosa JRBF, Mantello CC, Garcia D, de Souza LM, da Silva CC, Gazaffi R, da Silva CC, Toledo-Silva G, Cubry P, Garcia AAF, de Souza AP, Le Guen V. QTL detection for growth and latex production in a full-sib rubber tree population cultivated under suboptimal climate conditions. BMC PLANT BIOLOGY 2018; 18:223. [PMID: 30305095 PMCID: PMC6180592 DOI: 10.1186/s12870-018-1450-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 09/27/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rubber tree is cultivated in mainly Southeast Asia and is by far the most significant source of natural rubber production worldwide. However, the genetic architecture underlying the primary agronomic traits of this crop has not been widely characterized. This study aimed to identify quantitative trait loci (QTLs) associated with growth and latex production using a biparental population established in suboptimal growth conditions in Brazil. RESULTS A full-sib population composed of 251 individuals was developed from crossing two high-producing Asiatic rubber tree cultivars, PR 255 and PB 217. This mapping population was genotyped with microsatellite markers from enriched genomic libraries or transcriptome datasets and single-nucleotide polymorphism (SNP) markers, leading to construction of a saturated multipoint integrated genetic map containing 354 microsatellite and 151 SNP markers. Height and circumference measurements repeated over a six-year period and registration of cumulative latex production during six consecutive months on the same individuals allowed in-depth characterization of the genetic values of several growth traits and precocious latex production. Growth traits, circumference and height, were overall positively correlated, whereas latex production was not correlated or even negatively correlated with growth traits. A total of 86 distinct QTLs were identified, most of which were detected for only one trait. Among these QTLs, 15 were linked to more than one phenotypic trait (up to 4 traits simultaneously). Latex production and circumference increments during the last wintering period were associated with the highest numbers of identified QTLs (eleven and nine, respectively), jointly explaining the most significantly observed phenotypic variances (44.1% and 44.4%, respectively). The most important QTL for latex production, located on linkage group 16, had an additive effect of the male parent PB 217 and corresponded to a QTL at the same position detected in a previous study carried out in Thailand for the biparental population RRIM 600 x PB 217. CONCLUSIONS Our results identified a set of significant QTLs for rubber tree, showing that the performance of modern Asiatic cultivars can still be improved and paving the way for further marker-assisted selection, which could accelerate breeding programs.
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Affiliation(s)
- João Ricardo Bachega Feijó Rosa
- Department of Genetics, Luiz de Queiros College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Pircacicaba, SP 13400-970 Brazil
- FTS Sementes S.A., Avenida Newton Slaviero, Ponta Grossa, PR 84043-560 Brazil
| | - Camila Campos Mantello
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0 LE UK
| | - Dominique Garcia
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
| | - Lívia Moura de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Carla Cristina da Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Rodrigo Gazaffi
- Center of Agronomic Sciences, Department of Biotechnology and Vegetal and Animal Production, Federal University of São Carlos (UFSCAR), Jardim Residencial Pedras Preciosas, Araras, SP 13604900 Brazil
| | - Cícero Casimiro da Silva
- Plantation E. Michelin, R&D Department, Rua João de Barro quadra 22 lote 16, Ouro Branco do Sul, Itiquira, MT 78790-000 Brazil
| | - Guilherme Toledo-Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University Santa Catarina, Florianópolis, Brazil
| | - Philippe Cubry
- IRD, UMR DiADE, 911 avenue Agropolis, BP 64501, 34394, Montpellier cedex 5, France
| | - Antonio Augusto Franco Garcia
- Department of Genetics, Luiz de Queiros College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Pircacicaba, SP 13400-970 Brazil
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Vincent Le Guen
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
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40
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Conson ARO, Taniguti CH, Amadeu RR, Andreotti IAA, de Souza LM, dos Santos LHB, Rosa JRBF, Mantello CC, da Silva CC, José Scaloppi Junior E, Ribeiro RV, Le Guen V, Garcia AAF, Gonçalves PDS, de Souza AP. High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1255. [PMID: 30197655 PMCID: PMC6117502 DOI: 10.3389/fpls.2018.01255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/08/2018] [Indexed: 06/02/2023]
Abstract
Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67 to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.
