1
|
Chen P, Ye C, Huang Y, Xu B, Wu T, Dong Y, Jin Y, Zhao L, Hu C, Mao J, Wu R. Glutaminolysis regulates endometrial fibrosis in intrauterine adhesion via modulating mitochondrial function. Biol Res 2024; 57:13. [PMID: 38561846 PMCID: PMC10983700 DOI: 10.1186/s40659-024-00492-3] [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: 08/24/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Endometrial fibrosis, a significant characteristic of intrauterine adhesion (IUA), is caused by the excessive differentiation and activation of endometrial stromal cells (ESCs). Glutaminolysis is the metabolic process of glutamine (Gln), which has been implicated in multiple types of organ fibrosis. So far, little is known about whether glutaminolysis plays a role in endometrial fibrosis. METHODS The activation model of ESCs was constructed by TGF-β1, followed by RNA-sequencing analysis. Changes in glutaminase1 (GLS1) expression at RNA and protein levels in activated ESCs were verified experimentally. Human IUA samples were collected to verify GLS1 expression in endometrial fibrosis. GLS1 inhibitor and glutamine deprivation were applied to ESCs models to investigate the biological functions and mechanisms of glutaminolysis in ESCs activation. The IUA mice model was established to explore the effect of glutaminolysis inhibition on endometrial fibrosis. RESULTS We found that GLS1 expression was significantly increased in activated ESCs models and fibrotic endometrium. Glutaminolysis inhibition by GLS1 inhibitor bis-2-(5-phenylacetamido-1,2,4-thiadiazol-2-yl) ethyl sulfide (BPTES or glutamine deprivation treatment suppressed the expression of two fibrotic markers, α-SMA and collagen I, as well as the mitochondrial function and mTORC1 signaling in ESCs. Furthermore, inhibition of the mTORC1 signaling pathway by rapamycin suppressed ESCs activation. In IUA mice models, BPTES treatment significantly ameliorated endometrial fibrosis and improved pregnancy outcomes. CONCLUSION Glutaminolysis and glutaminolysis-associated mTOR signaling play a role in the activation of ESCs and the pathogenesis of endometrial fibrosis through regulating mitochondrial function. Glutaminolysis inhibition suppresses the activation of ESCs, which might be a novel therapeutic strategy for IUA.
Collapse
Affiliation(s)
- Pei Chen
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Chaoshuang Ye
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Yunke Huang
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Bingning Xu
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Tianyu Wu
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Yuanhang Dong
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Yang Jin
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Li Zhao
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Changchang Hu
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Jingxia Mao
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
| | - Ruijin Wu
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China.
| |
Collapse
|
2
|
Tang Q, Xu Y, Gao F, Xu Y, Cheng C, Deng C, Chen J, Yuan X, Zhang X, Su J. Transcriptomic and metabolomic analyses reveal the differential accumulation of phenylpropanoids and terpenoids in hemp autotetraploid and its diploid progenitor. BMC PLANT BIOLOGY 2023; 23:616. [PMID: 38049730 PMCID: PMC10696708 DOI: 10.1186/s12870-023-04630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Cannabis sativa, a dioecious plant that has been cultivated worldwide for thousands of years, is known for its secondary metabolites, especially cannabinoids, which possess several medicinal effects. In this study, we investigated the autopolyploidization effects on the biosynthesis and accumulation of these metabolites, transcriptomic and metabolomic analyses were performed to explore the gene expression and metabolic variations in industrial hemp autotetraploids and their diploid progenitors. RESULTS Through these analyses, we obtained 1,663 differentially expressed metabolites and 1,103 differentially expressed genes. Integrative analysis revealed that phenylpropanoid and terpenoid biosynthesis were regulated by polyploidization. No substantial differences were found in the cannabidiol or tetrahydrocannabinol content between tetraploids and diploids. Following polyploidization, some transcription factors, including nine bHLH and eight MYB transcription factors, affected the metabolic biosynthesis as regulators. Additionally, several pivotal catalytic genes, such as flavonol synthase/flavanone 3-hydroxylase, related to the phenylpropanoid metabolic pathway, were identified as being modulated by polyploidization. CONCLUSIONS This study enhances the overall understanding of the impact of autopolyploidization in C. sativa and the findings may encourage the application of polyploid breeding for increasing the content of important secondary metabolites in industrial hemp.
Collapse
Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Feng Gao
- Yunnan Academy of Industrial Hemp, Kunming, 650214, Yunnan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Jiquan Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Xiaoge Yuan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Xiaoyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China.
