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Yang W, Jiang T, Wang Y, Wang X, Wang R. Combined Transcriptomics and Metabolomics Analysis Reveals the Effect of Selenium Fertilization on Lycium barbarum Fruit. Molecules 2023; 28:8088. [PMID: 38138577 PMCID: PMC10745541 DOI: 10.3390/molecules28248088] [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: 09/17/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
As a beneficial nutrient and essential trace element, selenium plays a significant role in plant growth functions and human protein biosynthesis. Plant selenium enrichment is mainly obtained from both natural soil and exogenous selenium supplementation, while human beings consume selenium-enriched foods for the purposes of selenium supplementation. In this study, different types of selenium fertilizers were sprayed onto Lycium barbarum in Ningxia, and transcriptomics and metabolomics techniques were used to explore the effects of selenium on the fruit differentials and differential genes in Lycium barbarum. Taking the "Ning Qiyi No.1" wolfberry as the research object, sodium selenite, nano-selenium, and organic selenium were sprayed at a concentration of 100 mg·L-1 three times from the first fruiting period to the harvesting period, with a control treatment comprising the spraying of clear water. We determined the major metabolites and differential genes of the amino acids and derivatives, flavonoids, and alkaloids in ripe wolfberries. We found that spraying selenium significantly enhanced the Lycium barbarum metabolic differentiators; the most effective spray was the organic selenium, with 129 major metabolic differentiators and 10 common metabolic pathways screened after spraying. Nano-selenium was the next best fertilizer we screened, with 111 major metabolic differentiators, the same number as organic selenium in terms of differential genes and common metabolite pathways. Sodium selenite was the least effective of the three, with only 59 of its major metabolic differentials screened, but its differential genes and metabolites were enriched for five common pathways.
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Affiliation(s)
- Wenqin Yang
- College of Agronomy, Ningxia University, Yinchuan 750021, China; (W.Y.); (T.J.); (Y.W.)
| | - Tingting Jiang
- College of Agronomy, Ningxia University, Yinchuan 750021, China; (W.Y.); (T.J.); (Y.W.)
| | - Yaqi Wang
- College of Agronomy, Ningxia University, Yinchuan 750021, China; (W.Y.); (T.J.); (Y.W.)
| | - Xiaojing Wang
- Ningxia Research Institute of Quality Standards and Testing Technology of Agricultural Products, Yinchuan 750001, China
| | - Rui Wang
- College of Agronomy, Ningxia University, Yinchuan 750021, China; (W.Y.); (T.J.); (Y.W.)
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2
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Genetic diversity of the Chinese medicinal plant Astragali Radix based on transcriptome-derived SSR markers. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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3
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Yang W, Bai Z, Wang F, Zou M, Wang X, Xie J, Zhang F. Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers. BMC Genomics 2022; 23:597. [PMID: 35974306 PMCID: PMC9382759 DOI: 10.1186/s12864-022-08832-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Monochasma savatieri Franch. ex Maxim is a medicinally valuable herb. However, the collection and protection of the wild germplasm resources of M. savatieri are still insufficient, and their genetic diversity and population structure have been poorly studied. Results We collected and examined 46 M. savatieri individuals from Fujian, Hunan, Jiangxi, and Zhejiang provinces for genetic diversity and population structure, using 33 newly developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. Applying these markers, we detected a total of 208 alleles, with an average of 6.303 alleles per locus. The polymorphic information content varied from 0.138 to 0.884 (average: 0.668), indicating a high level of polymorphism. At the population level, there was a low degree of genetic diversity among populations (I = 0.535, He = 0.342), with Zhejiang individuals showing the highest genetic diversity among the four populations (Fst = 0.497), which indicated little gene flow within the M. savatieri populations (Nm = 0.253). Mantel test analysis revealed a significant positive correlation between geographical and genetic distance among populations (R2 = 0.3304, p < 0.05), and structure and principal coordinate analyses supported classification of populations into three clusters, which was consistent with the findings of cluster analysis. Conclusions As a rare medicinal plants, the protection of M. savatieri does not look optimistic, and accordingly, protective efforts should be beefed up on the natural wild populations. This study provided novel tools and insights for designing effective collection and conservation strategies for M. savatieri. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08832-x.