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Affiliation(s)
- André R. O. Conson
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Cristiane H. Taniguti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodrigo R. Amadeu
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Livia M. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - João R. B. F. Rosa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Camila C. Mantello
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Carla C. da Silva
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - Rafael V. Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vincent Le Guen
- French Agricultural Research Centre for International Development (CIRAD), UMR AGAP, Montpellier, France
| | - Antonio A. F. Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Anete P. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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41
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de Souza LM, dos Santos LHB, Rosa JRBF, da Silva CC, Mantello CC, Conson ARO, Scaloppi EJ, Fialho JDF, de Moraes MLT, Gonçalves PDS, Margarido GRA, Garcia AAF, Le Guen V, de Souza AP. Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree ( Hevea brasiliensis). FRONTIERS IN PLANT SCIENCE 2018; 9:815. [PMID: 30018620 PMCID: PMC6037771 DOI: 10.3389/fpls.2018.00815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr.de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation.
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Affiliation(s)
- Livia M. de Souza
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Luciano H. B. dos Santos
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - João R. B. F. Rosa
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Carla C. da Silva
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Camila C. Mantello
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- The John Bingham Laboratory, National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - André R. O. Conson
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Erivaldo J. Scaloppi
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute of Campinas, Votuporanga, Brazil
| | - Josefino de F. Fialho
- Centro de Pesquisa Agropecuária dos Cerrados (Cpac), Embrapa Cerrados, Empresa Brazileira de Pesquisa Agropecuária, Planaltina, Brazil
| | - Mario Luiz T. de Moraes
- Departamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, Brazil
| | - Paulo de S. Gonçalves
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute of Campinas, Votuporanga, Brazil
| | - Gabriel R. A. Margarido
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
| | - Antonio A. F. Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
| | - Vincent Le Guen
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
| | - Anete P. de Souza
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas, Campinas, Brazil
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Deng X, Wang J, Li Y, Wu S, Yang S, Chao J, Chen Y, Zhang S, Shi M, Tian W. Comparative transcriptome analysis reveals phytohormone signalings, heat shock module and ROS scavenger mediate the cold-tolerance of rubber tree. Sci Rep 2018; 8:4931. [PMID: 29563566 PMCID: PMC5862945 DOI: 10.1038/s41598-018-23094-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/06/2018] [Indexed: 11/26/2022] Open
Abstract
Two contrasting cold response rubber tree clones, the cold-resistant ‘93-114’ and cold-sensitive ‘Reken501’, were subject to a global transcriptome response assessing via high-throughput RNA-seq technique and comprehensive bioinformatics analysis using the referenced rubber tree genome with the purpose of exploring the potential molecular cues underlying the tolerance of rubber trees to cold stress. As a result, a total of 1919 genes had significantly higher expression, while 2929 genes had significantly lower expression in ‘93–114’ than in ‘Reken501’ without cold stress. Upon cold stress, the numbers of genes with significantly higher expression decreased to 1501 at 1 h treatment and to 1285 at 24 h treatment in ‘93–114’ than that of ‘Reken501’, conversely, the numbers of genes with significantly lower expression increased to 7567 at 1 h treatment and to 5482 at 24 h treatment. Functional annotation of the differentially expressed genes between ‘93–114’ and ‘Reken501’ suggests that down-regulation of auxin and ethylene signaling and activation of heat shock module and ROS scavengers is a primary strategy for H. brasiliensis to cope with cold stress. Our identified vital differentially expressed genes may be beneficial for elucidation of the molecular mechanisms underlying cold tolerance and for genetic improvement of H. brasiliensis clones.
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Affiliation(s)
- Xiaomin Deng
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China
| | - Jianxiao Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056021, Hebei, China
| | - Yan Li
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China
| | - Shaohua Wu
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China
| | - Shuguang Yang
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China
| | - Jinquan Chao
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China
| | - Yueyi Chen
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China
| | - Shixin Zhang
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China
| | - Minjing Shi
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China
| | - Weimin Tian
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, P.R. China.
