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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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3
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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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4
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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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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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6
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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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7
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Roy CB, Goonetilleke SN, Joseph L, Krishnan A, Saha T, Kilian A, Mather DE. Analysis of Genetic Diversity and Resistance to Foliar Pathogens Based on Genotyping-by-Sequencing of a Para Rubber Diversity Panel and Progeny of an Interspecific Cross. PLANTS (BASEL, SWITZERLAND) 2022; 11:3418. [PMID: 36559531 PMCID: PMC9781018 DOI: 10.3390/plants11243418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Para rubber trees (Hevea brasiliensis) are the largest major source of natural rubber in the world. Its major pathogens are Phytophthora spp., Corynespora cassiicola, and Colletotrichum spp. A rubber diversity panel of 116 clones using over 12,000 single nucleotide polymorphisms (SNPs) from DArTSeq genotyping revealed clear phylogenetic differences in clones that originated from different geographical regions of the world. An integrated linkage map constructed with an F1 progeny of 86 from an interspecific cross between H. brasiliensis and H. benthamiana using 23,978 markers [10,323 SNPs and 13,655 SilicoDArTs] spanned 3947.83 cM with 0.83 cM average marker-interval. The genome scaffolds that were anchored to the linkage map, covering 1.44 Gb of H. brasiliensis reference genome, revealed a high level of collinearity between the genetic map and reference genome. Association analysis identified 12 SNPs significantly associated with the resistance against Phytophthora, Corynespora, and Colletotrichum in six linkage groups: 2, 6, 12, 14, 17, and 18. Kompetitive Allele-Specific PCR marker assays were developed for those 12 SNPs, screened with 178 individuals, and detected clear separation between two genotypes. Within the proximity to those SNPs, 41 potentially key genes that have previously been reported to associate with plant disease resistance were predicted with high confidence.
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Affiliation(s)
- C. Bindu Roy
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Shashi N. Goonetilleke
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Limiya Joseph
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Anu Krishnan
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Thakurdas Saha
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Andrzej Kilian
- Diversity Arrays Technology, Canberra, ACT 2617, Australia
| | - Diane E. Mather
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia
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8
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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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9
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Development of Novel Markers for Yield in Hevea brasiliensis Muell. Arg. Based on Candidate Genes from Biosynthetic Pathways Associated with Latex Production. Biochem Genet 2022; 60:2171-2199. [PMID: 35296963 DOI: 10.1007/s10528-022-10211-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022]
Abstract
Scarcity of functional genetic markers associated with candidate genes (CGs) is a serious constraint for marker-assisted selection in the natural rubber producing tree, Hevea brasiliensis. In order to develop markers associated with rubber yield, five CGs involved in latex biosynthesis were characterized from 16 popular Hevea varieties. Novel SNPs and indels were identified and developed into markers using simple genotyping techniques like allele-specific PCR, CAPS, etc. A progeny population was genotyped using these markers to validate them, to understand their segregation pattern and to map them to a genetic linkage map. Parent-specific maps were constructed using pseudo-test cross strategy with the help of additional markers. The sequence structure information generated will be useful for future studies on gene mapping, functional relevance of coding SNPs and evolution of rubber biosynthesis genes in Hevea. Concurrently, the markers developed may serve as powerful tools for yield-based selection and for genetic diversity and pedigree studies in Hevea. Above all, the marker assays designed for genotyping could be economically carried out in any laboratory having basic molecular biology infrastructure and expertise.
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10
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Francisco FR, Aono AH, da Silva CC, Gonçalves PS, Scaloppi Junior EJ, Le Guen V, Fritsche-Neto R, Souza LM, de Souza AP. Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches. FRONTIERS IN PLANT SCIENCE 2021; 12:768589. [PMID: 34992619 PMCID: PMC8724537 DOI: 10.3389/fpls.2021.768589] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/02/2021] [Indexed: 06/08/2023]
Abstract
Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.
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Affiliation(s)
- Felipe Roberto Francisco
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Cristina da Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Paulo S. Gonçalves
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute (IAC), Votuporanga, Brazil
| | | | - Vincent Le Guen
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Roberto Fritsche-Neto
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Livia Moura Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- São Francisco University (USF), Itatiba, Brazil
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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11
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Lee JH, Siddique MI, Kwon JK, Kang BC. Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici. Front Microbiol 2021; 12:694136. [PMID: 34484141 PMCID: PMC8415033 DOI: 10.3389/fmicb.2021.694136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/20/2021] [Indexed: 12/03/2022] Open
Abstract
Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistant varieties of host crops. In the present study, we compared the genomes of three P. capsici isolates with different aggressiveness levels to reveal their genomic differences. We obtained genome sequences using short-read and long-read technologies, which yielded an average genome size of 76 Mbp comprising 514 contigs and 15,076 predicted genes. A comparative genomic analysis uncovered the signatures of accelerated evolution, gene family expansions in the pathogenicity-related genes among the three isolates. Resequencing two additional P. capsici isolates enabled the identification of average 1,023,437 SNPs, revealing the frequent accumulation of non-synonymous substitutions in pathogenicity-related gene families. Furthermore, pathogenicity-related gene families, cytoplasmic effectors and ATP binding cassette (ABC) transporters, showed expansion signals in the more aggressive isolates, with a greater number of non-synonymous SNPs. This genomic information explains the plasticity, difference in aggressiveness levels, and genome structural variation among the P. capsici isolates, providing insight into the genomic features related to the evolution and pathogenicity of this oomycete pathogen.