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Affiliation(s)
- Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhiyi Bai
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fuqiang Wang
- Yichun Academy of Sciences, Yichun, 336000, China
| | - Mingzhu Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xinru Wang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
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4
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Zhang Y, Liu X, Li Y, Liu X, Ma H, Qu S, Li Z. Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of Luculia yunnanensis, an Endangered Species Endemic to Yunnan, Southwestern China. PLANTS 2022; 11:plants11091204. [PMID: 35567204 PMCID: PMC9104135 DOI: 10.3390/plants11091204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]
Abstract
Luculia yunnanensis (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence of climate change and human factors, the distribution range of L. yunnanensis has exhibited a significant shrinking trend, and it has become a vulnerable species that is in urgent need of conservation and rational utilization research. In this study, the flower transcriptome sequencing of L. yunnanensis was conducted using an Illumina HiSeq platform. We designed and developed a series of EST-SSR primers based on the flower transcriptome data of L. yunnanensis. The results showed that 98,389 unigenes were obtained from the L. yunnanensis flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. The MISA (Microsatellite) tool was used to identify SSR loci from all unigenes, and a total of 15,384 SSRs were identified. Repeat motifs were given priority with mononucleotides, dinucleotides, and trinucleotides. The 81 primer pairs were synthesized randomly, of which 44 pairs showed effective amplification. A total of 17 primers showed stable amplification, and rich polymorphism was observed in 6 populations. We concluded via genetic diversity analysis that the average effective number of alleles (Ne), Shannon’s information index (I), and polymorphism information content (PIC) were 1.925, 0.837, and 0.403, respectively. In conclusion, 17 EST-SSR primers can be used for subsequent population genetic diversity analysis and molecular-marker-assisted breeding, which is of great significance for formulating resource conservation and utilization strategies for L. yunnanensis.
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Affiliation(s)
- Yao Zhang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (Y.Z.); (X.L.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Xi Liu
- School of Geography and Ecotourism, Southwest Forestry University, Kunming 650224, China;
| | - Yuying Li
- College of Grassland Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Xiongfang Liu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (Y.Z.); (X.L.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Hong Ma
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (Y.Z.); (X.L.)
- Key Laboratory of Breeding and Utilization of Resource Insects, National Forestry and Grassland Administration, Kunming 650224, China
- Correspondence: (H.M.); (S.Q.); (Z.L.)
| | - Suping Qu
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
- Correspondence: (H.M.); (S.Q.); (Z.L.)
| | - Zhenghong Li
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (Y.Z.); (X.L.)
- Correspondence: (H.M.); (S.Q.); (Z.L.)
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5
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Gong H, Rehman F, Li Z, Liu J, Yang T, Liu J, Li H, Hu Z, Ma Q, Wu Z, A B, Yang M, Gao H, Zhi H, Qu H, Di D, Wang Y. Discrimination of Geographical Origins of Wolfberry ( Lycium barbarum L.) Fruits Using Stable Isotopes, Earth Elements, Free Amino Acids, and Saccharides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2984-2997. [PMID: 35179024 DOI: 10.1021/acs.jafc.1c06207] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
To develop sophisticated approaches for distinguishing goji origins, 325 wolfberry fruit samples of a certain cultivar, plant age, drying method, and collection season were gathered from 26 producing areas across Northwest China in 2017 and 2018. We employed 49 indices, including stable isotopes, earth elements, soluble amino acids, and saccharides, to identify the regions of origin of these goji fruits. Analysis of variance (ANOVA) and heritability analysis were used to assess the effects of the environment (producing areas), cultivar, plant age, drying process, and collection season. Samples from the same place can be classified and partially discriminated using principal component analysis (PCA). We were able to distinguish fruits produced in Zhongning County from those produced in the other five producing provinces using orthogonal projection to latent structure-discriminant analysis (OPLS-DA). Calcium (Ca), manganese (Mn), ornithine (Orn), cystine (Cys-Cys), glutamate (Glu), phenylalanine (Phe), phosphoserine (Ps), serine (Ser), lysine (Lys), taurine (Tau), proline (Pro), and tyrosine (Tyr) indices were chosen using S-plots and heritability analysis, and their repeatability was established with samples collected in 2018. The indices selected in this study can distinguish goji berries produced in Zhongning County from fruits originating from five other Provinces with high repeatability, which was validated with various cultivars, drying methods, harvest seasons, and plant ages and with heritability analysis.