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Wuyun TN, Wang L, Liu H, Wang X, Zhang L, Bennetzen JL, Li T, Yang L, Liu P, Du L, Wang L, Huang M, Qing J, Zhu L, Bao W, Li H, Du Q, Zhu J, Yang H, Yang S, Liu H, Yue H, Hu J, Yu G, Tian Y, Liang F, Hu J, Wang D, Gao R, Li D, Du H. The Hardy Rubber Tree Genome Provides Insights into the Evolution of Polyisoprene Biosynthesis. MOLECULAR PLANT 2018; 11:429-442. [PMID: 29229569 DOI: 10.1016/j.molp.2017.11.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/14/2017] [Accepted: 11/28/2017] [Indexed: 05/21/2023]
Abstract
Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. Here, we present a high-quality assembly of its ∼1.2-Gb genome (scaffold N50 = 1.88 Mb) with at least 26 723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which was obtained using an integrated strategy combining Illumina sequencing, PacBio sequencing, and BioNano mapping. As a sister taxon to lamiids and campanulids, E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication in the last ∼125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and the biosynthesis of secondary metabolites, which may account for its considerable environmental adaptability. In contrast to the rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthesize long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rubber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. These results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.
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Affiliation(s)
- Ta-Na Wuyun
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China.
| | - Lin Wang
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Huimin Liu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Tiezhu Li
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Lirong Yang
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450003, China
| | - Panfeng Liu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Lanying Du
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Lu Wang
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Mengzhen Huang
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Jun Qing
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Lili Zhu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Wenquan Bao
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Hongguo Li
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Qingxin Du
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Jingle Zhu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Hong Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Shuguang Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Hui Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Hui Yue
- Shandong BELO EUCOMMIA Biological Engineering Co., Ltd., Qingzhou 262500, China
| | - Jiang Hu
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Guoliang Yu
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Yu Tian
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Fan Liang
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Jingjing Hu
- Wuhan Unique Gene Bioinformatics Science and Technology Co., Ltd., Wuhan 430073, China
| | - Depeng Wang
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Ruiwen Gao
- Shandong BELO EUCOMMIA Biological Engineering Co., Ltd., Qingzhou 262500, China.
| | - Dejun Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China.
| | - Hongyan Du
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China.
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Makita Y, Kawashima M, Lau NS, Othman AS, Matsui M. Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches. BMC Genomics 2018; 19:922. [PMID: 29363422 PMCID: PMC5780850 DOI: 10.1186/s12864-017-4333-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
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/ .
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mika Kawashima
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Nyok Sean Lau
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Minami Matsui
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication. Sci Rep 2017; 7:17902. [PMID: 29263331 PMCID: PMC5738346 DOI: 10.1038/s41598-017-17203-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/22/2017] [Indexed: 12/15/2022] Open
Abstract
Molecular markers are efficient tools for breeding and genetic studies. However, despite their ecological and economic importance, their development and application have long been hampered. In this study, we identified 524,170 simple sequence repeat (SSR), 267,636 intron length polymorphism (ILP), and 11,872 potential intron polymorphism (PIP) markers from 16 tree species based on recently available genome sequences. Larger motifs, including hexamers and heptamers, accounted for most of the seven different types of SSR loci. Within these loci, A/T bases comprised a significantly larger proportion of sequence than G/C. SSR and ILP markers exhibited an alternative distribution pattern. Most SSRs were monomorphic markers, and the proportions of polymorphic markers were positively correlated with genome size. By verifying with all 16 tree species, 54 SSR, 418 ILP, and four PIP universal markers were obtained, and their efficiency was examined by PCR. A combination of five SSR and six ILP markers were used for the phylogenetic analysis of 30 willow samples, revealing a positive correlation between genetic diversity and geographic distance. We also found that SSRs can be used as tools for duplication analysis. Our findings provide important foundations for the development of breeding and genetic studies in tree species.
