1
|
Salık Y, Eroglu P, Zengin G, Binzet R. Assessment and comparison of phytochemical constituents and biological activities of endemic Odonterrhena floribunda (Brassicaceae) from Türkiye. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-12. [PMID: 39219065 DOI: 10.1080/09603123.2024.2393433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
This study aimed to evaluate the phenolic profile, antioxidant, antibacterial, and antidiabetic properties of ethanolic and methanolic extracts of the different parts of the endemic Odontarrhena floribunda. The antioxidant activities of O. floribunda were determined with 1,1-diphenyl-1-picrylhydrazyl (DPPH) and the copper-reducing antioxidant capacity (CUPRAC) assays. The strongest antioxidant activity was recorded in methanolic root extract (IC50:1.68±0.25 μg/mL) for DPPH and ethanolic root (λ450:0.68±0.20) extract for CUPRAC. Antibacterial activities of the extracts were displayed by the Resazurin Microplate Method (REMA). All plant extracts analyzed demonstrated stronger effects on Acinetobacter baumannii (ATCC 02026) than those of the standard compound. The in vitro α-amylase and α-glucosidase inhibitory of the plant extract were assessed using the Iodine method. Except for the methanol leaf extract, all other extracts showed strong α-glucosidase inhibitory activity (0.88-2.13 mmolTE/g). These results show that this endemic O. floribunda is a potential natural antioxidant, antibacterial, and enzyme inhibitor source.
Collapse
Affiliation(s)
- Yasemin Salık
- Department of Chemistry, Faculty of Science, Mersin University, Mersin, Türkiye
| | - Pelin Eroglu
- Department of Chemistry, Faculty of Science, Mersin University, Mersin, Türkiye
| | - Gökhan Zengin
- Physiology and Biochemistry Research Laboratory, Department of Biology, Faculty of Science, Selcuk University, Konya, Türkiye
| | - Rıza Binzet
- Department of Biology, Faculty of Science, Mersin University, Mersin, Türkiye
| |
Collapse
|
2
|
Guo C, Liu Y, Fu H, Zhang X, Li M. Effect of cruciferous vegetable intake on cancer: An umbrella review of meta-analysis. J Food Sci 2024. [PMID: 39138635 DOI: 10.1111/1750-3841.17300] [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: 03/07/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/15/2024]
Abstract
Previous systematic evaluations and meta-analyses of the relationship between cruciferous vegetable (CV) intake and cancer risk have yielded inconsistent results. Herein, we summarize and evaluate the existing data and examine the relationship between CV intake and cancer risk. We searched four databases for cancer risk as a key outcome indicator. AMSTAR-2 was used to evaluate the methodological quality of the included systematic reviews, PRISMA 2020 was used to evaluate the report quality, and corrected coverage area analysis was used to evaluate the duplication rate of the original documents. Overall, 22 meta-analyses involving 175 independent cancer studies were included. Evidence on lung, gastric, prostate, breast, endometrial, and ovarian cancer, as well as renal cell carcinoma, suggests a potential association between cancer and CV intake, which influences the risk of various cancers. Future research should focus on improving methods and techniques, controlling influencing factors, elucidating underlying mechanisms, and improving evidence quality to demonstrate the association between CV intake and cancer. The potential role of dietary CVs in cancer control has implications for public health policies.
Collapse
Affiliation(s)
- Chunyan Guo
- College of Pharmacy, Qiqihar Medical University, Qiqihar, China
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, China
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot, China
| | - Yibo Liu
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, China
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot, China
- Inner Mongolia Medical University, Hohhot, China
| | - Haiqi Fu
- Inner Mongolia Medical University, Hohhot, China
| | - Xinyu Zhang
- Inner Mongolia Medical University, Hohhot, China
| | - Minhui Li
- College of Pharmacy, Qiqihar Medical University, Qiqihar, China
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, China
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot, China
- Inner Mongolia Medical University, Hohhot, China
| |
Collapse
|
3
|
Li X, Wang Y, Cai C, Ji J, Han F, Zhang L, Chen S, Zhang L, Yang Y, Tang Q, Bucher J, Wang X, Yang L, Zhuang M, Zhang K, Lv H, Bonnema G, Zhang Y, Cheng F. Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea. Nat Genet 2024; 56:517-529. [PMID: 38351383 PMCID: PMC10937405 DOI: 10.1038/s41588-024-01655-4] [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: 06/16/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024]
Abstract
Brassica oleracea, globally cultivated for its vegetable crops, consists of very diverse morphotypes, characterized by specialized enlarged organs as harvested products. This makes B. oleracea an ideal model for studying rapid evolution and domestication. We constructed a B. oleracea pan-genome from 27 high-quality genomes representing all morphotypes and their wild relatives. We identified structural variations (SVs) among these genomes and characterized these in 704 B. oleracea accessions using graph-based genome tools. We show that SVs exert bidirectional effects on the expression of numerous genes, either suppressing through DNA methylation or promoting probably by harboring transcription factor-binding elements. The following examples illustrate the role of SVs modulating gene expression: SVs promoting BoPNY and suppressing BoCKX3 in cauliflower/broccoli, suppressing BoKAN1 and BoACS4 in cabbage and promoting BoMYBtf in ornamental kale. These results provide solid evidence for the role of SVs as dosage regulators of gene expression, driving B. oleracea domestication and diversification.