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Affiliation(s)
- Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Zhong Li
- Bairuiyuan Company, Yinchuan 750000, P. R. China
| | - Jianfei Liu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, P. R. China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Juan Liu
- Zhongning County Goji Industry Development Service Bureau, Zhongwei 755100, Ningxia, P. R. China
| | - Haoran Li
- Zhongning County Goji Industry Development Service Bureau, Zhongwei 755100, Ningxia, P. R. China
| | - Zhongqing Hu
- Zhongning County Goji Industry Development Service Bureau, Zhongwei 755100, Ningxia, P. R. China
| | - Qihu Ma
- Beijing TongRenTang Health-Pharmaceutical (Ningxia) Co., Ltd., Yinchuan 750000, Ningxia, P. R. China
| | - Zhigeng Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Biao A
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Meizhen Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, P. R. China
| | - Hui Zhi
- School of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Hongxia Qu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Duolong Di
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, P. R. China
- Center of Resource Chemical and New Material, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Qingdao 266100, P. R. China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
- Gannan Normal University, Ganzhou, Jinagxi 341000, P. R. China
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6
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Gong H, Rehman F, Ma Y, A B, Zeng S, Yang T, Huang J, Li Z, Wu D, Wang Y. Germplasm Resources and Strategy for Genetic Breeding of Lycium Species: A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:802936. [PMID: 35222468 PMCID: PMC8874141 DOI: 10.3389/fpls.2022.802936] [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: 10/27/2021] [Accepted: 01/07/2022] [Indexed: 06/01/2023]
Abstract
Lycium species (goji), belonging to Solanaceae, are widely spread in the arid to semiarid environments of Eurasia, Africa, North and South America, among which most species have affinal drug and diet functions, resulting in their potential to be a superior healthy food. However, compared with other crop species, scientific research on breeding Lycium species lags behind. This review systematically introduces the present germplasm resources, cytological examination and molecular-assisted breeding progress in Lycium species. Introduction of the distribution of Lycium species around the world could facilitate germplasm collection for breeding. Karyotypes of different species could provide a feasibility analysis of fertility between species. The introduction of mapping technology has discussed strategies for quantitative trait locus (QTL) mapping in Lycium species according to different kinds of traits. Moreover, to extend the number of traits and standardize the protocols of trait detection, we also provide 1,145 potential traits (275 agronomic and 870 metabolic) in different organs based on different reference studies on Lycium, tomato and other Solanaceae species. Finally, perspectives on goji breeding research are discussed and concluded. This review will provide breeders with new insights into breeding Lycium species.
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Affiliation(s)
- Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Ma
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Biao A
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jianguo Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong Li
- Agricultural Comprehensive Development Center in Ningxia Hui Autonomous Region, Yinchuan, China
| | | | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, Gannan Normal University, Ganzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
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7
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Liu H, Zhang Y, Wang Z, Su Y, Wang T. Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences. Front Genet 2021; 12:759557. [PMID: 34868238 PMCID: PMC8635753 DOI: 10.3389/fgene.2021.759557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.
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Affiliation(s)
- Hanjing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuli Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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8
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Abstract
Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.
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Yeast Synthetic Biology for the Production of Lycium barbarum Polysaccharides. Molecules 2021; 26:molecules26061641. [PMID: 33804230 PMCID: PMC8000229 DOI: 10.3390/molecules26061641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
The fruit of Lycium barbarum L. (goji berry) is used as traditional Chinese medicine, and has the functions of immune regulation, anti-tumor, neuroprotection, anti-diabetes, and anti-fatigue. One of the main bioactive components is L. barbarum polysaccharide (LBP). Nowadays, LBP is widely used in the health market, and it is extracted from the fruit of L. barbarum. The planting of L. barbarum needs large amounts of fields, and it takes one year to harvest the goji berry. The efficiency of natural LBP production is low, and the LBP quality is not the same at different places. Goji berry-derived LBP cannot satisfy the growing market demands. Engineered Saccharomyces cerevisiae has been used for the biosynthesis of some plant natural products. Recovery of LBP biosynthetic pathway in L. barbarum and expression of them in engineered S. cerevisiae might lead to the yeast LBP production. However, information on LBP biosynthetic pathways and the related key enzymes of L. barbarum is still limited. In this review, we summarized current studies about LBP biosynthetic pathway and proposed the strategies to recover key enzymes for LBP biosynthesis. Moreover, the potential application of synthetic biology strategies to produce LBP using engineered S. cerevisiae was discussed.
