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Tang Q, Wang X, Ma S, Fan S, Chi F, Song Y. Molecular mechanism of abscisic acid signaling response factor VcbZIP55 to promote anthocyanin biosynthesis in blueberry (Vaccinium corymbosum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108611. [PMID: 38615439 DOI: 10.1016/j.plaphy.2024.108611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
A high content of anthocyanin in blueberry (Vaccinium corymbosum) is an important indicator to evaluate fruit quality. Abscisic acid (ABA) can promote anthocyanin biosynthesis, but since the molecular mechanism is unclear, clarifying the mechanism will improve for blueberry breeding and cultivation regulation. VcbZIP55 regulating anthocyanin synthesis in blueberry were screened and mined using the published Isoform-sequencing, RNA-Seq and qRT-PCR at different fruit developmental stages. Blueberry genetic transformation and transgenic experiments confirmed that VcbZIP55 could promote anthocyanin biosynthesis in blueberry adventitious buds, tobacco leaves, blueberry leaves and blueberry fruit. VcbZIP55 responded to ABA signals and its expression was upregulated in blueberry fruit. In addition, using VcbZIP55 for Yeast one hybrid assay (Y1H) and transient expression in tobacco leaves demonstrated an interaction between VcbZIP55 and a G-Box motif on the VcMYB1 promoter to activate the expression of VcMYB1. This study will lay the theoretical foundation for the molecular mechanisms of phytohormone regulation responsible for anthocyanin synthesis and provide theoretical support for blueberry quality improvement.
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Affiliation(s)
- Qi Tang
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
| | - Xuan Wang
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
| | - Shurui Ma
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
| | - Shutian Fan
- Institute of Special Animal and Plant Sciences CAAS, Jilin Changchun, 130122, China.
| | - Fumei Chi
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
| | - Yang Song
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
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Wang J, Zhao R, Li Y, Rong H, Yang L, Gao M, Sun B, Zhang Y, Xu Y, Yan X. Effect and Mechanism of L-Arginine against Alternaria Fruit Rot in Postharvest Blueberry Fruit. PLANTS (BASEL, SWITZERLAND) 2024; 13:1058. [PMID: 38674466 PMCID: PMC11054261 DOI: 10.3390/plants13081058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024]
Abstract
This study aimed to explore the impact of L-arginine (Arg) on the development of resistance to Alternaria tenuissima (A. tenuissima) in blueberries. The metabolism of reactive oxygen species, pathogenesis-related proteins (PRs), and jasmonic acid (JA) biosynthesis pathways were analyzed, including changes in activity and gene expression of key enzymes. The results indicated that Arg treatment could prevent the development of Alternaria fruit rot in postharvest blueberries. In addition, it was also found to induce a burst of hydrogen peroxide in the blueberries early on during storage, thereby improving their resistance to A. tenuissima. Arg treatment was observed to increase the activity of antioxidant enzymes (peroxidase, catalase, superoxide dismutase, and ascorbate peroxidase) and related gene expression, as well as the total levels of phenolics, flavonoids, and anthocyanin in the blueberries. The activity and gene expression of the PRs (chitinase and β-1,3-glucanase) were elevated in Arg-treated blueberries, boosting their resistance to pathogens. Additionally, a surge in endogenous JA content was detected in Arg-treated blueberries, along with upregulated expression of key genes related the JA biosynthesis pathway (VcLOX1, VcAOS1, VcAOC, VcAOC3, VcOPR1, VcOPR3, VcMYC2, and VcCOI1), thereby further bolstering disease resistance. In conclusion, Arg treatment was determined to be a promising prospective method for controlling Alternaria fruit rot in blueberries.
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Affiliation(s)
- Jiaqi Wang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Runan Zhao
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Yuxuan Li
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Haifeng Rong
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Ling Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Ming Gao
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Bingxin Sun
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Yunhe Zhang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Yufeng Xu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
| | - Xuerui Yan
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (R.Z.); (Y.L.); (H.R.); (L.Y.); (M.G.); (B.S.); (Y.Z.); (Y.X.)
