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Cheng S, Zhang Q, Geng X, Xie L, Chen M, Jiao S, Qi S, Yao P, Lu M, Zhang M, Zhai W, Yun Q, Feng S. Haplotype-resolved chromosome-level genome assembly of Ehretia macrophylla. Sci Data 2024; 11:589. [PMID: 38839803 PMCID: PMC11153487 DOI: 10.1038/s41597-024-03431-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
Ehretia macrophylla Wall, known as wild loquat, is an ecologically, economically, and medicinally significant tree species widely grown in China, Japan, Vietnam, and Nepal. In this study, we have successfully generated a haplotype-resolved chromosome-scale genome assembly of E. macrophylla by integrating PacBio HiFi long-reads, Illumina short-reads, and Hi-C data. The genome assembly consists of two haplotypes, with sizes of 1.82 Gb and 1.58 Gb respectively, and contig N50 lengths of 28.11 Mb and 21.57 Mb correspondingly. Additionally, 99.41% of the assembly was successfully anchored into 40 pseudo-chromosomes. We predicted 58,886 protein-coding genes, of which 99.60% were functionally annotated from databases. We furthermore detected 2.65 Gb repeat sequences, 659,290 rRNAs, 4,931 tRNAs and 4,688 other ncRNAs. The high-quality assembly of the genome offers a solid basis for furthering the fields of molecular breeding and functional genomics of E. macrophylla.
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Affiliation(s)
- Shiping Cheng
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China.
| | | | - Xining Geng
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Lihua Xie
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Minghui Chen
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Siqian Jiao
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Shuaizheng Qi
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Pengqiang Yao
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Mailin Lu
- Henan Forestry Vocational College, Luoyang, 471000, China
| | - Mengren Zhang
- Henan Forestry Vocational College, Luoyang, 471000, China
| | - Wenshan Zhai
- Henan Senzhuang Cukang Agriculture and Forestry Technology Co., Ltd, Luoyang, 471000, China
| | - Quanzheng Yun
- Kaitai Mingjing Genetech Corporation, Beijing, 100070, China
| | - Shangguo Feng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, China.
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China.
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2
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Zhang S, Ren Y, Wang S, Song L, Jing Y, Xu T, Kang X, Li Y. EuHDZ25 positively affects rubber biosynthesis by targeting EuFPS1 in Eucommia leaves. Int J Biol Macromol 2024; 272:132707. [PMID: 38825274 DOI: 10.1016/j.ijbiomac.2024.132707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/12/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024]
Abstract
Eucommia ulmoides is a temperate gum source plant that produces trans-polyisoprene (TPI), also known as Eucommia rubber. The structural configuration and function of TPI offer a new material with important potential for industrial development. In this study, we detected the TPI content in the leaves of diploid and triploid E. ulmoides plants. The average TPI content in the leaves of triploid E. ulmoides was significantly higher than that of diploid. Transcriptome data and weighted gene co-expression network analyses identified a significant positive correlation between the EuFPS1 gene and TPI content. Overexpression of EuFPS1 increased the density of rubber particles and TPI content, indicating its crucial role in TPI biosynthesis. In addition, the expression of EuHDZ25 in E. ulmoides was significantly positively correlated with EuFPS1 expression. Yeast one-hybrid and dual-luciferase assays demonstrated that EuHDZ25 mainly promotes TPI biosynthesis through positive regulation of EuFPS1 expression. The significantly up-regulated expression of EuHDZ25 and its consequent upregulation of EuFPS1 during the biosynthesis of TPI may partially explain the increased TPI content of triploids. This study provides an important theoretical foundation for further exploring the molecular mechanism of secondary metabolites content variation in polyploids and can help to promote the development and utilization of rubber resources.