Collapse
Affiliation(s)
- Xing Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengcheng Cai
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yinqing Yang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Tang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xuelin Wang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| |
Collapse
|
4
|
Marzouk MM, Hegazi NM, El Shabrawy MOA, Farid MM, Kawashty SA, Hussein SR, Saleh NAM. Discriminative Metabolomics Analysis and Cytotoxic Evaluation of Flowers, Leaves, and Roots Extracts of Matthiola longipetala subsp. livida. Metabolites 2023; 13:909. [PMID: 37623853 PMCID: PMC10456503 DOI: 10.3390/metabo13080909] [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: 06/28/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Matthiola longipetala subsp. livida is an annual herb in Brassicaceae that has received little attention despite the family's high reputation for health benefits, particularly cancer prevention. In this study, UPLC-HRMS-MS analysis was used for mapping the chemical constituents of different plant parts (i.e., flowers, leaves, and roots). Also, spectral similarity networks via the Global Natural Products Social Molecular Networking (GNPS) were employed to visualize their chemical differences and similarities. Additionally, the cytotoxic activity on HCT-116, HeLa, and HepG2 cell lines was evaluated. Throughout the current analysis, 154 compounds were annotated, with the prevalence of phenolic acids, glucosinolates, flavonol glucosides, lipids, peptides, and others. Predictably, secondary metabolites (phenolic acids, flavonoids, and glucosinolates) were predominant in flowers and leaves, while the roots were characterized by primary metabolites (peptides and fatty acids). Four diacetyl derivatives tentatively assigned as O-acetyl O-malonyl glucoside of quercetin (103), kaempferol (108 and 112), and isorhamnetin (114) were detected for the first time in nature. The flowers and leaves extracts showed significant inhibition of HeLa cell line propagation with LC50 values of 18.1 ± 0.42 and 29.6 ± 0.35 µg/mL, respectively, whereas the flowers extract inhibited HCT-116 with LC50 24.8 ± 0.45 µg/mL, compared to those of Doxorubicin (26.1 ± 0.27 and 37.6 ± 0.21 µg/mL), respectively. In conclusion, the flowers of M. longipetala are responsible for the abundance of bioactive compounds with cytotoxic properties.
Collapse
Affiliation(s)
- Mona M. Marzouk
- Phytochemistry and Plant Systematics Department, Division of Pharmaceutical Industries, National Research Centre, Cairo P.O. Box 12622, Egypt; (N.M.H.); (M.O.A.E.S.); (M.M.F.); (S.A.K.); (S.R.H.); (N.A.M.S.)
| | | | | | | | | | | | | |
Collapse
|
5
|
Zhang K, Yang Y, Zhang X, Zhang L, Fu Y, Guo Z, Chen S, Wu J, Schnable JC, Yi K, Wang X, Cheng F. The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits. PLANT COMMUNICATIONS 2023; 4:100431. [PMID: 36071668 PMCID: PMC10030322 DOI: 10.1016/j.xplc.2022.100431] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/09/2022] [Accepted: 08/24/2022] [Indexed: 05/04/2023]
Abstract
Orychophragmus violaceus, referred to as "eryuelan" (February orchid) in China, is an early-flowering ornamental plant. The high oil content and abundance of unsaturated fatty acids in O. violaceus seeds make it a potential high-quality oilseed crop. Here, we generated a whole-genome assembly for O. violaceus using Nanopore and Hi-C sequencing technologies. The assembled genome of O. violaceus was ∼1.3 Gb in size, with 12 pairs of chromosomes. Through investigation of ancestral genome evolution, we determined that the genome of O. violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype. Comparisons between the reconstructed subgenomes of O. violaceus identified indicators of subgenome dominance, indicating that subgenomes likely originated via allotetraploidy. O. violaceus was phylogenetically close to the Brassica genus, and tetraploidy in O. violaceus occurred approximately 8.57 million years ago, close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage. However, the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica, as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks. Moreover, identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O. violaceus. These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O. violaceus.
Collapse
Affiliation(s)
- Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Yinqing Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Xin Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Yu Fu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Zhongwei Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Shumin Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA.
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China.