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang 110866, China
- Shenyang Key Laboratory for Logistics Preservation and Packaging of Agricultural Products, Shenyang 110866, China
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3
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Panzade KP, Tribhuvan KU, Pawar DV, Jasrotia RS, Gaikwad K, Dalal M, Kumar RR, Singh MP, Awasthi OP, Padaria JC. Discovering the regulators of heat stress tolerance in Ziziphus nummularia (Burm.f) wight and walk.-arn. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:497-511. [PMID: 38633271 PMCID: PMC11018567 DOI: 10.1007/s12298-024-01431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Ziziphus nummularia an elite heat-stress tolerant shrub, grows in arid regions of desert. However, its molecular mechanism responsible for heat stress tolerance is unexplored. Therefore, we analysed whole transcriptome of Jaisalmer (heat tolerant) and Godhra (heat sensitive) genotypes of Z. nummularia to understand its molecular mechanism responsible for heat stress tolerance. De novo assembly of 16,22,25,052 clean reads yielded 276,029 transcripts. A total of 208,506 unigenes were identified which contains 4290 and 1043 differentially expressed genes (DEG) in TGO (treated Godhra at 42 °C) vs. CGO (control Godhra) and TJR (treated Jaisalmer at 42 °C) vs. CJR (control Jaisalmer), respectively. A total of 987 (67 highly enriched) and 754 (34 highly enriched) pathways were obsorved in CGO vs. TGO and CJR vs. TJR, respectively. Antioxidant pathways and TFs like Homeobox, HBP, ARR, PHD, GRAS, CPP, and E2FA were uniquely observed in Godhra genotype and SET domains were uniquely observed in Jaisalmer genotype. Further transposable elements were highly up-regulated in Godhra genotype but no activation in Jaisalmer genotype. A total of 43,093 and 39,278 simple sequence repeats were identified in the Godhra and Jaisalmer genotypes, respectively. A total of 10 DEGs linked to heat stress were validated in both genotypes for their expression under different heat stresses using quantitative real-time PCR. Comparing expression patterns of the selected DEGs identified ClpB1 as a potential candidate gene for heat tolerance in Z. nummularia. Here we present first characterized transcriptome of Z. nummularia in response to heat stress for the identification and characterization of heat stress-responsive genes. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01431-y.
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Affiliation(s)
- Kishor Prabhakar Panzade
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Kishor U. Tribhuvan
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand 834 003 India
| | - Deepak V. Pawar
- ICAR- Directorate of Weed Research, Maharajpur, Jabalpur, Madhya Pradesh 482004 India
| | - Rahul Singh Jasrotia
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX 78229 USA
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Monika Dalal
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, ICAR–Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agrcultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Om Prakash Awasthi
- Division of Horticulture, ICAR-Indian Agrcultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Jasdeep Chatrath Padaria
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
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Wang J, Wang Y, Li Y, Yang L, Sun B, Zhang Y, Xu Y, Yan X. l-Arginine treatment maintains postharvest quality in blueberry fruit by enhancing antioxidant capacity during storage. J Food Sci 2023; 88:3666-3680. [PMID: 37477270 DOI: 10.1111/1750-3841.16710] [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: 03/15/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
The postharvest quality of blueberry fruit is largely limited by deterioration. l-arginine (Arg) is a functional nontoxic amino acid with high biological activities. This study investigated the positive effects and the underlying mechanism of Arg treatment on the quality of postharvest blueberries. Arg effectively mitigated fruit decay and improved the quality of blueberries, including weight loss, firmness, and soluble solid content. Mechanistically, Arg-mediated activation of the anti-oxidative defense system reduced reactive oxygen species-mediated oxidative damage. Moreover, Arg treatment decreased the activities and gene expression of phospholipase D, lipoxygenase, and lipase-inhibiting membrane lipid peroxidation during the prolonged storage of blueberries. Meanwhile, Arg treatment increased nitric oxide (NO) content and NO synthase activity. Furthermore, correlation and principal component analyses revealed the enhancement of Arg treatment on antioxidant capacity. This study suggests that Arg treatment can maintain the postharvest quality of blueberries by improving antioxidant capacity.