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Affiliation(s)
- Shuwen Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yongyu Ren
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Shun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lianjun Song
- Weixian Eucommia National Forest Tree Germplasm Repository, Weixian Forestry Cultivation Base of Superior Species, Hebei, China
| | - Yanchun Jing
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Tingting Xu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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3
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Zhang S, Chen H, Wang S, Du K, Song L, Xu T, Xia Y, Guo R, Kang X, Li Y. Positive regulation of the Eucommia rubber biosynthesis-related gene EuFPS1 by EuWRKY30 in Eucommia ulmoides. Int J Biol Macromol 2024; 268:131751. [PMID: 38657917 DOI: 10.1016/j.ijbiomac.2024.131751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
Eucommia rubber is a secondary metabolite from Eucommia ulmoides that has attracted much attention because of its unique properties and enormous potential for application. However, the transcriptional mechanism regulating its biosynthesis has not yet been determined. Farnesyl pyrophosphate synthase is a key enzyme in the Eucommia rubber biosynthesis. In this study, the promoter of EuFPS1 was used as bait, EuWRKY30 was screened from the cDNA library of EuFPS1 via a yeast one-hybrid system. EuWRKY30 belongs to the WRKY IIa subfamily and contains a WRKY domain and a C2H2 zinc finger motif, and the expressed protein is located in the nucleus. EuWRKY30 and EuFPS1 exhibited similar tissue expression patterns, and yeast one-hybrid and dual-luciferase experiments confirmed that EuWRKY30 directly binds to the W-box element in the EuFPS1 promoter and activates its expression. Moreover, the overexpression of EuWRKY30 significantly upregulated the expression level of EuFPS1, further increasing the density of the rubber particles and Eucommia rubber content. The results of this study indicated that EuWRKY30 positively regulates EuFPS1, which plays a critical role in the synthesis of Eucommia rubber, provided a basis for further analysis of the underlying transcriptional regulatory mechanisms.
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Affiliation(s)
- Shuwen Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Hao Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Shun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Kang Du
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Lianjun Song
- Weixian Eucommia National Forest Tree Germplasm Repository, Weixian Forestry Cultivation Base of Superior Species, Hebei, China
| | - Tingting Xu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yufei Xia
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Ruihua Guo
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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4
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Wang R, Zhu Y, Zhao D. Genome-Wide Identification and Expression Analysis of Growth-Regulating Factors in Eucommia ulmoides Oliver (Du-Zhong). PLANTS (BASEL, SWITZERLAND) 2024; 13:1185. [PMID: 38732399 PMCID: PMC11085888 DOI: 10.3390/plants13091185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
The roots, stems, leaves, and seeds of Eucommia ulmoides contain a large amount of trans-polyisoprene (also known as Eu-rubber), which is considered to be an important laticiferous plant with valuable industrial applications. Eu-rubber used in industry is mainly extracted from leaves. Therefore, it is of great significance to identify genes related to regulating the leaf size of E. ulmoides. Plant growth-regulating factors (GRFs) play important roles in regulating leaf size, and their functions are highly conserved across different plant species. However, there have been very limited reports on EuGRFs until now. In this study, eight canonical EuGRFs with both QLQ and WRC domains and two putative eul-miR396s were identified in the chromosome-level genome of E. ulmoides. It is found that, unlike AtGRFs, all EuGRFs contain the miR396s binding site in the terminal of WRC domains. These EuGRFs were distributed on six chromosomes in the genome of E. ulmoides. Collinearity analysis of the E. ulmoides genome revealed that EuGRF1 and EuGRF3 exhibit collinear relationships with EuGRF2, suggesting that those three genes may have emerged via gene replication events. The collinear relationship between EuGRFs, AtGRFs, and OsGRFs showed that EuGRF5 and EuGRF8 had no collinear members in Arabidopsis and rice. Almost all EuGRFs show a higher expression level in growing and developing tissues, and most EuGRF promoters process phytohormone-response and stress-induced cis-elements. Moreover, we found the expression of EuGRFs was significantly induced by gibberellins (GA3) in three hours, and the height of E. ulmoides seedlings was significantly increased one week after GA3 treatment. The findings in this study provide potential candidate genes for further research and lay the foundation for further exploring the molecular mechanism underlying E. ulmoides development in response to GA3.