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China.
| |
Collapse
|
3
|
Sun H, Wang J, Li H, Li T, Gao Z. Advancements and challenges in bamboo breeding for sustainable development. TREE PHYSIOLOGY 2023; 43:1705-1717. [PMID: 37471643 DOI: 10.1093/treephys/tpad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Bamboo is a highly renewable biomass resource with outstanding ecological, economic and social benefits. However, its lengthy vegetative growth stage and uncertain flowering period have hindered the application of traditional breeding methods. In recent years, significant progress has been made in bamboo breeding. While technical advances in bamboo breeding have been impressive, it is essential to also consider the broader implications we can learn from bamboo's extraordinary features for sustainable development. This review provides an overview of the current status of bamboo breeding technology, including a detailed history of bamboo breeding divided into four eras, a comprehensive map of bamboo germplasm gardens worldwide, with a focus on China, and a summary of available transgenic technologies for gene function verification and genetic improvement. As the demand for bamboo as a sustainable and renewable resource increases continuously, breeding objectives should be focused on enhancing yield, wood properties and adaptability to diverse environmental conditions. In particular, priority should be given to improving fiber length, internode length and wall thickness, as well as regulating lignin and cellulose content for papermaking, substitute for plastic and other applications. Furthermore, we highlight the challenges and opportunities for future research and development in bamboo breeding, including the application of omics technologies, artificial intelligence and the development of new breeding methods. Finally, by integrating the technical advances in bamboo breeding with a discussion of its broader implications for sustainable development, this review provides a comprehensive framework for the development of bamboo industry.
Collapse
Affiliation(s)
- Huayu Sun
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Jiangfei Wang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Hui Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Tiankuo Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| |
Collapse
|
4
|
Li C, Mao B, Wang K, Xu L, Fan L, Wang Y, Li Y, Ma Y, Wang L, Liu L. RsERF40 contributes to cold stress tolerance and cell expansion of taproot in radish ( Raphanus sativus L.). HORTICULTURE RESEARCH 2023; 10:uhad013. [PMID: 36968181 PMCID: PMC10031735 DOI: 10.1093/hr/uhad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of taproots are inhibited by cold stress in radish (Raphanus sativus L.). Ethylene-responsive element binding factors (ERF) are key participators in the cold stress response and growth regulation of plants. However, the function of ERF genes in cold tolerance and root development in radish remains elusive. Here, we showed that the secondary growth of radish taproots was inhibited by cold stress. Comparative transcriptome analysis demonstrated that the RsERF40 gene is an important regulator of the cold stress response and root growth regulation. The cold tolerance of transgenic Arabidopsis plants overexpressing the RsERF40 gene was significantly improved. Overexpressing RsERF40 in the cold-sensitive radish genotype and silencing RsERF40 in the cold-tolerant radish genotype indicated that RsERF40 was beneficial for alleviating oxidative damage under cold stress in radish. Transgenic Arabidopsis seedlings showed an increase in the elongation and radial growth of dark-grown roots. RT-qPCR analysis showed that the expression of the cold-related genes (CORs) RsCOR78 and RsCOR413PM1 and the cell wall strengthening-related genes RsCESA6 and RsEXPB3 was upregulated in transgenic Arabidopsis seedlings. Yeast one-hybrid (Y1H) and dual-luciferase reporter assays (DLA) revealed that RsERF40 directly regulates RsCOR78, RsCOR413PM1, RsCESA6 and RsEXPB3 expression, illustrating that RsERF40 enhances cold tolerance and taproot growth by modulating osmotic adjustment and cell wall mechanical strength in radish. In this study, the RsERF40-regulon was firstly found to be a new cold response pathway independent of the CBF-COR pathway conferring cold stress tolerance with increasing radish taproot growth. These results provided novel insight into the molecular mechanism underlying cold stress response and would facilitate the genetic improvement of cold tolerance in radish and other root vegetable crops.