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Affiliation(s)
- Jiaqi Wang
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, P. R. China
| | - Yajuan Wang
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, P. R. China
| | - Yuxuan Li
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, P. R. China
| | - Ling Yang
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, P. R. China
| | - Bingxin Sun
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yunhe Zhang
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yufeng Xu
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Xuerui Yan
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, P. R. China
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5
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Wang H, Zhai L, Wang S, Zheng B, Hu H, Li X, Bian S. Identification of R2R3-MYB family in blueberry and its potential involvement of anthocyanin biosynthesis in fruits. BMC Genomics 2023; 24:505. [PMID: 37648968 PMCID: PMC10466896 DOI: 10.1186/s12864-023-09605-w] [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: 05/06/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Blueberries (Vaccinium corymbosum) are regarded as "superfoods" attributed to large amounts of anthocyanins, a group of flavonoid metabolites, which provide pigmentation in plant and beneficial effects for human health. MYB transcription factor is one of vital components in the regulation of plant secondary metabolism, which occupies a dominant position in the regulatory network of anthocyanin biosynthesis. However, the role of MYB family in blueberry responding to anthocyanin biosynthesis remains elusive. RESULTS In this study, we conducted a comprehensive analysis of VcMYBs in blueberry based on the genome data, including phylogenetic relationship, conserved motifs, identification of differentially expressed MYB genes during fruit development and their expression profiling, etc. A total of 437 unique MYB sequences with two SANT domains were identified in blueberry, which were divided into 3 phylogenetic trees. Noticeably, there are many trigenic and tetragenic VcMYBs pairs with more than 95% identity to each other. Meanwhile, the transcript accumulations of VcMYBs were surveyed underlying blueberry fruit development, and they showed diverse expression patterns, suggesting various functional roles in fruit ripening. More importantly, distinct transcript profiles between skin and pulp of ripe fruit were observed for several VcMYBs, such as VcMYB437, implying the potential roles in anthocyanin biosynthesis. CONCLUSIONS Totally, 437 VcMYBs were identified and characterized. Subsequently, their transcriptional patterns were explored during fruit development and fruit tissues (skin and pulp) closely related to anthocyanin biosynthesis. These genome-wide data and findings will contribute to demonstrating the functional roles of VcMYBs and their regulatory mechanisms for anthocyanins production and accumulation in blueberry in the future study.
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Affiliation(s)
- Haiyang Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, China
| | - Shouwen Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Botian Zheng
- College of Plant Science, Jilin University, Changchun, China
| | - Honglu Hu
- College of Plant Science, Jilin University, Changchun, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, China.
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, China.
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Qin X, Tian C, Meng F. Comparative Transcriptome Analysis Reveals the Effect of the DHN Melanin Biosynthesis Pathway on the Appressorium Turgor Pressure of the Poplar Anthracnose-Causing Fungus Colletotrichum gloeosporioides. Int J Mol Sci 2023; 24:ijms24087411. [PMID: 37108573 PMCID: PMC10138971 DOI: 10.3390/ijms24087411] [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: 03/02/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Anthracnose of poplar caused by Colletotrichum gloeosporioides is a leaf disease that seriously affects poplar growth. The pathogen invades the host in the form of adherent cells, which generate turgor pressure through the metabolism of intracellular substances prior to penetrating the epidermis of poplar leaves. In this study, the expansion-related pressure of the mature appressorium of the wild-type C. gloeosporioides was approximately 13.02 ± 1.54 MPa at 12 h, whereas it was 7.34 ± 1.23 MPa and 9.34 ± 2.22 MPa in the melanin synthesis-related gene knockout mutants ΔCgCmr1 and ΔCgPks1, respectively. The CgCmr1 and CgPks1 genes were highly expressed at 12 h in the wild-type control, implying that the DHN melanin biosynthesis pathway may play an important role in the mature appressorium stage. The transcriptome sequencing analysis indicated that the upregulated melanin biosynthesis genes in C. gloeosporioides, such as CgScd1, CgAyg1, CgThr1, CgThr2, and CgLac1, are involved in specific KEGG pathways (i.e., fatty acid biosynthesis, fatty acid metabolism, and biotin metabolism). Therefore, we speculate that the melanin synthesis-related genes and fatty acid metabolism pathway genes contribute to the regulation of the turgor pressure in the mature C. gloeosporioides appressorium, ultimately leading to the formation of infection pegs that enter plant tissues. These observations may reflect the co-evolution of C. gloeosporioides and its host.