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Affiliation(s)
- Joung-Ho Lee
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Muhammad Irfan Siddique
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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12
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Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees. PLANTS 2021; 10:plants10071440. [PMID: 34371639 PMCID: PMC8309273 DOI: 10.3390/plants10071440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 02/01/2023]
Abstract
Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.
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13
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Liang X, Chen Q, Wu C, Liu Y, Fang Y. Reference gene validation in Eotetranychus sexmaculatus (Acari: Tetranychidae) feeding on mite-susceptible and mite-resistant rubber tree germplasms. EXPERIMENTAL & APPLIED ACAROLOGY 2020; 82:211-228. [PMID: 32886259 DOI: 10.1007/s10493-020-00542-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Reliable reference genes are quite important in calculating gene transcript levels by using real-time quantitative reverse transcription-PCR (RT-qPCR). Eotetranychus sexmaculatus is known as a dangerous mite causing significant yield reduction of rubber tree latex; however, selection of appropriate reference genes for validation of target gene expression in E. sexmaculatus has not been conducted yet. In the present study, nine candidate reference genes were analyzed for their expression stability in different life stages of E. sexmaculatus by using common algorithms including comparative ΔCq method, geNorm, NormFinder and BestKeeper. In addition, a comprehensive analysis software (RefFinder) was used to assign an overall final rank for each candidate gene. The results showed that β-actin and β-TUB were the best two reference genes and were subjected to evaluate expression of two protective enzyme genes (EsCu/ZnSOD and EsCAT1) in E. sexmaculatus. We found that the expression of EsCu/ZnSOD and EsCAT1 in E. sexmaculatus feeding on mite-resistant rubber tree germplasm was significantly lower compared with those feeding on mite-susceptible germplasm. These results will facilitate research in revealing molecular mechanisms underlying rubber tree resistance to the spider mite.
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Affiliation(s)
- Xiao Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qing Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Chunling Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ying Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yongjun Fang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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14
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Nawae W, Yundaeng C, Naktang C, Kongkachana W, Yoocha T, Sonthirod C, Narong N, Somta P, Laosatit K, Tangphatsornruang S, Pootakham W. The Genome and Transcriptome Analysis of the Vigna mungo Chloroplast. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091247. [PMID: 32967378 PMCID: PMC7570002 DOI: 10.3390/plants9091247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 05/20/2023]
Abstract
Vigna mungo is cultivated in approximately 5 million hectares worldwide. The chloroplast genome of this species has not been previously reported. In this study, we sequenced the genome and transcriptome of the V. mungo chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., rbcL, ndhF, and atpF) and RNA polymerase genes (e.g., rpoC2) from the comparison of the chloroplast genome of V. mungo, temperate legume species, and tropical legume species. Our transcriptome data from PacBio isoform sequencing showed that the 51-kb DNA inversion could affect the transcriptional regulation of accD polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of clpP in the leaf, shoot, flower, fruit, and root tissues of V. mungo. We also found three G-to-A RNA editing events that change guanine to adenine in the transcripts transcribed from the adenine-rich regions of the ycf4 gene. The edited guanine bases were found particularly in the chloroplast genome of the Vigna species. These G-to-A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The V. mungo chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Chutintorn Yundaeng
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Wasitthee Kongkachana
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Thippawan Yoocha
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Nattapol Narong
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (P.S.); (K.L.)
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (P.S.); (K.L.)