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Affiliation(s)
- Ruoruo Wang
- Plant Conservation Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Biotechnology Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Ying Zhu
- Plant Conservation Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Biotechnology Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Degang Zhao
- Plant Conservation Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Biotechnology Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Region, Guiyang 550006, China
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
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5
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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6
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Wang Q, Hu F, Yao Z, Zhao X, Chu G, Ye J. Comprehensive genomic characterisation of the NAC transcription factor family and its response to drought stress in Eucommia ulmoides. PeerJ 2023; 11:e16298. [PMID: 37901460 PMCID: PMC10601904 DOI: 10.7717/peerj.16298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/23/2023] [Indexed: 10/31/2023] Open
Abstract
The NAC transcription factor family enhances plant adaptation to environmental challenges by participating in signalling pathways triggered by abiotic stressors and hormonal cues. We identified 69 NAC genes in the Eucommia ulmoides genome and renamed them according to their chromosomal distribution. These EuNAC proteins were clustered into 13 sub-families and distributed on 16 chromosomes and 2 scaffolds. The gene structures suggested that the number of exons varied from two to eight among these EuNACs, with a multitude of them containing three exons. Duplicated events resulted in a large gene family; 12 and four pairs of EuNACs were the result of segmental and tandem duplicates, respectively. The drought-stress response pattern of 12 putative EuNACs was observed under drought treatment, revealing that these EuNACs could play crucial roles in mitigating the effects of drought stress responses and serve as promising candidate genes for genetic engineering aimed at enhancing the drought stress tolerance of E. ulmoides. This study provides insight into the evolution, diversity, and characterisation of NAC genes in E. ulmoides and will be helpful for future characterisation of putative EuNACs associated with water deficit.
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Affiliation(s)
- Qi Wang
- Laboratory of Forestry Department, Agricultural College, Shihezi University, Shihezi, China
| | - FengCheng Hu
- Lveyang County Forest Tree Seedling Workstation, Forestry Bureau of Lveyang County, Lveyang, China
| | - ZhaoQun Yao
- Laboratory of Plant Protection Department, Agricultural College, Shihezi University, Shihezi, China
| | - XinFeng Zhao
- Lveyang County Forest Tree Seedling Workstation, Forestry Bureau of Lveyang County, Lveyang, China
| | - GuangMing Chu
- Laboratory of Forestry Department, Agricultural College, Shihezi University, Shihezi, China
| | - Jing Ye
- Laboratory of Forestry Department, Agricultural College, Shihezi University, Shihezi, China
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7
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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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8
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Guo M, Zhang M, Gao S, Wang L, Zhang J, Huang Z, Dong Y. Quantitative Detection of Natural Rubber Content in Eucommia ulmoides by Portable Pyrolysis-Membrane Inlet Mass Spectrometry. Molecules 2023; 28:molecules28083330. [PMID: 37110564 PMCID: PMC10142753 DOI: 10.3390/molecules28083330] [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: 02/28/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Eucommia ulmoides gum (EUG) is a natural polymer predominantly consisting of trans-1,4-polyisoprene. Due to its excellent crystallization efficiency and rubber-plastic duality, EUG finds applications in various fields, including medical equipment, national defense, and civil industry. Here, we devised a portable pyrolysis-membrane inlet mass spectrometry (PY-MIMS) approach to rapidly, accurately, and quantitatively identify rubber content in Eucommia ulmoides (EU). EUG is first introduced into the pyrolyzer and pyrolyzed into tiny molecules, which are then dissolved and diffusively transported via the polydimethylsiloxane (PDMS) membrane before entering the quadrupole mass spectrometer for quantitative analysis. The results indicate that the limit of detection (LOD) for EUG is 1.36 μg/mg, and the recovery rate ranges from 95.04% to 104.96%. Compared to the result of pyrolysis-gas chromatography (PY-GC), the average relative error is 1.153%, and the detection time was reduced to less than 5 min, demonstrating that the procedure was reliable, accurate, and efficient. The method has the potential to be employed to precisely identify the rubber content of natural rubber-producing plants such as Eucommia ulmoides, Taraxacum kok-saghyz (TKS), Guayule, and Thorn lettuce.