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Affiliation(s)
- Xinyu Qin
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Fanli Meng
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China
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Krishna P, Pandey G, Thomas R, Parks S. Improving Blueberry Fruit Nutritional Quality through Physiological and Genetic Interventions: A Review of Current Research and Future Directions. Antioxidants (Basel) 2023; 12:antiox12040810. [PMID: 37107184 PMCID: PMC10135188 DOI: 10.3390/antiox12040810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 03/29/2023] Open
Abstract
Blueberry, hailed as an antioxidant superfood, is the fruit of small shrubs in the genus Vaccinium (family Ericaceae). The fruits are a rich source of vitamins, minerals and antioxidants such as flavonoids and phenolic acids. The antioxidative and anti-inflammatory activities derived from the polyphenolic compounds, particularly from the abundantly present anthocyanin pigment, have been highlighted as the major contributing factor to the health-benefitting properties of blueberry. In recent years, blueberry cultivation under polytunnels has expanded, with plastic covers designed to offer protection of crop and fruit yield from suboptimal environmental conditions and birds. An important consideration is that the covers reduce photosynthetically active radiation (PAR) and filter out ultraviolet (UV) radiation that is critical for the fruit’s bioactive composition. Blueberry fruits grown under covers have been reported to have reduced antioxidant capacity as compared to fruits from open fields. In addition to light, abiotic stresses such as salinity, water deficit, and low temperature trigger accumulation of antioxidants. We highlight in this review how interventions such as light-emitting diodes (LEDs), photo-selective films, and exposure of plants to mild stresses, alongside developing new varieties with desired traits, could be used to optimise the nutritional quality, particularly the content of polyphenols, of blueberry grown under covers.
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8
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Wang C, Duan T, Shi L, Zhang X, Fan W, Wang M, Wang J, Ren L, Zhao X, Wang Y. Characterization of Volatile Organic Compounds Produced by Bacillus siamensis YJ15 and Their Antifungal Activity Against Botrytis cinerea. PLANT DISEASE 2022; 106:2321-2329. [PMID: 35380464 DOI: 10.1094/pdis-01-22-0230-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
To develop an effective and environmentally safe strategy to control postharvest gray mold caused by Botrytis cinerea, Bacillus siamensis strain YJ15 isolated from blueberry was used to test the biocontrol potential. It is interesting to find that the volatile organic compounds (VOCs) emitted from strain YJ15 exhibited significant antifungal activity against Botrytis cinerea as well as 11 other plant-pathogenic fungi, with a percentage of mycelial growth inhibition from 74.96 to 92.81%. Additionally, VOCs from strain YJ15 could reduce significantly the disease incidence and lesion diameter with the increasing of fermentation time, indicating great biocontrol potential for controlling blueberry postharvest gray mold. Furthermore, the VOCs were collected by using headspace solid-phase microextraction fiber, and the composition of VOCs was further revealed by using gas chromatography coupled with quadruple mass spectrometry. In total, 24 kinds of VOCs, including 5 alkanes, 2 aldehydes, 3 ketones, 5 alcohols, 1 alkene, 5 acids and esters, 2 aromatic compounds, and 1 sulfur compound, were emitted at 1, 3, 5, and 7 days after inoculation. Among these VOCs, eight antifungal VOCs could inhibit mycelial growth of B. cinerea. It is important to highlight that, although 1-butanol and 3-methyl-1-butanol were the most abundant compounds, 2-ethylhexanol, 1-heptanol, and 1,3-xylene have proved to be more toxic to B. cinerea than 3-methyl-1-butanol, propanethioic acid, 2,2-dimethyl-, ethyl 2-methylbutyrate, 2-heptanone, and 1-butanol, which provide new, promising biofumigants for the control of postharvest gray mold caused by B. cinerea.