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
- Correspondence: or
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15
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Pootakham W, Nawae W, Naktang C, Sonthirod C, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Somta P, Laosatit K, Tangphatsornruang S. A chromosome-scale assembly of the black gram (Vigna mungo) genome. Mol Ecol Resour 2020; 21:238-250. [PMID: 32794377 DOI: 10.1111/1755-0998.13243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked-read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long-range Chicago and HiC techniques yielded the first high-quality, chromosome-level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single-copy orthologous genes revealed that black gram and mungbean (Vigna radiata) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in V. mungo revealed no evidence supporting a recent genome-wide duplication event observed in the tetraploid créole bean (Vigna reflexo-pilosa). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related Vigna species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in V. mungo using full-length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high-quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker-assisted breeding and for future comparative genomics and phylogenetic studies in legume species.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
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16
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Pootakham W, Sonthirod C, Naktang C, Nawae W, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Sheedy JR, Buaboocha J, Mekiyanon S, Tangphatsornruang S. De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements. Mol Ecol Resour 2020; 21:212-225. [PMID: 32841550 DOI: 10.1111/1755-0998.13240] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023]
Abstract
Luffa spp. (sponge gourd or ridge gourd) is an economically important vegetable crop widely cultivated in China, India and Southeast Asia. Here, we employed PacBio long-read single-molecule real-time (SMRT) sequencing to perform de novo genome assemblies of two commonly cultivated Luffa species, L. acutangula and L. cylindrica. We obtained preliminary draft genomes of 734.6 Mb and 689.8 Mb with scaffold N50 of 786,130 and 578,616 bases for L. acutangula and L. cylindrica, respectively. We also applied long-range Chicago and HiC techniques to obtain the first chromosome-scale whole-genome assembly of L. acutangula. The final assembly contained 13 pseudomolecules, corresponding to the haploid chromosome number in Luffa spp. (1n = 13, 2n = 26). The sizes of the assembled Luffa genomes are approximately twice as large as the genome assemblies of related Cucurbitaceae. A large proportion of L. acutangula (62.17%; 456.69 Mb) and L. cylindrica (56.78%; 391.65 Mb) genome assemblies contained repetitive elements. Phylogenetic analyses revealed that the substantial accumulation of transposable elements likely contributed to the expansion of the Luffa genomes. We also investigated alternative splicing events in Luffa using full-length transcript sequences obtained from PacBio Isoform Sequencing (Iso-seq). While the predominant form of alternative splicing in most plant species examined was intron retention, alternative 3' acceptor site selection appeared to be a major event observed in Luffa. High-quality genome assemblies for L. acutangula and L. cylindrica reported here provide valuable resources for Luffa breeding and future genetics and comparative genomics studies in Cucurbitaceae.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - John R Sheedy
- Chia Tai Company Limited, Phra Khanong District, Bangkok, Thailand
| | | | - Supat Mekiyanon
- Chia Tai Company Limited, Phra Khanong District, Bangkok, Thailand
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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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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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20
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Abstract
Natural rubber (NR), principally comprising cis-1,4-polyisoprene, is an industrially important natural hydrocarbon polymer because of its unique physical properties, which render it suitable for manufacturing items such as tires. Presently, industrial NR production depends solely on latex obtained from the Pará rubber tree, Hevea brasiliensis. In latex, NR is enclosed in rubber particles, which are specialized organelles comprising a hydrophobic NR core surrounded by a lipid monolayer and membrane-bound proteins. The similarity of the basic carbon skeleton structure between NR and dolichols and polyprenols, which are found in most organisms, suggests that the NR biosynthetic pathway is related to the polyisoprenoid biosynthetic pathway and that rubber transferase, which is the key enzyme in NR biosynthesis, belongs to the cis-prenyltransferase family. Here, we review recent progress in the elucidation of molecular mechanisms underlying NR biosynthesis through the identification of the enzymes that are responsible for the formation of the NR backbone structure.
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Affiliation(s)
- Satoshi Yamashita
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan;
| | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan;
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21
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Zhang L, Liu M, Long H, Dong W, Pasha A, Esteban E, Li W, Yang X, Li Z, Song A, Ran D, Zhao G, Zeng Y, Chen H, Zou M, Li J, Liang F, Xie M, Hu J, Wang D, Cao H, Provart NJ, Zhang L, Tan X. Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 17:558-575. [PMID: 32224189 PMCID: PMC7212303 DOI: 10.1016/j.gpb.2019.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 12/12/2018] [Accepted: 03/29/2019] [Indexed: 12/05/2022]
Abstract
Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further whole-genome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites; 17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.
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Affiliation(s)
- Lin Zhang
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China; (3)Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
| | - Meilan Liu
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Hongxu Long
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Wei Dong
- (4)State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Asher Pasha
- (3)Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Eddi Esteban
- (3)Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Wenying Li
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiaoming Yang
- (5)College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Ze Li
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
| | - Aixia Song
- (4)State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Duo Ran
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guang Zhao
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yanling Zeng
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Hao Chen
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ming Zou
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Jingjing Li
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Fan Liang
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Meili Xie
- (6)Nextomics Biosciences Co., Wuhan 430073, China; (7)Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiang Hu
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Depeng Wang
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Heping Cao
- (8)US Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA.
| | - Nicholas J Provart
- (3)Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
| | - Liangsheng Zhang
- (4)State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xiaofeng Tan
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China.