Collapse
Affiliation(s)
- Cui Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Baozhen Mao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yinbo Ma
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lun Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | | |
Collapse
|
5
|
Buono D, Albach DC. Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11516. [PMID: 37051581 PMCID: PMC10083463 DOI: 10.1002/aps3.11516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 12/20/2022] [Indexed: 06/19/2023]
Abstract
PREMISE Polyploidy has become a central factor in plant evolutionary biological research in recent decades. Methods such as flow cytometry have revealed the widespread occurrence of polyploidy; however, its inference relies on expensive lab equipment and is largely restricted to fresh or recently dried material. METHODS Here, we assess the applicability of infrared spectroscopy to infer ploidy in two related species of Veronica (Plantaginaceae). Infrared spectroscopy relies on differences in the absorbance of tissues, which could be affected by primary and secondary metabolites related to polyploidy. We sampled 33 living plants from the greenhouse and 74 herbarium specimens with ploidy known through flow cytometrical measurements and analyzed the resulting spectra using discriminant analysis of principal components (DAPC) and neural network (NNET) classifiers. RESULTS Living material of both species combined was classified with 70% (DAPC) to 75% (NNET) accuracy, whereas herbarium material was classified with 84% (DAPC) to 85% (NNET) accuracy. Analyzing both species separately resulted in less clear results. DISCUSSION Infrared spectroscopy is quite reliable but is not a certain method for assessing intraspecific ploidy level differences in two species of Veronica. More accurate inferences rely on large training data sets and herbarium material. This study demonstrates an important way to expand the field of polyploid research to herbaria.
Collapse
Affiliation(s)
- Daniele Buono
- AG Plant Biodiversity and EvolutionCarl von Ossietzky UniversityAmmerlaender Heerstrasse 114‐11826129OldenburgGermany
- Institute of BotanyTechnical University of DresdenObergraben 601097DresdenGermany
- Present address:
Systematik, Biodiversität und Evolution der PflanzenLudwig‐Maximilians‐UniversityMenzinger Str. 6780638MunichGermany
| | - Dirk C. Albach
- AG Plant Biodiversity and EvolutionCarl von Ossietzky UniversityAmmerlaender Heerstrasse 114‐11826129OldenburgGermany
| |
Collapse
|
6
|
Valenzuela F, D’Afonseca V, Hernández R, Gómez A, Arencibia AD. Validation of Reference Genes in a Population of Blueberry (Vaccinium corymbosum) Plants Regenerated in Colchicine. PLANTS (BASEL, SWITZERLAND) 2022; 11:2645. [PMID: 36235509 PMCID: PMC9573746 DOI: 10.3390/plants11192645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
For the first time we report the validation of reference genes in plants from a population of blueberry (Vaccinium corymbosum) clones cultured in vitro on a colchicine-supplemented medium. Nodal segment explants of the cultivar Duke were regenerated by organogenesis under different periods of colchicine 1 mg/L exposure (1, 2, 3, 5, 30 days). The clones selected for the study showed variability for phenotypic traits after 2 years of adaptation to field conditions, compared to plants of the donor genotype that were regenerated on a medium without colchicine. Vaccinium myrtillus (GAPDH) and Vaccinium macrocarpon (ATP1, NADH, RPOB and COX2) were used as reference genomes for primer design. The results show that colchicine treatments can cause genomic changes in blueberry plants. At the molecular level, exposure of plants to colchicine in early periods could promote an increase in gene expression of specific genes such as ATP1, COX2, GAPDH, MATK, NADH and RPOB. However, prolonged exposure (30 days) could decrease gene expression of the genes studied. For qPCR assays, the primers designed for ATP1, COX2, GAPDH and MATK genes showed high efficiency. In addition, the GAPDH, ATP1, NADH and COX2 genes showed high stability and could be recommended as potential reference genes for gene expression assays in Vaccinium.
Collapse
Affiliation(s)
- Francisca Valenzuela
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Vivían D’Afonseca
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Ricardo Hernández
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
- Doctorado en Biotecnología Traslacional. Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Aleydis Gómez
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Ariel D. Arencibia
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| |
Collapse
|
7
|
Zheng Y, Yang D, Rong J, Chen L, Zhu Q, He T, Chen L, Ye J, Fan L, Gao Y, Zhang H, Gu L. Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:649-670. [PMID: 34990066 DOI: 10.1111/jipb.13217] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/04/2022] [Indexed: 05/25/2023]
Abstract
Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing techniques are available for D. latiflorus, enabling reverse genetic approaches. Thus, D. latiflorus has the potential to be a model bamboo species. However, the genome sequence of D. latiflorus has remained unreported due to its polyploidy and large genome size. Here, we sequenced the D. latiflorus genome and assembled it into three allele-aware subgenomes (AABBCC), representing the largest genome of a major bamboo species. We assembled 70 allelic chromosomes (2, 737 Mb) for hexaploid D. latiflorus using both single-molecule sequencing from the Pacific Biosciences (PacBio) Sequel platform and chromosome conformation capture sequencing (Hi-C). Repetitive sequences comprised 52.65% of the D. latiflorus genome. We annotated 135 231 protein-coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome sequencing using RNA-Seq and PacBio single-molecule real-time long-read isoform sequencing revealed highly differential alternative splicing (AS) between non-abortive and abortive shoots, suggesting that AS regulates the abortion rate of bamboo shoots. This high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.
