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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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Duan CJ, Han X, Chang YH, Xu J, Yue GL, Zhang Y, Fu YJ. A novel ternary deep eutectic solvent pretreatment for the efficient separation and conversion of high-quality gutta-percha, value-added lignin and monosaccharide from Eucommia ulmoides seed shells. BIORESOURCE TECHNOLOGY 2023; 370:128570. [PMID: 36596366 DOI: 10.1016/j.biortech.2022.128570] [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: 11/24/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
A novel ternary deep eutectic solvent (DES), consisted of choline chloride, oxalic acid and ethylene glycol, was developed as a green, low-cost and recyclable pretreatment system for multi-stage utilization of Eucommia ulmoides seed shells. Under optimum conditions, 79.7 % hemicellulose and 65.6 % lignin were quickly removed while 84.0 % cellulose was retained. After DES pretreatment, the yield and purity of gutta-percha achieved 85.1 mg/g and 96.2 %, which increased 1.4 and 1.8 folds higher than that of un-treatment ones. Meanwhile, 69.1 % enzymatic digestibility of cellulose was obtained, that was 2.3 folds higher than that of raw substrates. Moreover, 53.6 % low-condensation lignin with aromatic structures and valuable aryl-ether linkages was well collected. Importantly, the DES that has been recycled five runs can still remove 73.9 % hemicellulose and 58.0 % lignin. Overall, the DES was determined to efficiently promote the separation and conversion of high-quality gutta-percha, value-added lignin and high-yield glucose from Eucommia ulmoides seed shells.
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Affiliation(s)
- Cong-Jia Duan
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Hexing Road 26, Harbin 150040, PR China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
| | - Xu Han
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Hexing Road 26, Harbin 150040, PR China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
| | - Yuan-Hang Chang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Hexing Road 26, Harbin 150040, PR China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
| | - Jian Xu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Hexing Road 26, Harbin 150040, PR China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
| | - Gan-Lu Yue
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Hexing Road 26, Harbin 150040, PR China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
| | - Ying Zhang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Hexing Road 26, Harbin 150040, PR China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
| | - Yu-Jie Fu
- The College of Forestry, Beijing Forestry University, Beijing 100083, PR China.
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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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Zhang X, Pan L, Guo W, Li Y, Wang W. A convergent mechanism of sex determination in dioecious plants: Distinct sex-determining genes display converged regulation on floral B-class genes. FRONTIERS IN PLANT SCIENCE 2022; 13:953445. [PMID: 36092432 PMCID: PMC9459113 DOI: 10.3389/fpls.2022.953445] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 06/12/2023]
Abstract
Sex determination in dioecious plants has been broadly and progressively studied with the blooming of genome sequencing and editing techniques. This provides us with a great opportunity to explore the evolution and genetic mechanisms underlining the sex-determining system in dioecious plants. In this study, comprehensively reviewing advances in sex-chromosomes, sex-determining genes, and floral MADS-box genes in dioecious plants, we proposed a convergent model that governs plant dioecy across divergent species using a cascade regulation pathway connecting sex-determining genes and MADS-box genes e.g., B-class genes. We believe that this convergent mechanism of sex determination in dioecious plants will shed light on our understanding of gene regulation and evolution of plant dioecy. Perspectives concerning the evolutionary pathway of plant dioecy are also suggested.
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Affiliation(s)
- Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Linsi Pan
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wencai Wang
- Department of Molecular of Biology, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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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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Transcriptomic differences between male and female Trachycarpus fortunei. Sci Rep 2020; 10:12338. [PMID: 32704095 PMCID: PMC7378167 DOI: 10.1038/s41598-020-69107-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/01/2020] [Indexed: 11/09/2022] Open
Abstract
Trachycarpus fortunei (Hook.) is a typical dioecious plant, which has important economic value. There is currently no sex identification method for the early stages of T. fortunei growth. The aim of this study was to obtain expression and site differences between male and female T. fortunei transcriptomes. Using the Illumina sequencing platform, the transcriptomes of T. fortunei male and female plants were sequenced. By analyzing transcriptomic differences, the chromosomal helical binding protein (CHD1), serine/threonine protein kinase (STPK), cytochrome P450 716B1, and UPF0136 were found to be specifically expressed in T. fortunei males. After single nucleotide polymorphism (SNP) detection, a total of 12 male specific sites were found and the THUMP domain protein homologs were found to be male-biased expressed. Cytokinin dehydrogenase 6 (CKX6) was upregulated in male flowers and the lower concentrations of cytokinin (CTK) may be more conducive to male flower development. During new leaf growth, flavonoid and flavonol biosynthesis were initiated. Additionally, the flavonoids, 3',5'-hydroxylase (F3'5'H), flavonoids 3'-hydroxylase, were upregulated, which may cause the pale yellow phenotype. Based on these data, it can be concluded that inter-sex differentially expressed genes (DEGs) and specific SNP loci may be associated with sex determination in T. fortunei.
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