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Affiliation(s)
- Minmin Guo
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Rubber Plant Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mingjian Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Rubber Plant Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shunkai Gao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Rubber Plant Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lu Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Rubber Plant Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jichuan Zhang
- Rubber Plant Research Center, Beijing University of Chemical Technology, Beijing 100029, China
- College of Materials and Engineering, Beijing University of Chemical and Technology, Beijing 100029, China
| | - Zejian Huang
- Center for Advanced Measurement Science, National Institute of Metrology, Technology Innovation Center of Mass Spectrum for State Market Regulation, Beijing 100029, China
| | - Yiyang Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Rubber Plant Research Center, Beijing University of Chemical Technology, Beijing 100029, China
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9
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Du Q, Wu Z, Liu P, Qing J, He F, Du L, Sun Z, Zhu L, Zheng H, Sun Z, Yang L, Wang L, Du H. The chromosome-level genome of Eucommia ulmoides provides insights into sex differentiation and α-linolenic acid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1118363. [PMID: 37063180 PMCID: PMC10102601 DOI: 10.3389/fpls.2023.1118363] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Eucommia ulmoides Oliver is a typical dioecious plant endemic to China that has great medicinal and economic value. Here, we report a high-quality chromosome-level female genome of E. ulmoides obtained by PacBio and Hi-C technologies. The size of the female genome assembly was 1.01 Gb with 17 pseudochromosomes and 31,665 protein coding genes. In addition, Hi-C technology was used to reassemble the male genome released in 2018. The reassembled male genome was 1.24 Gb with the superscaffold N50 (48.30 Mb), which was increased 25.69 times, and the number of predicted genes increased by 11,266. Genome evolution analysis indicated that E. ulmoides has undergone two whole-genome duplication events before the divergence of female and male, including core eudicot γ whole-genome triplication event (γ-WGT) and a recent whole genome duplication (WGD) at approximately 27.3 million years ago (Mya). Based on transcriptome analysis, EuAP3 and EuAG may be the key genes involved in regulating the sex differentiation of E. ulmoides. Pathway analysis showed that the high expression of ω-3 fatty acid desaturase coding gene EU0103017 was an important reason for the high α-linolenic acid content in E. ulmoides. The genome of female and male E. ulmoides presented here is a valuable resource for the molecular biological study of sex differentiation of E. ulmoides and also will provide assistance for the breeding of superior varieties.
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Affiliation(s)
- Qingxin Du
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Zixian Wu
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Panfeng Liu
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Jun Qing
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Feng He
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Lanying Du
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Zhiqiang Sun
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Lili Zhu
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Hongchu Zheng
- Product Department, Henan Jinduzhong Agricultural Science and Technology Co., Ltd., Yanling, China
| | - Zongyi Sun
- Operation Department, Grandomics Biosciences Co., Ltd., Wuhan, China
| | - Long Yang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Lu Wang
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Hongyan Du
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
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10
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Zhang S, Xu T, Ren Y, Song L, Liu Z, Kang X, Li Y. The NAC transcription factor family in Eucommia ulmoides: Genome-wide identification, characterization, and network analysis in relation to the rubber biosynthetic genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1030298. [PMID: 37077635 PMCID: PMC10106570 DOI: 10.3389/fpls.2023.1030298] [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: 08/28/2022] [Accepted: 02/13/2023] [Indexed: 05/03/2023]
Abstract
The NAC transcription factor family is a large plant gene family, participating in plant growth and development, secondary metabolite synthesis, biotic and abiotic stresses responses, and hormone signaling. Eucommia ulmoides is a widely planted economic tree species in China that can produce trans-polyisoprene: Eucommia rubber (Eu-rubber). However, genome-wide identification of the NAC gene family has not been reported in E. ulmoides. In this study, 71 NAC proteins were identified based on genomic database of E. ulmoides. Phylogenetic analysis showed that the EuNAC proteins were distributed in 17 subgroups based on homology with NAC proteins in Arabidopsis, including the E. ulmoides-specific subgroup Eu_NAC. Gene structure analysis suggested that the number of exons varied from 1 to 7, and multitudinous EuNAC genes contained two or three exons. Chromosomal location analysis revealed that the EuNAC genes were unevenly distributed on 16 chromosomes. Three pairs of genes of tandem duplicates genes and 12 segmental duplications were detected, which indicated that segmental duplications may provide the primary driving force of expansion of EuNAC. Prediction of cis-regulatory elements indicated that the EuNAC genes were involved in development, light response, stress response and hormone response. For the gene expression analysis, the expression levels of EuNAC genes in various tissues were quite different. To explore the effect of EuNAC genes on Eu-rubber biosynthesis, a co-expression regulatory network between Eu-rubber biosynthesis genes and EuNAC genes was constructed, which indicated that six EuNAC genes may play an important role in the regulation of Eu-rubber biosynthesis. In addition, this six EuNAC genes expression profiles in E. ulmoides different tissues were consistent with the trend in Eu-rubber content. Quantitative real-time PCR analysis showed that EuNAC genes were responsive to different hormone treatment. These results will provide a useful reference for further studies addressing the functional characteristics of the NAC genes and its potential role in Eu-rubber biosynthesis.