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Cloning and Aggregation Characterization of Rubber Elongation Factor and Small Rubber Particle Protein from Ficus carica. Mol Biotechnol 2017; 60:83-91. [DOI: 10.1007/s12033-017-0051-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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De novo Transcriptome Sequencing of MeJA-Induced Taraxacum koksaghyz Rodin to Identify Genes Related to Rubber Formation. Sci Rep 2017; 7:15697. [PMID: 29146946 PMCID: PMC5691164 DOI: 10.1038/s41598-017-14890-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 10/18/2017] [Indexed: 01/07/2023] Open
Abstract
Increase in the consumption of natural rubber (NR) has necessitated the identification of alternative sources of NR. The quality of NR produced by Taraxacum koksaghyz Rodin (TKS) is comparable to that from Hevea brasiliensis (H.brasiliensis), and therefore, TKS is being considered as an alternative source of NR. Here, we sequenced the TKS root transcriptome after wild TKS seedlings were treated with methyl jasmonate (MeJA) for 0, 6, and 24 h. The clean reads generated for each experimental line were assembled into 127,833 unigenes. The Kyoto encyclopedia of genes and genomes pathway prediction suggested that methyl jasmonate regulated secondary metabolism in TKS. Differential expression analysis showed that the expression of HMGCR, FPPS, IDI, GGPPS, and REF/SRPP increased with methyl jasmonate treatment. Interestingly, differential expression analysis of the jasmonate (JA)-related transcription factors (TFs), indicated that certain genes encoding these transcription factors (namely, bHLH, MYB, AP2/EREBP, and WRKY) showed the same expression pattern in the lines treated for 6 h and 24 h. Moreover, HMGCR was up-regulated in the transgenic seedlings overexpressing DREB. We predicted that methyl jasmonate regulated secondary metabolism and affected rubber biosynthesis via the interaction of the JA-related TFs with genes associated with rubber biosynthesis in TKS.
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48
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Brown D, Feeney M, Ahmadi M, Lonoce C, Sajari R, Di Cola A, Frigerio L. Subcellular localization and interactions among rubber particle proteins from Hevea brasiliensis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5045-5055. [PMID: 29036360 PMCID: PMC5853894 DOI: 10.1093/jxb/erx331] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/14/2017] [Indexed: 05/21/2023]
Abstract
Natural rubber (polyisoprene) from the rubber tree Hevea brasiliensis is synthesized by specialized cells called laticifers. It is not clear how rubber particles arise, although one hypothesis is that they derive from the endoplasmic reticulum (ER) membrane. Here we cloned the genes encoding four key proteins found in association with rubber particles and studied their intracellular localization by transient expression in Nicotiana benthamiana leaves. We show that, while the cis-prenyltransferase (CPT), responsible for the synthesis of long polyisoprene chains, is a soluble, cytosolic protein, other rubber particle proteins such as rubber elongation factor (REF), small rubber particle protein (SRPP) and Hevea rubber transferase 1-REF bridging protein (HRBP) are associated with the endoplasmic reticulum (ER). We also show that SRPP can recruit CPT to the ER and that interaction of CPT with HRBP leads to both proteins relocating to the plasma membrane. We discuss these results in the context of the biogenesis of rubber particles.