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10
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Shori AB, Ling YH, Baba AS. Effects of
Lycium
barbarum
and fish collagen in cheese on the proteolytic degradation profile with anti‐ACE activity. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Amal Bakr Shori
- Faculty of Science, Department of Biological Sciences King Abdulaziz University Jeddah Saudi Arabia
| | - Yap Huey Ling
- Biomolecular Research Group, Division of Biochemistry, Institute of Biological Sciences, Faculty of Science University of Malaya Kuala Lumpur Malaysia
| | - Ahmad Salihin Baba
- Biomolecular Research Group, Division of Biochemistry, Institute of Biological Sciences, Faculty of Science University of Malaya Kuala Lumpur Malaysia
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11
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Li G, Qin B, Li S, Yin Y, Zhao J, An W, Cao Y, Mu Z. LbNR-Derived Nitric Oxide Delays Lycium Fruit Coloration by Transcriptionally Modifying Flavonoid Biosynthetic Pathway. FRONTIERS IN PLANT SCIENCE 2020; 11:1215. [PMID: 32903673 PMCID: PMC7438876 DOI: 10.3389/fpls.2020.01215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/27/2020] [Indexed: 05/29/2023]
Abstract
Anthocyanin-derived fleshy fruit pigmentation has become an excellent system for studying the regulatory network underlying fruit ripening and quality. The transcriptional control of anthocyanin biosynthesis by MYB-bHLH-WDR complexes has been well established, but the intermediate signals through which the environmental or developmental cues regulate these transcription factors remain poorly understood. Here we found that nitric oxide (NO) production during Lycium fruit ripening decreased progressively presenting a negative relationship with anthocyanins. After cloning of the nitric reductase (NR) gene from Lycium barbarum (LbNR) plants, we demonstrated that LbNR-derived NO partially inhibited anthocyanin biosynthesis but enhanced proanthocyanidin (PA) accumulation, and delayed fruit coloration. Application of the NO donor, sodium nitroprusside (SNP), produced a similar effect. The endogenous or exogenous NO downregulated the transcripts both of the regulatory genes and the structural genes that related to anthocyanin biosynthesis, while upregulated both of those genes that related to PA biosynthesis. Given there is a significant negative relationship between the levels of anthocyanins and PAs during Lycium fruit ripening, NO not only inhibited anthocyanin de novo biosynthesis but redirected the flavonoid biosynthetic pathway from anthocyanins to PA production. Two types of LrMYB transcription factors of opposite nature, namely anthocyanin-specific and PA-specific, which belong to the R2R3-MYB subfamily and 1R-MYB subfamily, respectively, were identified from L. ruthenicum fruits. It was further found that NO acts by antagonizing the ABA signaling, a phytohormone we have previously shown playing a positive role in Lycium fruit coloration. Our results provided particularly novel information about NO-ABA-anthocyanin interplay during Lycium fruit development and ripening, which may fill a gap between the developmental cues and the transcriptional regulation of anthocyanin biosynthesis.
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Affiliation(s)
- Gen Li
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Beibei Qin
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Shuodan Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Yue Yin
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Jianhua Zhao
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Wei An
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Youlong Cao
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Zixin Mu
- College of Life Sciences, Northwest A&F University, Yangling, China
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12
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Zhao J, Li H, Yin Y, An W, Qin X, Wang Y, Fan Y, Li Y, Cao Y. Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns. FEBS Open Bio 2020; 10:1550-1567. [PMID: 32533890 PMCID: PMC7396440 DOI: 10.1002/2211-5463.12910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/27/2020] [Accepted: 06/07/2020] [Indexed: 11/06/2022] Open
Abstract
Goji berries have been used as food and medicine for millennia. Due to their high morphological similarity, fruits of two distinct species belonging to the family Solanaceae, Lycium barbarum (LB) and Lycium chinense (Chinese boxthorn), are usually marketed together as goji berries, but nearly 90% of all commercially available goji berries belong to the former species. A third closely related species, a wild perennial thorny shrub native to north‐western China, Lycium ruthenicum (LR; known as Russian box thorn, and its fruit as black wolfberry), has become a popular choice for combating soil desertification and for alleviating soil salinity/alkalinity due to its high resistance to the harsh environment of saline deserts. Despite the phylogenetic closeness of LB and LR, their fruits are very different. To identify the genes involved in these distinct phenotypes, here we studied expression patterns of 22 transcriptional regulators that may be crucial drivers of these differences during five developmental stages. BAM1 may contribute to higher sugar content in LB. High expression of BFRUCT in ripe LR is likely to be an evolutionary adaptation to fruit ripening in an arid environment. Two arogenate dehydratase paralogues, CHS and LDOX, are probably crucial elements of the mechanism by which LR accumulates much higher levels of anthocyanin. DXS2 (carotenoid accumulation in LB) and CCD4 (carotenoid degradation in ripe LR fruit) may be crucial drivers behind the much higher content of carotenoids in LB. EIL3 and ERF5 are two transcription factors that may contribute to the higher abiotic stress resilience of LR. GATA22‐like appears to have more important roles in growth than ripening in LB fruit and vice versa in LR. HAT5‐like exhibited opposite temporal patterns in two fruits: high in the 1st stage in LB and high in the 5th stage in LR. PED1 was expressed at a much lower level in LR. Finally, we hypothesise that the poorly functionally characterised SCL32 gene may play a part in the increased resistance to environmental stress of LR. We suggest that BAM1, BFRUCT, EIL3, ERF5, ADT paralogues (for functional redundancy), PED1, GATA22‐like, HAT5‐like and SCL32 warrant further functional studies.