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Affiliation(s)
- Shuwen Zhang
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Tingting Xu
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Yongyu Ren
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Lianjun Song
- Weixian Eucommia National Forest Tree Germplasm Repository, Weixian Forestry Cultivation Base of Superior Species, Hebei, China
| | - Zhao Liu
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- *Correspondence: Yun Li,
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11
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Zhang X, Wang X, Pan L, Guo W, Li Y, Wang W. Genome-wide identification and expression analysis of MADS-box transcription factors reveal their involvement in sex determination of hardy rubber tree ( Eucommia ulmoides oliv.). Front Genet 2023; 14:1138703. [PMID: 36896236 PMCID: PMC9988917 DOI: 10.3389/fgene.2023.1138703] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Eucommia ulmoides is a famous rubber-producing and medicinal tree species that produces unisexual flowers on separate individuals from the earliest stage of stamen/pistil primordium formation. To explore the genetic regulation pathway of sex in E. ulmoides, comprehensive genome-wide analyses and tissue-/sex-specific transcriptome comparisons of MADS-box transcription factors were performed for the first time in this work. Quantitative real-time PCR technique was employed to further validate the expression of genes that are assigned to floral organ ABCDE model. A total of 66 non-redundant E. ulmoides MADS-box (EuMADS) genes were identified, they were classified into Type I (M-type, 17 genes) and Type II (MIKC, 49 genes). Complex protein-motif composition, exon-intron structure and phytohormone-response cis-elements were detected in MIKC-EuMADS genes. Furthermore, 24 differentially-expressed EuMADS genes (DEGs) between male and female flowers, and two DEGs between male and female leaves were revealed. Amongst the 14 floral organ ABCDE model-related genes, there were 6 (A/B/C/E-class) and 5 (A/D/E-class) genes displayed male- and female-biased expression respectively. In particular, one B-class gene EuMADS39 and one A-class gene EuMADS65 were almost exclusively expressed in male trees, no matter in flower or leaf tissues. Collectively, these results suggested a critical role of MADS-box transcription factors in sex determination of E. ulmoides, which is conducive to decoding the molecular regulation mechanism of sex in E. ulmoides.
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Affiliation(s)
- Xianzhi Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xinyi Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Linsi Pan
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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12
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Zhou T, Bai G, Hu Y, Ruhsam M, Yang Y, Zhao Y. De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids. DNA Res 2022; 29:6748869. [PMID: 36197098 PMCID: PMC9724787 DOI: 10.1093/dnares/dsac034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/24/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Gentiana macrophylla is a perennial herb in the Gentianaceae family, whose dried roots are used in traditional Chinese medicine. Here, we assembled a chromosome-level genome of G. macrophylla using a combination of Nanopore, Illumina, and Hi-C scaffolding approaches. The final genome size was ~1.79 Gb (contig N50 = 720.804 kb), and 98.89% of the genome sequences were anchored on 13 pseudochromosomes (scaffold N50 = 122.73 Mb). The genome contained 55,337 protein-coding genes, and 73.47% of the assemblies were repetitive sequences. Genome evolution analysis indicated that G. macrophylla underwent two rounds of whole-genome duplication after the core eudicot γ genome triplication event. We further identified candidate genes related to the biosynthesis of iridoids, and the corresponding gene families mostly expanded in G. macrophylla. In addition, we found that root-specific genes are enriched in pathways involved in defense responses, which may greatly improve the biological adaptability of G. macrophylla. Phylogenomic analyses showed a sister relationship of asterids and rosids, and all Gentianales species formed a monophyletic group. Our study contributes to the understanding of genome evolution and active component biosynthesis in G. macrophylla and provides important genomic resource for the genetic improvement and breeding of G. macrophylla.
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Affiliation(s)
- Tao Zhou
- Corresponding author: Tel. +86 29 8265 5424. (T.Z.); (Y.Z.)
| | | | | | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Yanci Yang
- School of Biological Science and Technology, Baotou Teachers’ College, Baotou, China
| | - Yuemei Zhao
- Corresponding author: Tel. +86 29 8265 5424. (T.Z.); (Y.Z.)