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Affiliation(s)
- Chunwei Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi 030031, P.R. China
| | - Tiankun Duan
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
| | - Luxin Shi
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
| | - Xiqian Zhang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
| | - Weixin Fan
- Experiment Teaching Center, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
| | - Meiqin Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
| | - Jianming Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
| | - Lu Ren
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
| | - Xiaojun Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi 030031, P.R. China
| | - Yan Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, P.R. China
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9
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Edger PP, Iorizzo M, Bassil NV, Benevenuto J, Ferrão LFV, Giongo L, Hummer K, Lawas LMF, Leisner CP, Li C, Munoz PR, Ashrafi H, Atucha A, Babiker EM, Canales E, Chagné D, DeVetter L, Ehlenfeldt M, Espley RV, Gallardo K, Günther CS, Hardigan M, Hulse-Kemp AM, Jacobs M, Lila MA, Luby C, Main D, Mengist MF, Owens GL, Perkins-Veazie P, Polashock J, Pottorff M, Rowland LJ, Sims CA, Song GQ, Spencer J, Vorsa N, Yocca AE, Zalapa J. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. HORTICULTURE RESEARCH 2022; 9:uhac083. [PMID: 35611183 PMCID: PMC9123236 DOI: 10.1093/hr/uhac083] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/22/2022] [Indexed: 06/02/2023]
Abstract
The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops' relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Nahla V Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Juliana Benevenuto
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Luis Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Lara Giongo
- Fondazione Edmund Mach - Research and Innovation CentreItaly
| | - Kim Hummer
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Lovely Mae F Lawas
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Changying Li
- Phenomics and Plant Robotics Center, College of Engineering, University of Georgia, Athens, USA
| | - Patricio R Munoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Amaya Atucha
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ebrahiem M Babiker
- USDA-ARS Southern Horticultural Laboratory, Poplarville, MS 39470-0287, USA
| | - Elizabeth Canales
- Department of Agricultural Economics, Mississippi State University, Mississippi State, MS 39762, USA
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Lisa DeVetter
- Department of Horticulture, Washington State University Northwestern Washington Research and Extension Center, Mount Vernon, WA, 98221, USA
| | - Mark Ehlenfeldt
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Karina Gallardo
- School of Economic Sciences, Washington State University, Puyallup, WA 98371, USA
| | - Catrin S Günther
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Michael Hardigan
- USDA-ARS, Horticulture Crops Research Unit, Corvallis, OR 97333, USA
| | - Amanda M Hulse-Kemp
- USDA-ARS, Genomics and Bioinformatics Research Unit, Raleigh, NC 27695, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - MacKenzie Jacobs
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Claire Luby
- USDA-ARS, Horticulture Crops Research Unit, Corvallis, OR 97333, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA
| | - Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | | | | | - James Polashock
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Marti Pottorff
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Lisa J Rowland
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705, USA
| | - Charles A Sims
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Guo-qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Jessica Spencer
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Nicholi Vorsa
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Alan E Yocca
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Juan Zalapa
- USDA-ARS, VCRU, Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
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10
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Chiluisa-Utreras V, Vela D, Vaca I, Acurio R, Chicaiza J, Peñaherrera S. Expression of the ANS, CHS and DFR genes involved in the biosynthesis of anthocyanins in Vaccinium floribundum Kunth from Ecuador, using RT-qPCR. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.04.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Vaccinium floribundum Kunth, a wild native species of berry in Ecuador, presents a lot of phenolic compounds, specifically anthocyanins; hence it is considered a natural nutraceutical due to all its nutritional properties. The comparison of the expression of genes is involved in the biosynthesis pathway of anthocyanin of several populations. The aim of the research was to analyze the expression levels of three genes involved in the biosynthesis of anthocyanin in this species collected in two areas of the province of Pichincha: Machachi population of the Mejía canton, with geographic coordinates 0 ° 31′04.8 ″ S 78 ° 37′07.4 ″ W and altitude 3200 meters above sea level, and Pintag population of the Quito cantón, with geographic coordinates 0 ° 24′00.0 ″ S 78 ° 24′00.0 ″ W and altitude 3000 meters above sea level. The gene expression analysis was performed using the quantitative polymerase chain reaction technique and reverse transcription (RT-qPCR). For the population of Machachi, the glyceraldehyde-3-phosphate dehydrogenase gene had an average concentration of 648.59 ng/µL, followed by the chalcone synthase gene with 143.71 ng/µL, then by the dihydroflavonol 4-reductase gene with 59.58 ng/µL and finally by the anthocyanin synthase gene with 39 ng/µL. For the population of Pintag, the glyceraldehyde-3-phosphate dehydrogenase gene has an average concentration of 667.32 ng/µL, followed by the chalcone synthase gene with 157.22 ng/µL, then by the dihydroflavonol 4-reductase gene with 60.42 ng/µL, and finally by the anthocyanin synthase gene with 44.40 ng/µL. Each gene has a similar expression level in both populations, but there are differences when comparing the expression level among genes. Many enzymes, structural genes, and regulatory elements have been observed as transcription factors involved in anthocyanin biosynthesis.