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Affiliation(s)
- Daniel Brown
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | - Mathin Ahmadi
- Tun Abdul Razak Research Centre, Brickendonbury, Hertford, UK
| | - Chiara Lonoce
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Roslinda Sajari
- Malaysian Rubber Board, Experiment Station, Sungai Buloh, Selangor DE, Malaysia
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49
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Sui JL, Xiao XH, Qi JY, Fang YJ, Tang CR. The SWEET gene family in Hevea brasiliensis - its evolution and expression compared with four other plant species. FEBS Open Bio 2017; 7:1943-1959. [PMID: 29226081 PMCID: PMC5715295 DOI: 10.1002/2211-5463.12332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/27/2017] [Accepted: 10/03/2017] [Indexed: 11/11/2022] Open
Abstract
SWEET proteins play an indispensable role as a sugar efflux transporter in plant development and stress responses. The SWEET genes have previously been characterized in several plants. Here, we present a comprehensive analysis of this gene family in the rubber tree, Hevea brasiliensis. There are 36 members of the SWEET gene family in this species, making it one of the largest families in plant genomes sequenced so far. Structure and phylogeny analyses of these genes in Hevea and in other species demonstrated broad evolutionary conservation. RNA‐seq analyses revealed that SWEET2, 16, and 17 might represent the main evolutionary direction of SWEET genes in plants. Our results in Hevea suggested the involvement of HbSWEET1a, 2e, 2f, and 3b in phloem loading, HbSWEET10a and 16b in laticifer sugar transport, and HbSWEET9a in nectary‐specific sugar transport. Parallel studies of RNA‐seq analyses extended to three other plant species (Manihot esculenta, Populus trichocarpa, and Arabidopsis thaliana) produced findings which implicated MeSWEET10a, 3a, and 15b in M. esculenta storage root development, and the involvement of PtSWEET16b and PtSWEET16d in P. trichocarpa xylem development. RT‐qPCR results further revealed that HbSWEET10a, 16b, and 1a play important roles in phloem sugar transport. The results from this study provide a foundation not only for further investigation into the functionality of the SWEET gene family in Hevea, especially in its sugar transport for latex production, but also for related studies of this gene family in the plant kingdom.
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Affiliation(s)
- Jin-Lei Sui
- Institute of Tropical Agriculture and Forestry Hainan University Haikou Hainan China.,Key Lab of Rubber Biology Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
| | - Xiao-Hu Xiao
- Key Lab of Rubber Biology Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
| | - Ji-Yan Qi
- Key Lab of Rubber Biology Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
| | - Yong-Jun Fang
- Key Lab of Rubber Biology Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
| | - Chao-Rong Tang
- Key Lab of Rubber Biology Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
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50
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Jin X, Zhu L, Yao Q, Meng X, Ding G, Wang D, Xie Q, Tong Z, Tao C, Yu L, Li H, Wang X. Expression Profiling of Mitogen-Activated Protein Kinase Genes Reveals Their Evolutionary and Functional Diversity in Different Rubber Tree (Hevea brasiliensis) Cultivars. Genes (Basel) 2017; 8:genes8100261. [PMID: 28984837 PMCID: PMC5664111 DOI: 10.3390/genes8100261] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/03/2022] Open
Abstract
Rubber tree (Heveabrasiliensis) is the only commercially cultivated plant for producing natural rubber, one of the most essential industrial raw materials. Knowledge of the evolutionary and functional characteristics of kinases in H. brasiliensis is limited because of the long growth period and lack of well annotated genome information. Here, we reported mitogen-activated protein kinases in H. brasiliensis (HbMPKs) by manually checking and correcting the rubber tree genome. Of the 20 identified HbMPKs, four members were validated by proteomic data. Protein motif and phylogenetic analyses classified these members into four known groups comprising Thr-Glu-Tyr (TEY) and Thr-Asp-Tyr (TDY) domains, respectively. Evolutionary and syntenic analyses suggested four duplication events: HbMPK3/HbMPK6, HbMPK8/HbMPK9/HbMPK15, HbMPK10/HbMPK12 and HbMPK11/HbMPK16/HbMPK19. Expression profiling of the identified HbMPKs in roots, stems, leaves and latex obtained from three cultivars with different latex yield ability revealed tissue- and variety-expression specificity of HbMPK paralogues. Gene expression patterns under osmotic, oxidative, salt and cold stresses, combined with cis-element distribution analyses, indicated different regulation patterns of HbMPK paralogues. Further, Ka/Ks and Tajima analyses suggested an accelerated evolutionary rate in paralogues HbMPK10/12. These results revealed HbMPKs have diverse functions in natural rubber biosynthesis, and highlighted the potential possibility of using MPKs to improve stress tolerance in future rubber tree breeding.
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Affiliation(s)
- Xiang Jin
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Liping Zhu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Qi Yao
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Xueru Meng
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Guohua Ding
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Quanliang Xie
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Zheng Tong
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Chengcheng Tao
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Li Yu
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Xuchu Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
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