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22
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Exploitation of Hi-C sequencing for improvement of genome assembly and in-vitro validation of differentially expressing genes in Jatropha curcas L. 3 Biotech 2020; 10:91. [PMID: 32089986 DOI: 10.1007/s13205-020-2082-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/20/2020] [Indexed: 10/25/2022] Open
Abstract
Jatropha curcas is one of the major sources of renewable energy due to potential use of its oil as a biofuel. The genome of this crop is constituted by the high content of repetitive elements. We employed the Hi-C proximity ligation technique to re-scaffold our existing hybrid genome assembly of an elite genotype (RJC1) developed using Illumina and Pacbio technologies. We assembled 99.81% of non-truncated reads to achieve 266.80 Mbp of the genome with an N50 value of 1.58 Mb. Furthermore, we compared the efficiency of Hi-C-augmented genome assembly with the hybrid genome assembly and observed a ~ 50% reduction in scaffolds and a tenfold increase in the N50 value. The gene ontology analysis revealed the identification of terms for molecular function (45.52%), cellular component (33.47%), and biological function (20.99%). Comparative genomic analysis of 13-plant species showed the conservation of 414 lipid metabolizing genes identified in the KEGG pathway analysis. Differential gene expression (DGE) studies were conducted in the healthy and Jatropha mosaic virus-infected leaves via RNA-seq analysis and observed gene expression changes for 2185 genes. Out of these, we observed 546 genes having more than two-fold change of transcript level and among these 259 genes were down-regulated and 287 genes were up-regulated. To validate RNA-seq data, two DEGs were selected for gene expression analysis using qRT-PCR and the data was in correlation with in silico results. RNA-seq analysis further shows the identification of some of the candidate genes and may be useful to develop JMV resistant plants after functional validation. This Hi-C genome assembly provides a detailed accurate reference genome which could be utilized to improve Jatropha and other economically important Euphorbiaceae family members.
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Ou YJ, Ren QQ, Fang ST, Wu JG, Jiang YX, Chen YR, Zhong Y, Wang DD, Zhang GX. Complete Genome Insights into Lactococcus petauri CF11 Isolated from a Healthy Human Gut Using Second- and Third-Generation Sequencing. Front Genet 2020; 11:119. [PMID: 32174973 PMCID: PMC7054480 DOI: 10.3389/fgene.2020.00119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 12/31/2022] Open
Abstract
Lactococcus petauri CF11 was originally isolated from the gut of healthy humans. To determine the underlying molecular and genetic mechanisms of the probiotic potential of CF11, we performed complete genome sequencing, annotation, and comparative genome analysis. The complete genome of L. petauri CF11 comprised of 1,997,720 bp, with a DNA G+C content of 38.21 mol% containing 1982 protein coding genes and 16 rRNA operons. We found that 1206 genes (56.05%) were assigned a putative function using the gene ontology (GO) resource. The gene products of CF11 were primarily concentrated in molecular function and biological processes, such as catalysis, binding, metabolism, and cellular processes. Furthermore, 1,365 (68.87%) genes were assigned an illative function using COGs. CF11 proteins were associated with carbohydrate transport and metabolism, and amino acid transport and metabolism. This indicates that CF11 bacteria can perform active energy exchange. We classified 1,111 (56.05%) genes into six KEGG functional categories; fructose-bisphosphate aldolase and the phosphoenol pyruvate:phosphotransferase system (PTS), which are necessary in producing short-chain fatty acids (SCFAs), were excited in the carbohydrate metabolic pathway. This suggests that L. petauri CF11 produces SCFAs via glycolysis. The genomic island revealed that some regions contain fragments of antibiotic resistance and bacteriostatic genes. In addition, ANI analysis showed that L. petauri CF11 had the closest relationship with L. petauri 159469T, with an average nucleotide consistency of 98.03%. Taken together, the present study offers further insights into the functional and potential role of L. petauri CF11 in health care.
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Affiliation(s)
- Yun-Jing Ou
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qiao-Qiao Ren
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shu-Ting Fang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ji-Guo Wu
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yun-Xia Jiang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yi-Ran Chen
- Department of Water Hygiene, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Yi Zhong
- Department of Water Hygiene, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - De-Dong Wang
- Department of Water Hygiene, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Guo-Xia Zhang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
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24
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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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25
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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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26
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Lindblad KA, Pathmanathan JS, Moreira S, Bracht JR, Sebra RP, Hutton ER, Landweber LF. Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms. BMC Genomics 2019; 20:1037. [PMID: 31888453 PMCID: PMC6937825 DOI: 10.1186/s12864-019-6189-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even "third generation" sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly. RESULTS We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall. CONCLUSIONS This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.