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Affiliation(s)
- Jianhua Zhao
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, China
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yue Yin
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, China
| | - Wei An
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, China
| | - Xiaoya Qin
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, China
| | - Yajun Wang
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, China
| | - Yunfang Fan
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, China
| | - Yanlong Li
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, China
| | - Youlong Cao
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, China
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Shori AB, Ming KS, Baba AS. The effects of Lycium barbarum water extract and fish collagen on milk proteolysis and in vitro angiotensin I-converting enzyme inhibitory activity of yogurt. Biotechnol Appl Biochem 2020; 68:221-229. [PMID: 32249982 DOI: 10.1002/bab.1914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 03/25/2020] [Indexed: 12/19/2022]
Abstract
Plain and Lycium barbarum yogurt were made in the presence and absence of fish collagen. Yogurt samples were analyzed for acidification, milk protein proteolysis, angiotensin I-converting enzyme (ACE) inhibitory activity, and sensory evaluation during refrigerated storage for up to 21 days. The o-phthaldialdehyde peptides amount of L. barbarum yogurt both in the presence and absence of fish collagen were significantly increased during 14 days of storage. SDS-PAGE showed improvement in whey proteins degradation of L. barbarum yogurt with/without fish collagen after 3 weeks of storage. L. barbarum yogurt in absence of fish collagen was acting as a great ACE inhibitor reached up to 85% on day 7 of storage. The incorporation of L. barbarum and/or fish collagen affected to a small extent the overall sensory characteristics of yogurt. Yogurt supplemented with L. barbarum and/or fish collagen may lead to the improvement in the production and formulation of yogurt differing in their anti-ACE activity.
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Affiliation(s)
- Amal Bakr Shori
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Jeddah, Saudi Arabia
| | - Kong Siew Ming
- Biomolecular Research Group, Division of Biochemistry, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Ahmad Salihin Baba
- Biomolecular Research Group, Division of Biochemistry, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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Wang C, Dong Y, Zhu L, Wang L, Yan L, Wang M, Zhu Q, Nan X, Li Y, Li J. Comparative transcriptome analysis of two contrasting wolfberry genotypes during fruit development and ripening and characterization of the LrMYB1 transcription factor that regulates flavonoid biosynthesis. BMC Genomics 2020; 21:295. [PMID: 32272876 PMCID: PMC7147035 DOI: 10.1186/s12864-020-6663-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/10/2020] [Indexed: 11/25/2022] Open
Abstract
Background Lycium barbarum and L. ruthenicum have been used as traditional medicinal plants in China and other Asian counties for centuries. However, the molecular mechanisms underlying fruit development and ripening, as well as the associated production of medicinal and nutritional components, have been little explored in these two species. Results A competitive transcriptome analysis was performed to identify the regulators and pathways involved in the fruit ripening of red wolfberry (L. barbarum) and black wolfberry (L. ruthenicum) using an Illumina sequencing platform. In total, 155,606 genes and 194,385 genes were detected in red wolfberry (RF) and black wolfberry (BF), respectively. Of them, 20,335, 24,469, and 21,056 genes were differentially expressed at three different developmental stages in BF and RF. Functional categorization of the differentially expressed genes revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, anthocyanin biosynthesis, and sugar metabolism were the most differentially regulated processes during fruit development and ripening in the RF and BF. Furthermore, we also identified 38 MYB transcription factor-encoding genes that were differentially expressed during black wolfberry fruit development. Overexpression of LrMYB1 resulted in the activation of structural genes for flavonoid biosynthesis and led to an increase in flavonoid content, suggesting that the candidate genes identified in this RNA-seq analysis are credible and might offer important utility. Conclusion This study provides novel insights into the molecular mechanism of Lycium fruit development and ripening and will be of value to novel gene discovery and functional genomic studies.
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Affiliation(s)
- Cuiping Wang
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China. .,Agricultural Biotechnology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
| | - Yan Dong
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lizhen Zhu
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Libin Wang
- Biochip Research Center, the General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - Li Yan
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Mengze Wang
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Qiang Zhu
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Xiongxiong Nan
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Yonghua Li
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
| | - Jian Li
- State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China
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Zhao J, Li H, Yin Y, An W, Qin X, Wang Y, Li Y, Fan Y, Cao Y. Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. Sci Rep 2020; 10:4354. [PMID: 32152358 PMCID: PMC7062791 DOI: 10.1038/s41598-020-61064-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 11/15/2019] [Indexed: 12/31/2022] Open
Abstract
Red wolfberry (or goji berry, Lycium barbarum; LB) is an important agricultural product with a high content of pharmacologically important secondary metabolites such as phenylpropanoids. A close relative, black wolfberry (L. ruthenicum; LR), endemic to the salinized deserts of northwestern China, is used only locally. The two fruits exhibit many morphological and phytochemical differences, but genetic mechanisms underlying them remain poorly explored. In order to identify the genes of interest for further studies, we studied transcriptomic (Illumina HiSeq) and metabolomic (LC-MS) profiles of the two fruits during five developmental stages (young to ripe). As expected, we identified much higher numbers of significantly differentially regulated genes (DEGs) than metabolites. The highest numbers were identified in pairwise comparisons including the first stage for both species, but total numbers were consistently somewhat lower for the LR. The number of differentially regulated metabolites in pairwise comparisons of developmental stages varied from 66 (stages 3 vs 4) to 133 (stages 2 vs 5) in both species. We identified a number of genes (e.g. AAT1, metE, pip) and metabolites (e.g. rutin, raffinose, galactinol, trehalose, citrulline and DL-arginine) that may be of interest to future functional studies of stress adaptation in plants. As LB is also highly suitable for combating soil desertification and alleviating soil salinity/alkalinity/pollution, its potential for human use may be much wider than its current, highly localized, relevance.