Collapse
Affiliation(s)
- Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jundong Rong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liguang Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiang Zhu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tianyou He
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingyan Chen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Ye
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lili Fan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| |
Collapse
|
8
|
Tavan M, Sarikhani H, Mirjalili MH, Rigano MM, Azizi A. Triterpenic and phenolic acids production changed in Salvia officinalis via in vitro and in vivo polyploidization: A consequence of altered genes expression. PHYTOCHEMISTRY 2021; 189:112803. [PMID: 34144408 DOI: 10.1016/j.phytochem.2021.112803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 05/02/2023]
Abstract
The induction of polyploidy is an efficient technique for creating a diversity of genetic, phenotypic, and phytochemical novelties in plant taxa. Sage (Salvia officinalis L.) is a well-known medicinal plant rich of valuable bioactive molecules such as triterpenic and phenolic acids. In the present study, the effect of in vitro and in vivo polyploidization on morphological characteristics, anatomical structures, phytochemical traits, and expression level of the genes involved in the biosynthesis of major triterpenic acids (ursolic, betulinic, and oleanolic acids) of the plant was studied. The sterile seeds treated with different concentrations (0, 0.05, 0.1, and 0.2%) of colchicine for 24 and 48 h were considered for polyploidy induction. Flow cytometry and chromosome counting were used to confirm the ploidy level of diploid (2n = 2x = 14, 2C DNA = 1.10 pg) and tetraploid (2n = 4x = 28, 2C DNA = 2.12 pg) plants after seven months. The highest polyploidy induction was obtained by applying 0.1% (w/v) colchicine for 48 h with an efficiency of 19.05% in vitro tetraploidy. Polyploids showed differences in leaf shape and color, leaf and stem thickness, trichrome density, root length, plant height, and number of leaves compared to diploid plants. There was also a significant decrease in rosmarinic acid content in polyploid (plants) as compared to diploid plants. Although a significant decrease in ursolic acid content was observed in polyploids, betulinic acid content associated with the expression levels of genes encoding enzymes being active in triterpene biosynthesis such as squalene epoxidase (SQE) and lupeol synthase (LUS). The expression of SQE and LUS was significantly increased in in vitro tertaploids (2.9-fold) and in vivo mixoploids (2.4-fold). The results confirm the idea that induced polyploidy can randomly alter breeding traits of plants as well as the content of bioactive compounds.
Collapse
Affiliation(s)
- Mansoureh Tavan
- Department of Horticultural Science, Faculty of Agriculture, Bu Ali Sina University, 65174, Hamedan, Iran.
| | - Hassan Sarikhani
- Department of Horticultural Science, Faculty of Agriculture, Bu Ali Sina University, 65174, Hamedan, Iran.
| | - Mohammad Hossein Mirjalili
- Department of Agriculture, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, 1983969411, Tehran, Iran.
| | - Maria Manuela Rigano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Naples, Italy.
| | - Ali Azizi
- Department of Horticultural Science, Faculty of Agriculture, Bu Ali Sina University, 65174, Hamedan, Iran.
| |
Collapse
|
9
|
Todd RT, Selmecki A. Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs. eLife 2020; 9:e58349. [PMID: 32687060 PMCID: PMC7371428 DOI: 10.7554/elife.58349] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Previously, we identified long repeat sequences that are frequently associated with genome rearrangements, including copy number variation (CNV), in many diverse isolates of the human fungal pathogen Candida albicans (Todd et al., 2019). Here, we describe the rapid acquisition of novel, high copy number CNVs during adaptation to azole antifungal drugs. Single-cell karyotype analysis indicates that these CNVs appear to arise via a dicentric chromosome intermediate and breakage-fusion-bridge cycles that are repaired using multiple distinct long inverted repeat sequences. Subsequent removal of the antifungal drug can lead to a dramatic loss of the CNV and reversion to the progenitor genotype and drug susceptibility phenotype. These findings support a novel mechanism for the rapid acquisition of antifungal drug resistance and provide genomic evidence for the heterogeneity frequently observed in clinical settings.
Collapse
Affiliation(s)
- Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
| |
Collapse
|