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Affiliation(s)
- Kelsi A. Lindblad
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA
| | - Jananan S. Pathmanathan
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
| | - Sandrine Moreira
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
| | - John R. Bracht
- Department of Biology, American University, 4400 Massachusetts Avenue, NW, Washington, DC 20016 USA
| | - Robert P. Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Elizabeth R. Hutton
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA
- Watson School of Biological Sciences, One Bungtown Road, Cold Spring Harbor,, NY 11724 USA
| | - Laura F. Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
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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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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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Jung H, Winefield C, Bombarely A, Prentis P, Waterhouse P. Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes. TRENDS IN PLANT SCIENCE 2019; 24:700-724. [PMID: 31208890 DOI: 10.1016/j.tplants.2019.05.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 05/01/2019] [Accepted: 05/10/2019] [Indexed: 05/16/2023]
Abstract
The commercial release of third-generation sequencing technologies (TGSTs), giving long and ultra-long sequencing reads, has stimulated the development of new tools for assembling highly contiguous genome sequences with unprecedented accuracy across complex repeat regions. We survey here a wide range of emerging sequencing platforms and analytical tools for de novo assembly, provide background information for each of their steps, and discuss the spectrum of available options. Our decision tree recommends workflows for the generation of a high-quality genome assembly when used in combination with the specific needs and resources of a project.
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Affiliation(s)
- Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia.
| | - Christopher Winefield
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, 7647 Christchurch, New Zealand
| | - Aureliano Bombarely
- Department of Bioscience, University of Milan, Milan 20133, Italy; School of Plants and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Peter Prentis
- School of Earth, Environmental, and Biological Sciences, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Peter Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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Carballo J, Santos BACM, Zappacosta D, Garbus I, Selva JP, Gallo CA, Díaz A, Albertini E, Caccamo M, Echenique V. A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality. Sci Rep 2019; 9:10250. [PMID: 31308395 PMCID: PMC6629639 DOI: 10.1038/s41598-019-46610-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/13/2019] [Indexed: 01/06/2023] Open
Abstract
The Poaceae constitute a taxon of flowering plants (grasses) that cover almost all Earth’s inhabitable range and comprises some of the genera most commonly used for human and animal nutrition. Many of these crops have been sequenced, like rice, Brachypodium, maize and, more recently, wheat. Some important members are still considered orphan crops, lacking a sequenced genome, but having important traits that make them attractive for sequencing. Among these traits is apomixis, clonal reproduction by seeds, present in some members of the Poaceae like Eragrostis curvula. A de novo, high-quality genome assembly and annotation for E. curvula have been obtained by sequencing 602 Mb of a diploid genotype using a strategy that combined long-read length sequencing with chromosome conformation capture. The scaffold N50 for this assembly was 43.41 Mb and the annotation yielded 56,469 genes. The availability of this genome assembly has allowed us to identify regions associated with forage quality and to develop strategies to sequence and assemble the complex tetraploid genotypes which harbor the apomixis control region(s). Understanding and subsequently manipulating the genetic drivers underlying apomixis could revolutionize agriculture.
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Affiliation(s)
- J Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS - CCT - CONICET Bahía Blanca) and Departamento de Agronomía, Universidad Nacional del Sur, Camino de la Carrindanga km 7, 8000, Bahía Blanca, Argentina
| | | | - D Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS - CCT - CONICET Bahía Blanca) and Departamento de Agronomía, Universidad Nacional del Sur, Camino de la Carrindanga km 7, 8000, Bahía Blanca, Argentina
| | - I Garbus
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS - CCT - CONICET Bahía Blanca) and Departamento de Agronomía, Universidad Nacional del Sur, Camino de la Carrindanga km 7, 8000, Bahía Blanca, Argentina
| | - J P Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS - CCT - CONICET Bahía Blanca) and Departamento de Agronomía, Universidad Nacional del Sur, Camino de la Carrindanga km 7, 8000, Bahía Blanca, Argentina
| | - C A Gallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS - CCT - CONICET Bahía Blanca) and Departamento de Agronomía, Universidad Nacional del Sur, Camino de la Carrindanga km 7, 8000, Bahía Blanca, Argentina
| | - A Díaz
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS - CCT - CONICET Bahía Blanca) and Departamento de Agronomía, Universidad Nacional del Sur, Camino de la Carrindanga km 7, 8000, Bahía Blanca, Argentina
| | - E Albertini
- Università degli Studi di Perugia, Dip. di Scienze Agrarie, Alimentari e Ambientali, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - M Caccamo
- NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK.
| | - V Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS - CCT - CONICET Bahía Blanca) and Departamento de Agronomía, Universidad Nacional del Sur, Camino de la Carrindanga km 7, 8000, Bahía Blanca, Argentina.