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Affiliation(s)
- Jianhua Zhao
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 750002, China
| | - Yue Yin
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Wei An
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Xiaoya Qin
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Yajun Wang
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Yanlong Li
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Yunfang Fan
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China
| | - Youlong Cao
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China.
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16
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Zhao X, Wang M, Chai J, Li Q, Zhou Y, Li Y, Cai X. De novo assembly and characterization of the transcriptome and development of microsatellite markers in a Chinese endemic Euphorbia kansui. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1788992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Xueyan Zhao
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, PR China
| | - Meng Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, PR China
| | - Jia Chai
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University (Air Force Medical University), Xi’an, PR China
| | - Qian Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, PR China
| | - Yafu Zhou
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, PR China
| | - Yan Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, PR China
| | - Xia Cai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, PR China
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17
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Chen G, Yue Y, Hua Y, Hu D, Shi T, Chang Z, Yang X, Wang L. SSR marker development in Clerodendrum trichotomum using transcriptome sequencing. PLoS One 2019; 14:e0225451. [PMID: 31747430 PMCID: PMC6867647 DOI: 10.1371/journal.pone.0225451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 11/05/2019] [Indexed: 11/26/2022] Open
Abstract
Clerodendrum trichotomum, a member of the Lamiaceae (Verbenaceae) family, is an ornamental plant widely distributed in South Asia. Previous studies have focused primarily on its growth characteristics, stress resistance, and pharmacological applications; however, molecular investigations remain limited. Considering germplasm conservation and the extensive applications of this plant, it is necessary to explore transcriptome resources and SSR makers for C. trichotomum. In the present study, RNA sequencing was used to determine the transcriptome of C. trichotomum. Subsequently, unigene annotations and classifications were obtained, and SSRs were mined with MIcroSAtellite. Finally, primer pairs designed with Oligo 6.0 were selected for polymorphism validation. In total, 127,325,666 high-quality reads were obtained, and 58,345 non-redundant unigenes were generated, of which 36,900 (63.24%) were annotated. Among the annotated unigenes, 35,980 (97.51%) had significant similarity to 607 species in Nr databases. In addition, a total of 6,444 SSRs were identified in 5,530 unigenes, and 200 random primer pairs were designed for polymorphism validation. Furthermore, after primary polymorphism identification, 30 polymorphic primer pairs were selected for the further polymorphism screening, and 200 alleles were identified, 197 of which showed polymorphism. In this work, a large number of unigenes were generated, and numerous SSRs were detected. These findings should be beneficial for further investigations into germplasm conservation and various applications of C. trichotomum. These results should also provide a solid foundation for future molecular biology studies in C. trichotomum.
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Affiliation(s)
- Gongwei Chen
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yuanzheng Yue
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yajie Hua
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Die Hu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingting Shi
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhaojing Chang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xiulian Yang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
- * E-mail: (LG-W); (XL-Y)
| | - Lianggui Wang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- * E-mail: (LG-W); (XL-Y)
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18
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Impact of Nitrogen Fertilizer Levels on Metabolite Profiling of the Lycium barbarum L. Fruit. Molecules 2019; 24:molecules24213879. [PMID: 31661883 PMCID: PMC6864581 DOI: 10.3390/molecules24213879] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/11/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
The yield and quality of goji (Lycium barbarum L.) fruit are heavily dependent on fertilizer, especially the availability of nitrogen, phosphorus, and potassium (N, P, and K, respectively). In this study, we performed a metabolomic analysis of the response of goji berry to nitrogen fertilizer levels using an Ultra Performance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry (UPLC-ESI-MS/MS) method. There was no significant difference in the fruit yield or the commodity grade between N0 (42.5 g/plant), N1 (85 g/plant), and N2 (127.5 g/plant). The primary nutrients of the goji berry changed with an increasing nitrogen fertilization. Comparative metabolomic profiling of three nitrogen levels resulted in the identification of 612 metabolites, including amino acids, flavonoids, carbohydrates, organic acids, and lipids/alcohols, among others, of which 53 metabolites (lipids, fatty acids, organic acids, and phenolamides) demonstrated significant changes. These results provide new insights into the molecular mechanisms of the relationship between yield and quality of goji berry and nitrogen fertilizer.