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Affiliation(s)
| | - Doris Vela
- Laboratory of Evolutive Genetics. School of Biological Sciences. Pontificia Universidad Católica, Quito, Ecuador
| | - Ivonne Vaca
- Research group BIOARN, Universidad Politécnica Salesiana, Quito - Ecuador
| | - Ramiro Acurio
- Research group BIOARN, Universidad Politécnica Salesiana, Quito - Ecuador
| | - Javier Chicaiza
- Laboratory of Life Sciences, Universidad Politécnica Salesiana, Quito - Ecuador
| | - Sofía Peñaherrera
- Laboratory of Life Sciences, Universidad Politécnica Salesiana, Quito - Ecuador
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11
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Tang Q, Chi FM, Liu HD, Zhang HJ, Song Y. Single-Molecule Real-Time and Illumina Sequencing to Analyze Transcriptional Regulation of Flavonoid Synthesis in Blueberry. FRONTIERS IN PLANT SCIENCE 2021; 12:754325. [PMID: 34659323 PMCID: PMC8514788 DOI: 10.3389/fpls.2021.754325] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/08/2021] [Indexed: 05/24/2023]
Abstract
Blueberries (Vaccinium corymbosum) contain large amounts of flavonoids, which play important roles in the plant's ability to resist stress and can also have beneficial effects on human health when the fruits are eaten. However, the molecular mechanisms that regulate flavonoid synthesis in blueberries are still unclear. In this study, we combined two different transcriptome sequencing platforms, single-molecule real-time (SMRT) and Illumina sequencing, to elucidate the flavonoid synthetic pathways in blueberries. We analyzed transcript quantity, length, and the number of annotated genes. We mined genes associated with flavonoid synthesis (such as anthocyanins, flavonols, and proanthocyanidins) and employed fluorescence quantitative PCR to analyze the expression of these genes and their correlation with flavonoid synthesis. We discovered one R2R3 MYB transcription factor from the sequencing library, VcMYB1, that can positively regulate anthocyanin synthesis in blueberries. VcMYB1 is mainly expressed in colored (mature) fruits. Experiments showed that overexpression and transient expression of VcMYB1 promoted anthocyanin synthesis in Arabidopsis, tobacco (Nicotiana benthamiana) plants and green blueberry fruits. Yeast one-hybrid (Y1H) assay, electrophoretic mobility shift assay, and transient expression experiments showed that VcMYB1 binds to the MYB binding site on the promoter of the structural gene for anthocyanin synthesis, VcMYB1 to positively regulate the transcription of VcDFR, thereby promoting anthocyanin synthesis. We also performed an in-depth investigation of transcriptional regulation of anthocyanin synthesis. This study provides background information and data for studying the synthetic pathways of flavonoids and other secondary metabolites in blueberries.
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12
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Cárcamo de la Concepción M, Sargent DJ, Šurbanovski N, Colgan RJ, Moretto M. De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars 'Bluecrop' and 'Legacy' at harvest and following post-harvest storage. PLoS One 2021; 16:e0255139. [PMID: 34339434 PMCID: PMC8328333 DOI: 10.1371/journal.pone.0255139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/12/2021] [Indexed: 11/19/2022] Open
Abstract
Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, 'Bluecrop' and 'Legacy', at harvest, three weeks storage in a non-modified environment at 4 °C and after three weeks storage at 4 °C followed by three days at 21 °C, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality. De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for 'Bluecrop' and 'Legacy' respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 290 unigenes were up-regulated in 'Legacy' only, 685 were up-regulated in 'Bluecrop', 252 were up-regulated in both cultivars and 948 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes. In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.
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Affiliation(s)
| | - Daniel James Sargent
- Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom
- NIAB EMR, East Malling, Kent, United Kingdom
| | | | - Richard John Colgan
- Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom
- * E-mail:
| | - Marco Moretto
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, Italy
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13
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Song X, Gao J, Peng H. Transcriptomic dynamics changes related to anthocyanin accumulation in the fleshy roots of carmine radish ( Raphanus sativus L.) characterized using RNA-Seq. PeerJ 2021; 9:e10978. [PMID: 33868802 PMCID: PMC8035900 DOI: 10.7717/peerj.10978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/29/2021] [Indexed: 01/03/2023] Open
Abstract
Carmine radish is famous for containing a natural red pigment (red radish pigment). However, the expression of anthocyanin biosynthesis-related genes during the dynamic development stages of the fleshy roots in carmine radish has not been fully investigated. Here, based on HPLC quantification of anthocyanin levels from our previous study, young fleshy roots of the carmine radish “Hongxin 1” obtained at the dynamic development stages of fleshy roots (seedling stage (SS), initial expansion (IE), full expansion (FE), bolting stage (BS), initial flowering stage (IFS), full bloom stage (FBS) and podding stage (PS)) were used for RNA-Seq. Approximately 126 comodulated DEGs related to anthocyanin biosynthesis (common DEGs in the dynamic growth stages of fleshy roots in carmine radish) were identified, from which most DEGs appeared to be likely to participate in anthocyanin biosynthesis, including two transcription factors, RsMYB and RsRZFP. In addition, some related proteins, e.g., RsCHS, RsDFR, RsANS, RsF′3H, RsF3GGT1, Rs3AT1, RsGSTF12, RsUFGT78D2 and RsUDGT-75C1, were found as candidate contributors to the regulatory mechanism of anthocyanin synthesis in the fleshy roots of carmine radish. In addition, 11 putative DEGs related to anthocyanin synthesis were evaluated by qRT-PCR via the (2-ΔΔCT) method; the Pearson correlation analysis indicated excellent concordance between the RNA-Seq and qRT-PCR results. Furthermore, GO enrichment analysis showed that “anthocyanin-containing compound biosynthetic process” and “anthocyanin-containing compound metabolic process” were commonly overrepresented in the dynamic growth stages of fleshy roots after the initial expansion stage. Moreover, five significantly enriched pathways were identified among the DEGs in the dynamic growth stages of fleshy roots in carmine radish, namely, flavonoid biosynthesis, flavone and flavonol biosynthesis, diterpenoid biosynthesis, anthocyanin biosynthesis, and benzoxazinoid biosynthesis. In conclusion, these results will expand our understanding of the complex molecular mechanisms of anthocyanin biosynthesis in the fleshy roots of carmine radish and the putative candidate genes involved in this process.