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Campos Mantello C, Boatwright L, da Silva CC, Scaloppi EJ, de Souza Goncalves P, Barbazuk WB, Pereira de Souza A. Deep expression analysis reveals distinct cold-response strategies in rubber tree (Hevea brasiliensis). BMC Genomics 2019; 20:455. [PMID: 31164105 PMCID: PMC6549365 DOI: 10.1186/s12864-019-5852-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/28/2019] [Indexed: 01/08/2023] Open
Abstract
Background Natural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. The rubber tree species Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg., which is native the Amazon rainforest, is the major producer of latex worldwide. Rubber tree breeding is time consuming, expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. In this work, transcriptome sequencing was used to identify a full set of transcripts and to evaluate the gene expression involved in the different cold-response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes. Results We built a comprehensive transcriptome using multiple database sources, which resulted in 104,738 transcripts clustered in 49,304 genes. The RNA-seq data from the leaf tissues sampled at four different times for each genotype were used to perform a gene-level expression analysis. Differentially expressed genes (DEGs) were identified through pairwise comparisons between the two genotypes for each time series of cold treatments. DEG annotation revealed that RRIM600 and GT1 exhibit different chilling tolerance strategies. To cope with cold stress, the RRIM600 clone upregulates genes promoting stomata closure, photosynthesis inhibition and a more efficient reactive oxygen species (ROS) scavenging system. The transcriptome was also searched for putative molecular markers (single nucleotide polymorphisms (SNPs) and microsatellites) in each genotype. and a total of 27,111 microsatellites and 202,949 (GT1) and 156,395 (RRIM600) SNPs were identified in GT1 and RRIM600. Furthermore, a search for alternative splicing (AS) events identified a total of 20,279 events. Conclusions The elucidation of genes involved in different chilling tolerance strategies associated with molecular markers and information regarding AS events provides a powerful tool for further genetic and genomic analyses of rubber tree breeding. Electronic supplementary material The online version of this article (10.1186/s12864-019-5852-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Camila Campos Mantello
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.,Department of Biology, University of Florida, Gainesville, FL, USA.,The John Bingham Laboratory, National Institute of Agricultural Botany, Cambridge, UK
| | - Lucas Boatwright
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Carla Cristina da Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Erivaldo Jose Scaloppi
- Rubber Research Advanced Center (CAPSA), Agronomical Institute (IAC), Votuporanga, SP, Brazil
| | | | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, USA.,Genetics Institute, University of Florida, Gainesville, FL, USA
| | - 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.
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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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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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Kumpeangkeaw A, Tan D, Fu L, Han B, Sun X, Hu X, Ding Z, Zhang J. Asymmetric birth and death of type I and type II MADS-box gene subfamilies in the rubber tree facilitating laticifer development. PLoS One 2019; 14:e0214335. [PMID: 30934009 PMCID: PMC6443149 DOI: 10.1371/journal.pone.0214335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023] Open
Abstract
The rubber tree (Hevea brasiliensis Muell. Arg.) is a rubber producing crop and contains specialized laticifers. MADS-box genes are a family of transcription factor genes that regulate plant development, especially floral organ and gametophyte development. 97 MADS-box genes were identified in the rubber tree through transcriptomes and genome mining. 93.8% of the genes were mapped onto the genome scaffolds in correspondence to the coverage (93.8%) of current version of sequenced genome. Phylogenetic analysis indicates that type II MADS-box genes have been more actively duplicated than their orthologous genes in Arabidopsis and rice, so that most (70, 72.2%) of the MADS-box genes in the rubber tree belong to type II subfamily. This is a high percentage compared to those in Arabidopsis (43.7%) and rice (56.8%). Moreover, 69 out of 70 type II genes in the rubber tree are transcribed, and they are mostly predominantly expressed in flowers, but some genes are predominantly expressed in laticifers, suggesting their roles in both flower and laticifer development. The number of type I genes in the rubber tree is only 27 (27.8%), a much smaller number compared to their orthologous genes in Arabidopsis (56.3%) and rice (43.2%). At the same time, most of the type I genes (55.6%, 15) in the rubber tree are silent and are probably pseudogenes. The high birth rate and low death rate of type II genes and low birth rate and high death rate of type I genes may corresponds to special developmental requirements in the rubber tree, e.g. the development of laticifer system for biosynthesis of cis-polyisoprene, the rubber. Moreover, atypical MIKC* factors (e.g. HbMADS1 in S-clade, and HbMADS20 in P-clade) are identified. These genes are diverged to typical MIKC* genes in sequences and facilitate functions required in laticifer development and rubber biosynthesis, which is not necessary in Arabidopsis and rice.
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Affiliation(s)
- Anuwat Kumpeangkeaw
- International College, Huazhong Agricultural University, Lion Mountain, Wuhan, China
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
- Song Khla Rubber Research Centre, Department of Agriculture, Ministry of Agriculture and Cooperatives, Had Yai, Song Khla, Thailand
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Xiaowen Hu
- Zhanjiang Experimental Station, CATAS, Zhanjiang, Guangdong Province, China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
- * E-mail:
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Zhao L, Zhang H, Kohnen MV, Prasad KVSK, Gu L, Reddy ASN. Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing. Front Genet 2019; 10:253. [PMID: 30949200 PMCID: PMC6438080 DOI: 10.3389/fgene.2019.00253] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.