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13
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Transcriptome and proteome associated analysis of flavonoid metabolism in haploid Ginkgo biloba. Int J Biol Macromol 2022; 224:306-318. [DOI: 10.1016/j.ijbiomac.2022.10.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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14
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Guo L, Yao H, Chen W, Wang X, Ye P, Xu Z, Zhang S, Wu H. Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era. HORTICULTURE RESEARCH 2022; 9:uhac223. [PMID: 36479585 PMCID: PMC9720450 DOI: 10.1093/hr/uhac223] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
Abstract
Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in the pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology, and chemical informatics are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.
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Affiliation(s)
- Li Guo
- Corresponding authors. E-mails: ;
| | | | | | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Peng Ye
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Sisheng Zhang
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wu
- Corresponding authors. E-mails: ;
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15
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High-Depth Transcriptome Reveals Differences in Natural Haploid Ginkgo biloba L. Due to the Effect of Reduced Gene Dosage. Int J Mol Sci 2022; 23:ijms23168958. [PMID: 36012222 PMCID: PMC9409250 DOI: 10.3390/ijms23168958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/31/2022] [Accepted: 08/10/2022] [Indexed: 12/13/2022] Open
Abstract
As a representative of gymnosperms, the discovery of natural haploids of Ginkgo biloba L. has opened a new door for its research. Haploid germplasm has always been a research material of interest to researchers because of its special characteristics. However, we do not yet know the special features and mechanisms of haploid ginkgo following this significant discovery. In this study, we conducted a homogenous garden experiment on haploid and diploid ginkgo to explore the differences in growth, physiology and biochemistry between the two. Additionally, a high-depth transcriptome database of both was established to reveal their transcriptional differences. The results showed that haploid ginkgo exhibited weaker growth potential, lower photosynthesis and flavonoid accumulation capacity. Although the up-regulated expression of DEGs in haploid ginkgo reached 46.7% of the total DEGs in the whole transcriptome data, the gene sets of photosynthesis metabolic, glycolysis/gluconeogenesis and flavonoid biosynthesis pathways, which were significantly related to these differences, were found to show a significant down-regulated expression trend by gene set enrichment analysis (GSEA). We further found that the major metabolic pathways in the haploid ginkgo transcriptional database were down-regulated in expression compared to the diploid. This study reveals for the first time the phenotypic, growth and physiological differences in haploid ginkgos, and demonstrates their transcriptional patterns based on high-depth transcriptomic data, laying the foundation for subsequent in-depth studies of haploid ginkgos.
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Li X, Cai K, Zhang Q, Pei X, Chen S, Jiang L, Han Z, Zhao M, Li Y, Zhang X, Li Y, Zhang S, Chen S, Qu G, Tigabu M, Chiang VL, Sederoff R, Zhao X. The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis. Gigascience 2022; 11:6619298. [PMID: 35764602 PMCID: PMC9239856 DOI: 10.1093/gigascience/giac057] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/20/2022] [Accepted: 05/24/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value. FINDINGS Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified. CONCLUSIONS Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.
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Affiliation(s)
| | | | | | | | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Luping Jiang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Zhiming Han
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Minghui Zhao
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yan Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Xinxin Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yuxi Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Shikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Mulualem Tigabu
- Southern Swedish Forest Research Center, Faculty of Forest Science, Swedish University of Agricultural Sciences, Lomma SE-234 22, Sweden
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiyang Zhao
- Correspondence address. Xiyang Zhao, E-mail:
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17
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Deng P, Wang Y, Hu F, Yu H, Liang Y, Zhang H, Wang T, Zhou Y, Li Z. Phenotypic Trait Subdivision Provides New Sight Into the Directional Improvement of Eucommia ulmoides Oliver. FRONTIERS IN PLANT SCIENCE 2022; 13:832821. [PMID: 35463430 PMCID: PMC9026163 DOI: 10.3389/fpls.2022.832821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Eucommia ulmoides Oliver has been used extensively in many fields. To satisfy increasing demand, great efforts must be made to further improve its traits. However, limited information is available on these traits, which is a factor that restricts their improvement. To improve traits directionally, nine clones were assigned to six sites to analyze the effect of different variation sources (the genotype, site, and genotype × environment interaction) on the phenotypic trait. In addition, a mixed linear model was used to assess the contribution of variations. In general, for most traits, the site effect accounted for a larger proportion of the variance, followed by the genotype and genotype × environment interaction effects. All the studied genotypes and sites had a significant effect, indicating that they could be improved by selecting preferable genotypes or cultivation areas, respectively. Interestingly, growth traits or economic traits could be improved simultaneously. Trait performance and stability are necessary when selecting genotypes. Moreover, the discriminating ability of genotypes should be considered in selecting cultivation areas. Annual mean temperature and annual sunshine duration proved to be crucial factors that affected the traits. They were correlated positively with economic traits and leaf yield and correlated negatively with growth traits. These findings contributed to selecting a wider range of cultivation areas. Regarding the genotype × environment interaction effect, there were significant differences only in the gutta-percha content, the total number of leaves, and the chlorogenic acid content. These traits could also be improved by choosing appropriate genotypes for the local environment. The research has provided preliminary data on the main factors that affect the traits of E. ulmoides and offered solutions for trait improvement. This information could be a reference for the trait improvement of other plants.