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China.
| |
Collapse
|
6
|
Zandberg JD, Fernandez CT, Danilevicz MF, Thomas WJW, Edwards D, Batley J. The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics. PLANTS (BASEL, SWITZERLAND) 2022; 11:2740. [PMID: 36297764 PMCID: PMC9610009 DOI: 10.3390/plants11202740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by >450 fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements.
Collapse
Affiliation(s)
- Jaco D. Zandberg
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | | | - Monica F. Danilevicz
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - William J. W. Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- Center for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| |
Collapse
|
7
|
Wu J, Liang J, Lin R, Cai X, Zhang L, Guo X, Wang T, Chen H, Wang X. Investigation of Brassica and its relative genomes in the post-genomics era. HORTICULTURE RESEARCH 2022; 9:uhac182. [PMID: 36338847 PMCID: PMC9627752 DOI: 10.1093/hr/uhac182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/07/2022] [Indexed: 06/16/2023]
Abstract
The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.
Collapse
Affiliation(s)
| | | | | | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Lei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xinlei Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Tianpeng Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | | |
Collapse
|
8
|
Liu SY, Ren ZT, Zhao CY, Hu CX, Wang HC. Hemilophiacardiocarpa (Brassicaceae), a new species from Yunnan, southwest China. PHYTOKEYS 2022; 194:95-103. [PMID: 35586325 PMCID: PMC9038854 DOI: 10.3897/phytokeys.194.82737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
Hemilophiacardiocarpa (Brassicaceae), the sixth species of the Chinese endemic genus Hemilophia, is described and illustrated. This plant is found in the Jiaozishan Mountains in Dongchuan District, northern Yunnan, southwest China. Morphologically, it shows close relationships with H.rockii and H.pulchella, but differs from it in the leaf shape and size, inflorescence, flower size, shape of fruit and length of its pedicel. An updated key to the taxa of Hemilophia is provided.
Collapse
Affiliation(s)
- Shao-Yun Liu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, Yunnan, ChinaYunnan UniversityKunmingChina
| | - Zheng-Tao Ren
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, Yunnan, ChinaYunnan UniversityKunmingChina
| | - Chang-You Zhao
- Management Bureau of Yunnan Jiaozishan National Natural Reserve, Luquan, 651515, Yunnan, ChinaManagement Bureau of Yunnan Jiaozishan National Natural ReserveLuquanChina
| | - Chun-Xiang Hu
- Management Bureau of Yunnan Jiaozishan National Natural Reserve, Luquan, 651515, Yunnan, ChinaManagement Bureau of Yunnan Jiaozishan National Natural ReserveLuquanChina
| | - Huan-Chong Wang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, Yunnan, ChinaYunnan UniversityKunmingChina
- Herbarium of Yunnan University, Kunming 650091, Yunnan, ChinaHerbarium of Yunnan UniversityKunmingChina
| |
Collapse
|
9
|
Chen H, Wang T, He X, Cai X, Lin R, Liang J, Wu J, King G, Wang X. BRAD V3.0: an upgraded Brassicaceae database. Nucleic Acids Res 2022; 50:D1432-D1441. [PMID: 34755871 PMCID: PMC8728314 DOI: 10.1093/nar/gkab1057] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.
Collapse
Affiliation(s)
- Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Tianpeng Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Xiaoning He
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Graham King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| |
Collapse
|
10
|
Francis A, Lujan-Toro BE, Warwick SI, Macklin JA, Martin SL. Update on the Brassicaceae species checklist. Biodivers Data J 2021; 9:e58773. [PMID: 33716543 PMCID: PMC7952366 DOI: 10.3897/bdj.9.e58773] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/13/2021] [Indexed: 11/16/2022] Open
Abstract
Background Here we present a revised species checklist for the Brassicaceae, updated from Warwick SI, Francis, A, Al-Shehbaz IA (2006), Brassicaceae: Species checklist and database on CD-ROM, Plant Systematics and Evolution 259: 249─25. This update of the checklist was initiated, based on recent taxonomic and molecular studies on the Brassicaceae that have resulted in new species names, combinations and associated synonyms. New information New data have been added indicating tribal affiliations within the family and where type specimens have been designated. In addition, information from many early publications has been checked and added to the database. The database now includes information on 14983 taxa, 4636 of which are currently accepted and divided into 340 genera and 52 tribes. A selected bibliography of recent publications on the Brassicaceae is included.
Collapse
Affiliation(s)
- Ardath Francis
- Agriculture and Agri-Food Canada, Ottawa, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - Beatriz E Lujan-Toro
- Agriculture and Agri-Food Canada, Ottawa, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - Suzanne I Warwick
- Agriculture and Agri-Food Canada, Ottawa, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - James A Macklin
- Agriculture and Agri-Food Canada, Ottawa, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - Sara L Martin
- Agriculture and Agri-Food Canada, Ottawa, Canada Agriculture and Agri-Food Canada Ottawa Canada
| |
Collapse
|