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Affiliation(s)
- Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Markus V. Kohnen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kasavajhala V. S. K. Prasad
- Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, CO, United States
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De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance. Genes (Basel) 2019; 10:genes10010069. [PMID: 30669588 PMCID: PMC6356885 DOI: 10.3390/genes10010069] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 12/26/2022] Open
Abstract
Jatropha curcas is an important perennial, drought tolerant plant that has been identified as a potential biodiesel crop. We report here the hybrid de novo genome assembly of J. curcas generated using Illumina and PacBio sequencing technologies, and identification of quantitative loci for Jatropha Mosaic Virus (JMV) resistance. In this study, we generated scaffolds of 265.7 Mbp in length, which correspond to 84.8% of the gene space, using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Additionally, 96.4% of predicted protein-coding genes were captured in RNA sequencing data, which reconfirms the accuracy of the assembled genome. The genome was utilized to identify 12,103 dinucleotide simple sequence repeat (SSR) markers, which were exploited in genetic diversity analysis to identify genetically distinct lines. A total of 207 polymorphic SSR markers were employed to construct a genetic linkage map for JMV resistance, using an interspecific F₂ mapping population involving susceptible J. curcas and resistant Jatropha integerrima as parents. Quantitative trait locus (QTL) analysis led to the identification of three minor QTLs for JMV resistance, and the same has been validated in an alternate F₂ mapping population. These validated QTLs were utilized in marker-assisted breeding for JMV resistance. Comparative genomics of oil-producing genes across selected oil producing species revealed 27 conserved genes and 2986 orthologous protein clusters in Jatropha. This reference genome assembly gives an insight into the understanding of the complex genetic structure of Jatropha, and serves as source for the development of agronomically improved virus-resistant and oil-producing lines.
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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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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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RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3-GENES GENOMES GENETICS 2018; 8:2709-2722. [PMID: 29954843 PMCID: PMC6071602 DOI: 10.1534/g3.118.200171] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.
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40
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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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41
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Huang Y, Fang Y, Long X, Liu L, Wang J, Zhu J, Ma Y, Qin Y, Qi J, Hu X, Tang C. Characterization of the rubber tree metallothionein family reveals a role in mitigating the effects of reactive oxygen species associated with physiological stress. TREE PHYSIOLOGY 2018; 38:911-924. [PMID: 29425342 DOI: 10.1093/treephys/tpy003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 01/28/2018] [Indexed: 05/15/2023]
Abstract
Metallothioneins (MTs) as reactive oxygen species (ROS) scavengers play important roles in stress response and heavy metal homeostasis. In Hevea brasiliensis (the para rubber tree that is the source of commercial natural rubber) and in other trees, the functions of MTs are not well understood. Latex exudes when the rubber tree is tapped. The flow of latex and its regeneration can be enhanced by tapping, wounding and ethylene treatment, all of which produce ROS as a by-product. Here, we show the presence of four MT genes in H. brasiliensis, comprising three Type 2 (HbMT2, -2a and -2b) and one Type 3 (HbMT3L) isoforms, representing one of the smallest MT gene families among angiosperms. The four HbMTs exhibited distinct tissue expression patterns: HbMT2 and HbMT3L mainly in leaves, HbMT2a specifically in flowers and HbMT2b in diverse tissues. The expression of HbMT2b, an isoform present in latex, decreased significantly in the latex following the stress-inducing treatments of tapping, wounding and ethephon (an ethylene generator). The expressions of the leaf-abundant isoforms, HbMT2 and -3L were up-regulated following pathogenic fungus infection and high-temperature stress, but down-regulated by low-temperature stress. These reactions were consistent with multiple defense- and hormone-responsive cis-acting elements in the HbMT promoters. Nine transcription factors were shown to implicate in the high-temperature responsiveness of HbMT2 and -3L in leaves. Overexpression of HbMT2 in Escherichia coli enhanced the bacterium's tolerance to heavy metals and ROS, consistent with its predicted role as an ROS scavenger. Taken together, our results, along with other relevant studies, suggest an important role of HbMTs in latex regeneration as well as species adaptation via the regulation of ROS homeostasis.