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Affiliation(s)
- Peng Deng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Yiran Wang
- College of Forestry, Northwest A&F University, Yangling, China
| | - Fengcheng Hu
- Lveyang County Forest Tree Seedling Workstation, Forestry Bureau of Lveyang County, Lveyang, China
| | - Hang Yu
- College of Forestry, Northwest A&F University, Yangling, China
| | - Yangling Liang
- College of Humanities and Social Development, Northwest A&F University, Yangling, China
| | - Haolin Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Ting Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuhao Zhou
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zhouqi Li
- College of Forestry, Northwest A&F University, Yangling, China
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18
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Whole genome re-sequencing reveals the genetic diversity and evolutionary patterns of Eucommia ulmoides. Mol Genet Genomics 2022; 297:485-494. [PMID: 35146538 DOI: 10.1007/s00438-022-01864-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/23/2022] [Indexed: 10/19/2022]
Abstract
Eucommia ulmoides (E. ulmoides) is a deciduous perennial tree belonging to the order Garryales, and is known as "living fossil" plant, along with ginkgo (Ginkgo biloba), metaspaca (Metasequoia glyptostroboides) and dove tree (Davidia involucrata Baill). However, the genetic diversity and population structure of E. ulmoides are still ambiguous nowdays. In this study, we re-sequenced the genomes of 12 E. ulmoides accessions from different major climatic geography regions in China to elucidate the genetic diversity, population structure and evolutionary pattern. By integration of phylogenetic analysis, principal component analysis and population structure analysis based on a number of high-quality SNPs, a total of 12 E. ulmoides accessions were clustered into four different groups. This result is consistent with their geographical location except for group samples from Shanghai and Hunan province. E. ulmoides accessions from Hunan province exhibited a closer genetic relationship with E. ulmoides accessions from Shanghai in China compared with other regions, which is also supported by the result of population structure analyses. Genetic diversity analysis further revealed that E. ulmoides samples in Shanghai and Hunan province were with higher genetic diversity than those in other regions in this study. In addition, we treated the E. ulmoides materials from Shanghai and Hunan province as group A, and the other materials from other places as group B, and then analyzed the evolutionary pattern of E. ulmoides. The result showed the significant differentiation (Fst = 0.1545) between group A and group B. Some candidate highly divergent genome regions were identified in group A by selective sweep analyses, and the function analysis of candidate genes in these regions showed that biological regulation processes could be correlated with the Eu-rubber biosynthesis. Notably, nine genes were identified from selective sweep regions. They were involved in the Eu-rubber biosynthesis and expressed in rubber containing tissues. The genetic diversity research and evolution model of E. ulmoides were preliminarily explored in this study, which laid the foundation for the protection of germplasm resources and the development and utilization of multipurpose germplasm resources in the future.