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Affiliation(s)
- Xia Song
- Research Center for Tourism Agriculture Development, Sichuan Tourism College, Chengdu, China
| | - Jian Gao
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Fuling, Chongqing, China
| | - Hua Peng
- Research Center for Tourism Agriculture Development, Sichuan Tourism College, Chengdu, China
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14
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Wang H, Kou X, Wu C, Fan G, Li T. Nitric Oxide and Hydrogen Peroxide Are Involved in Methyl Jasmonate-Regulated Response against Botrytis cinerea in Postharvest Blueberries. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13632-13640. [PMID: 33185095 DOI: 10.1021/acs.jafc.0c04943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The involvement and the relationship between nitric oxide (NO) and hydrogen peroxide (H2O2) in methyl jasmonate (MeJA)-induced immune responses in blueberries against Botrytis cinerea was explored using diphenylene iodonium (DPI, NADPH oxidase inhibitor) and 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO, NO scavenger). MeJA induced NO and H2O2 burst and enhanced the resistance of blueberries by elevating defense-related enzymes and the phenylpropanoid pathway. However, the above impacts stimulated by MeJA were weakened by DPI and destroyed by cPTIO. Furthermore, cPTIO abolished the increment in H2O2 by regulating the activities of NADPH oxidase, superoxide dismutase, catalase, and ascorbate peroxidase, whereas DPI weakened the increase in H2O2 but barely affected the generation of NO and the activity of nitric oxide synthase elevated by MeJA. These results indicated that NO and H2O2 were involved in the MeJA-induced resistance in blueberries, and NO worked upstream of H2O2 in this process.
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Affiliation(s)
- Hanbo Wang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
| | - Xiaohong Kou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Caie Wu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
| | - Gongjian Fan
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
| | - Tingting Li
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, Jiangsu 210037, PR China
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15
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Tian Y, Ma Z, Ma H, Gu Y, Li Y, Sun H. Comparative transcriptome analysis of lingonberry (Vaccinium vitis-idaea) provides insights into genes associated with flavonoids metabolism during fruit development. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1803130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Youwen Tian
- College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, PR China
| | - Zhili Ma
- College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, PR China
| | - Haohao Ma
- College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, PR China
| | - Yu Gu
- Engineering Center of Genetic Breeding and Innovative Utilization of Small Fruits of Jilin Province, College of Horticulture, Jilin Agricultural University, Changchun, Jilin, PR China
| | - Yadong Li
- Engineering Center of Genetic Breeding and Innovative Utilization of Small Fruits of Jilin Province, College of Horticulture, Jilin Agricultural University, Changchun, Jilin, PR China
| | - Haiyue Sun
- Engineering Center of Genetic Breeding and Innovative Utilization of Small Fruits of Jilin Province, College of Horticulture, Jilin Agricultural University, Changchun, Jilin, PR China
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16
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Characterization and Analysis of Anthocyanin-Related Genes in Wild-Type Blueberry and the Pink-Fruited Mutant Cultivar ‘Pink Lemonade’: New Insights into Anthocyanin Biosynthesis. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Blueberries are one of the richest sources of antioxidants, such as anthocyanins, among fruits and vegetables. Anthocyanin mutants, like the pink-fruited cultivar ‘Pink Lemonade’, are valuable resources for investigating anthocyanin biosynthesis in blueberries. In this study, we examined expression of flavonoid pathway genes during fruit development in wild-type, blue-fruited blueberries using quantitative real-time PCR. Expression was also compared between wild-type and the pink-fruited ‘Pink Lemonade’. This revealed significantly lower expression in ‘Pink Lemonade’ than in wild-type of nearly all the structural genes examined suggesting that a transcriptional regulator of the pathway was affected. Hence, we compared expression of three known regulatory genes and found that the gene encoding the transcription factor MYB1 was expressed at a significantly lower level in ‘Pink Lemonade’ than in the wild-type. To validate the capacity of this MYB1 to regulate the transcription of anthocyanin genes in blueberries, a transient expression assay was conducted. Results indicated MYB1 overexpression enhanced anthocyanin production. Comparative sequence analysis between wild-type and mutant MYB1 variants found differences in highly conserved features suggesting a mechanistic explanation for the mutant phenotype. Collectively, the results presented here contribute to a better understanding of mechanisms regulating anthocyanin biosynthesis in Vaccinium.