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19
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Ma Y, Reddy VR, Devi MJ, Song L, Cao B. De novo characterization of the Goji berry (Lycium barbarium L.) fruit transcriptome and analysis of candidate genes involved in sugar metabolism under different CO2 concentrations. TREE PHYSIOLOGY 2019; 39:1032-1045. [PMID: 30824924 DOI: 10.1093/treephys/tpz014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/05/2018] [Indexed: 05/09/2023]
Abstract
Goji berry (Lycium barbarum L.) is one of the important economic crops due to its exceptional nutritional value and medicinal benefits. Although reduced sugar levels in goji berry exposed to long-term elevated carbon dioxide (CO2) have been documented, the underlying molecular mechanisms remain unknown. The objective of this study was to explore the transcriptome of goji berry fruit under ambient and elevated CO2 concentrations and further to screen the differentially expressed genes (DEGs) for functions related to sugar metabolism. Fruit samples from goji berry exposed to ambient (400 μmol mol-1) and elevated (700 μmol mol-1) levels of CO2 for 120 days were analyzed for total sugar, carotenoid and flavone analysis. In this study, a reduction in total sugar and carotenoid levels in the fruits grown under elevated CO2 levels were observed. Fruit samples were also used to construct cDNA libraries using a HiSeqTM2500 platform. Consequently, 81,100 unigenes were assembled, of which 35,111 (43.3%) were annotated using various databases. Through DEGs analysis, it was found that 55 genes were upregulated and 18 were down-regulated in response to elevated CO2 treatment. Genes involved in the sugar metabolism and the related pathways were identified by Gene Ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. Furthermore, three genes, LBGAE (Lycium barbarum UDP-glucuronate 4-epimerase), LBGALA (Lycium barbarum alpha-galactosidase) and LBMS (Lycium barbarum malate synthase), associated with sugar metabolism were identified and discussed with respect to the reduction in the total sugar levels along with the enzymes acid invertase (AI), sucrose synthase (SS) and sucrose phosphate synthase (SPS) of the sucrose metabolism. This study can provide gene sources for elucidating the molecular mechanisms of sugar metabolism in the fruit of goji berry under elevated CO2.
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Affiliation(s)
- Yaping Ma
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- USDA-ARS-NEA, Adaptive Cropping Systems Laboratory, 10300 BARC, Beltsville, MD 20705, USA
| | - Vangimalla R Reddy
- USDA-ARS-NEA, Adaptive Cropping Systems Laboratory, 10300 BARC, Beltsville, MD 20705, USA
| | - Mura Jyostna Devi
- USDA-ARS-NEA, Adaptive Cropping Systems Laboratory, 10300 BARC, Beltsville, MD 20705, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Lihua Song
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- USDA-ARS-NEA, Adaptive Cropping Systems Laboratory, 10300 BARC, Beltsville, MD 20705, USA
| | - Bing Cao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
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Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers. FORESTS 2019. [DOI: 10.3390/f10050411] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies.
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Ma YJ, Duan HR, Zhang F, Li Y, Yang HS, Tian FP, Zhou XH, Wang CM, Ma R. Transcriptomic analysis of Lycium ruthenicum Murr. during fruit ripening provides insight into structural and regulatory genes in the anthocyanin biosynthetic pathway. PLoS One 2018; 13:e0208627. [PMID: 30532153 PMCID: PMC6285980 DOI: 10.1371/journal.pone.0208627] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/20/2018] [Indexed: 02/04/2023] Open
Abstract
Fruit development in Lycium ruthenicum Murr. involves a succession of physiological and biochemical changes reflecting the transcriptional modulation of thousands of genes. Although recent studies have investigated the dynamic transcriptomic responses during fruit ripening in L. ruthenicum, most have been limited in scope, and thus systematic data representing the structural genes and transcription factors involved in anthocyanin biosynthesis are lacking. In this study, the transcriptomes of three ripening stages associated with anthocyanin accumulation, including S1 (green ripeness stage), S2 (skin color change) and S3 (complete ripeness stage) in L. ruthenicum were investigated using Illumina sequencing. Of a total of 43,573 assembled unigenes, 12,734 were differentially expressed during fruit ripening in L. ruthenicum. Twenty-five significantly differentially expressed structural genes (including PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, F3'5'H, DFR, ANS and UFGT) were identified that might be associated with anthocyanin biosynthesis. Additionally, several transcription factors, including MYB, bHLH, WD40, NAC, WRKY, bZIP and MADS, were correlated with the structural genes, implying their important interaction with anthocyanin biosynthesis-related genes. Our findings provide insight into anthocyanin biosynthesis and regulation patterns in L. ruthenicum and offer a systematic basis for elucidating the molecular mechanisms governing anthocyanin biosynthesis in L. ruthenicum.