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19
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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20
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Deng P, Xie X, Long F, Zhang L, Li Y, Zhao Z, Yang S, Wang Y, Fan R, Li Z. Trait Variations and Probability Grading Index System on Leaf-Related Traits of Eucommia ulmoides Oliver Germplasm. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112280. [PMID: 34834643 PMCID: PMC8620490 DOI: 10.3390/plants10112280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 05/14/2023]
Abstract
Eucommia ulmoides Oliver (EUO), an economic tree grown specifically in China, is widely used in various fields. To satisfy the requirements of industrial development, superior varieties need to be selected for different uses. However, there is no unified standard for breeders to reference. In this study, leaf-related traits were classified by a probability grading method. The results indicated there were significant differences between different planting models for the studied traits, and the traits in the Arbor forest model showed more abundant variation. Compared with genotype, the planting model accounted for relatively bigger variance, indicating that the standard should be divided according to planting models. Furthermore, the optimum planting model for different traits would be obtained by analyzing the variation range. Association analyses were conducted among traits to select the crucial evaluation indexes. The indexes were divided into three grades in different planting models. The evaluation system on leaf-related traits of EUO germplasm was established preliminarily, which considered planting models and stability across years for the first time. It can be treated as a reference to identify and evaluate EUO germplasm resources. Additionally, the study served as an example for the classification of quantitative traits in other economically important perennial plants.
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Affiliation(s)
- Peng Deng
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Xiangchen Xie
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Feiyu Long
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Liang Zhang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Yonghang Li
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Zhangxu Zhao
- College of Economics and Management, Northwest A&F University, Xianyang 712100, China;
| | - Shiyao Yang
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China;
| | - Yiran Wang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Ruishen Fan
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Zhouqi Li
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
- Correspondence:
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21
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Wei X, Peng P, Peng F, Dong J. Natural Polymer Eucommia Ulmoides Rubber: A Novel Material. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3797-3821. [PMID: 33761246 DOI: 10.1021/acs.jafc.0c07560] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
As the second natural rubber resource, Eucommia ulmoides rubber (EUR) from Eucommia ulmoides Oliver is mainly composed of trans-1,4-polyisoprene, which is the isomer of natural rubber cis-1,4-polyisoprene from Hevea brasiliensis. In the past few years, the great potential application of EUR has received increasing attention, and there is a growing awareness that the natural polymer EUR could become an emerging research topic in field of the novel materials due to its unique and excellent duality of both rubber and plastic. To gain insight into its further development, in this review, the extraction, structure, physicochemical properties, and modification of EUR are discussed in detail. More emphasis on the potential applications in the fields of the environment, agriculture, engineering, and biomedical engineering is summarized. Finally, some insights into the challenges and perspectives of EUR are also suggested.
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Affiliation(s)
- Xingneng Wei
- College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Pai Peng
- College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Feng Peng
- College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
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22
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Yao L, Li P, Du Q, Quan M, Li L, Xiao L, Song F, Lu W, Fang Y, Zhang D. Genetic Architecture Underlying the Metabolites of Chlorogenic Acid Biosynthesis in Populus tomentosa. Int J Mol Sci 2021; 22:2386. [PMID: 33673666 PMCID: PMC7957499 DOI: 10.3390/ijms22052386] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Chlorogenic acid (CGA) plays a crucial role in defense response, immune regulation, and the response to abiotic stress in plants. However, the genetic regulatory network of CGA biosynthesis pathways in perennial plants remains unclear. Here, we investigated the genetic architecture for CGA biosynthesis using a metabolite-based genome-wide association study (mGWAS) and expression quantitative trait nucleotide (eQTN) mapping in a population of 300 accessions of Populus tomentosa. In total, we investigated 204 SNPs which were significantly associated with 11 metabolic traits, corresponding to 206 genes, and were mainly involved in metabolism and cell growth processes of P. tomentosa. We identified 874 eQTNs representing 1066 genes, in which the expression and interaction of causal genes affected phenotypic variation. Of these, 102 genes showed significant signatures of selection in three geographical populations, which provided insights into the adaptation of CGA biosynthesis to the local environment. Finally, we constructed a genetic network of six causal genes that coordinately regulate CGA biosynthesis, revealing the multiple regulatory patterns affecting CGA accumulation in P. tomentosa. Our study provides a multiomics strategy for understanding the genetic basis underlying the natural variation in the CGA biosynthetic metabolites of Populus, which will enhance the genetic development of abiotic-resistance varieties in forest trees.
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Affiliation(s)
- Liangchen Yao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Peng Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Lianzheng Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Liang Xiao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Fangyuan Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Wenjie Lu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Yuanyuan Fang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China; (L.Y.); (P.L.); (Q.D.); (M.Q.); (L.L.); (L.X.); (F.S.); (W.L.); (Y.F.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
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23
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Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
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Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
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