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Affiliation(s)
- Yacheng Huang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, PR China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Yongjun Fang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Xiangyu Long
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Linya Liu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, PR China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Jia Wang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, PR China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Jinheng Zhu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, PR China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Yanyan Ma
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, PR China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Yunxia Qin
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Jiyan Qi
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
| | - Xinwen Hu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, PR China
| | - Chaorong Tang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, PR China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, PR China
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42
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Hoffberg SL, Troendle NJ, Glenn TC, Mahmud O, Louha S, Chalopin D, Bennetzen JL, Mauricio R. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library. G3 (BETHESDA, MD.) 2018; 8:1855-1861. [PMID: 29703783 PMCID: PMC5982815 DOI: 10.1534/g3.118.200101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/19/2018] [Indexed: 11/18/2022]
Abstract
The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species.
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Affiliation(s)
| | | | - Travis C Glenn
- Department of Genetics
- Department of Environmental Health Science
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
| | - Ousman Mahmud
- Department of Genetics
- Department of Computational Biology
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
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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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44
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Zou Z, Xie G, Yang L. Papain-like cysteine protease encoding genes in rubber (Hevea brasiliensis): comparative genomics, phylogenetic, and transcriptional profiling analysis. PLANTA 2017; 246:999-1018. [PMID: 28752264 DOI: 10.1007/s00425-017-2739-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/29/2017] [Indexed: 05/22/2023]
Abstract
43 HbPLCPs representing nine subfamilies or 20 orthologous groups were found in rubber, where paralogs were resulted from the recent WGD and local duplication. Several senescence-associated genes were also identified. Papain-like cysteine proteases (PLCPs) comprise a large family of proteolytic enzymes involved in plant growth and development, seed germination, organ senescence, immunity, and stress response. Despite their importance and the extensive research in the model plant Arabidopsis thaliana, little information is available on rubber tree (Hevea brasiliensis), a rubber-producing plant of the Euphorbiaceae family. This study performed a genome-wide identification of PLCP family genes in rubber, resulting in a relatively high number of 43 members. The phylogenetic analysis assigned these genes into nine subfamilies, i.e., RD21 (6), CEP (4), XCP (4), XBCP3 (2), THI (1), SAG12 (18), RD19 (4), ALP (2), and CTB (2). Most of them were shown to have orthologs in Arabidopsis; however, several members in SAG12, CEP and XBCP3 subfamilies form new groups as observed in other core eudicots such as Manihot esculenta, Ricinus communis, Populus trichocarpa, and Vitis vinifera. Based on an expert sequence comparison, 20 orthologous groups (OGs) were proposed for core eudicots, and rubber paralogs were shown to be resulted from the recent whole-genome duplication (WGD) as well as local duplication. Transcriptional profiling showed distinct expression pattern of different members across various tissues, e.g., root, leaf, bark, laticifer, flower, and seed. By using the senescence-specific HbSAG12H1 as the indicator, the transcriptome of senescent rubber leaves was deeply sequenced and several senescence-associated PLCP genes were identified. Results obtained from this study provide valuable information for future functional analysis and utilization of PLCP genes in Hevea and other species.
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Affiliation(s)
- Zhi Zou
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China.
| | - Guishui Xie
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China
| | - Lifu Yang
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China
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45
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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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46
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Hatakeyama M, Aluri S, Balachadran MT, Sivarajan SR, Patrignani A, Grüter S, Poveda L, Shimizu-Inatsugi R, Baeten J, Francoijs KJ, Nataraja KN, Reddy YAN, Phadnis S, Ravikumar RL, Schlapbach R, Sreeman SM, Shimizu KK. Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Res 2017; 25:39-47. [PMID: 28985356 PMCID: PMC5824816 DOI: 10.1093/dnares/dsx036] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 08/23/2017] [Indexed: 01/26/2023] Open
Abstract
Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes.
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Affiliation(s)
- Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse. 190, 8057 Zurich, Switzerland.,Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland
| | - Sirisha Aluri
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Mathi Thumilan Balachadran
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse. 190, 8057 Zurich, Switzerland.,Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland.,Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Sajeevan Radha Sivarajan
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse. 190, 8057 Zurich, Switzerland.,Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland.,Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Andrea Patrignani
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Simon Grüter
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Lucy Poveda
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse. 190, 8057 Zurich, Switzerland
| | | | | | - Karaba N Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | | | - Shamprasad Phadnis
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Ramapura L Ravikumar
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Sheshshayee M Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse. 190, 8057 Zurich, Switzerland.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
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Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. BMC Genomics 2017; 18:578. [PMID: 28778149 PMCID: PMC5545040 DOI: 10.1186/s12864-017-3971-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/31/2017] [Indexed: 12/16/2022] Open
Abstract
Background Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Results Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Conclusions Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3971-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karen M Moll
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.,Montana State University, Center for Biofilm Engineering, Bozeman, MT, 59717, USA
| | - Peng Zhou
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, USA
| | - Thiruvarangan Ramaraj
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Diego Fajardo
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Nicholas P Devitt
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Michael J Sadowsky
- Department of Soil, Water & Climate, Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | | | - Nevin D Young
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | | | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.
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