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Affiliation(s)
- Yan-Jun Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Hui-Rong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Feng Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yi Li
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Hong-Shan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Fu-Ping Tian
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xue-Hui Zhou
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chun-Mei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Rui Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, China
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22
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Development and application of EST-SSRs markers for analysis of genetic diversity in erect milkvetch (Astragalus adsurgens Pall.). Mol Biol Rep 2018; 46:1323-1326. [PMID: 30443824 DOI: 10.1007/s11033-018-4484-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/08/2018] [Indexed: 10/27/2022]
Abstract
Erect milkvetch (Astragalus adsurgens Pall.) is a major legume forage plant widely grown in Northern China. However, the lack of molecular markers has limited its research into its genetic diversity and work on germplasm improvement. In this study, a total of 39,163 EST-SSR loci were identified from 30,262 unigene sequences in the erect milkvetch transcriptome using Illumina sequencing. Moreover, 22,367 EST-SSR primer pairs (PPs) were successfully designed. In addition, 100 PPs were synthesized and preliminarily screened in two accessions; of these, 90 were determined to be clear and stable EST-SSR markers. Fifty-one PPs were randomly selected in order to assess the genetic diversity of 27 erect milkvetch accessions. The average polymorphism information content of the 51 PPs was 0.682. Greater genetic diversity was detected in accessions from Inner Mongolia and in the group of landrace and wild erect milkvetch accessions. This study provides an important resource for germplasm improvement and genetic diversity analysis in erect milkvetch.
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Xu D, Chen H, Aci M, Pan Y, Shangguan Y, Ma J, Li L, Qian G, Wang Q. De Novo assembly, characterization and development of EST-SSRs from Bletilla striata transcriptomes profiled throughout the whole growing period. PLoS One 2018; 13:e0205954. [PMID: 30365506 PMCID: PMC6203367 DOI: 10.1371/journal.pone.0205954] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/04/2018] [Indexed: 01/13/2023] Open
Abstract
Bletilla striata is an endangered orchid that has been used for millennia as a medicinal herb, in cosmetics and as a horticultural plant. To construct the first nucleotide database for this species and to develop abundant EST-SSR markers for facilitating further studies, various tissues and organs of plants in the main developmental stages were harvested for mRNA isolation and subsequent RNA sequencing. A total of 106,054,784 clean reads were generated by using Illumina paired-end sequencing technology. The reads were assembled into 127,261 unigenes by the Trinity package; the unigenes had an average length of 612 bp and an N50 of 957 bp. Of these unigenes, 67,494 (51.86%) were annotated in a series of databases. Of these annotated unigenes, 41,818 and 24,615 were assigned to gene ontology categories and clusters of orthologous groups, respectively. Additionally, 20,764 (15.96%) unigenes were mapped onto 275 pathways using the KEGG database. In addition, 25,935 high-quality EST-SSR primer pairs were developed from the 15,433 unigenes by MISA mining. To validate the accuracy of the newly designed markers, 87 of 100 randomly selected primers were effectively amplified; 63 of those yielded PCR products of the expected size, and 25 yielded products with significant amounts of polymorphism among the 4 landraces. Furthermore, the transferability test of the 25 polymorphic markers was performed in 6 individuals of two closely related genus Phalaenopsis and dendrobium. Which results showed a total of 5 markers can successfully amplified among these populations. This research provides a comprehensive nucleotide database and lays a solid foundation for functional gene mining and genomic research in B. striata. The developed EST-SSR primers could facilitate phylogenetic studies and breeding.
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Affiliation(s)
- Delin Xu
- Department of Medical Cell Biology, Zunyi Medical University, Zunyi, Guizhou, China
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Hongbo Chen
- Department of Medical Cell Biology, Zunyi Medical University, Zunyi, Guizhou, China
| | - Murat Aci
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Yinchi Pan
- Department of Medical Cell Biology, Zunyi Medical University, Zunyi, Guizhou, China
| | - Yanni Shangguan
- Department of Medical Cell Biology, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jie Ma
- Department of Medical Cell Biology, Zunyi Medical University, Zunyi, Guizhou, China
| | - Lin Li
- Department of Medical Cell Biology, Zunyi Medical University, Zunyi, Guizhou, China
- * E-mail: (LL); (QG)
| | - Gang Qian
- Department of Medical Cell Biology, Zunyi Medical University, Zunyi, Guizhou, China
- * E-mail: (LL); (QG)
| | - Qianxing Wang
- Department of Medical Cell Biology, Zunyi Medical University, Zunyi, Guizhou, China
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