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17
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Li Y, Feng Y, Wang X, Cui J, Deng X, Zhang X. Adaptation of pine wood nematode Bursaphelenchus xylophilus to β-pinene stress. BMC Genomics 2020; 21:478. [PMID: 32660425 PMCID: PMC7358211 DOI: 10.1186/s12864-020-06876-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/01/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The pine wood nematode (PWN; Bursaphelenchus xylophilus) is the most damaging biological pest in pine forest ecosystems in China. However, the pathogenic mechanism remains unclear. Tracheid cavitation induced by excess metabolism of volatile terpenes is a typical characteristic of pine trees infected by B. xylophilus. β-pinene, one of the main volatile terpenes, influences PWN colonization and reproduction, stimulating pathogenicity during the early stages of infection. To elucidate the response mechanism of PWN to β-pinene, pathogenesis, mortality, and reproduction rate were investigated under different concentrations of β-pinene using a transcriptomics approach. RESULTS A low concentration of β-pinene (BL, C < 25.74 mg/ml) inhibited PWN reproduction, whereas a high concentration (BH, C > 128.7 mg/ml) promoted reproduction. Comparison of PWN expression profiles under low (BL, 21.66 mg/ml) and high (BH, 214.5 mg/ml) β-pinene concentrations at 48 h identified 659 and 418 differentially expressed genes (DEGs), respectively, compared with controls. Some key DEGs are potential regulators of β-pinene via detoxification metabolism (cytochrome P450, UDP-glucuronosyltransferases and short-chain dehydrogenases), ion channel/transporter activity (unc and ATP-binding cassette families), and nuclear receptor -related genes. Gene Ontology enrichment analysis of DEGs revealed metabolic processes as the most significant biological processes, and catalytic activity as the most significant molecular function for both BL and BH samples. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) analysis showed that xenobiotics biodegradation and metabolism, carbohydrate metabolism, lipid metabolism, amino acid metabolism, metabolism of cofactors and vitamins, and transport and catabolism were the dominant terms in metabolism categories. CONCLUSION In addition to detoxification via reduction/oxidation (redox) activity, PWN responds to β-pinene through amino acid metabolism, carbohydrate metabolism, and other pathways including growth regulation and epidermal protein changes to overcome β-pinene stress. This study lays a foundation for further exploring the pathogenic mechanism of PWN.
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Affiliation(s)
- Yongxia Li
- Lab. of Forest Pathogen Integrated Biology, Research institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Yuqian Feng
- Lab. of Forest Pathogen Integrated Biology, Research institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Xuan Wang
- Lab. of Forest Pathogen Integrated Biology, Research institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Jing Cui
- Lab. of Forest Pathogen Integrated Biology, Research institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Xun Deng
- Lab. of Forest Pathogen Integrated Biology, Research institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Xingyao Zhang
- Lab. of Forest Pathogen Integrated Biology, Research institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
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18
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Wang Y, Nie F, Shahid MQ, Baloch FS. Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset. BMC PLANT BIOLOGY 2020; 20:250. [PMID: 32493212 PMCID: PMC7268529 DOI: 10.1186/s12870-020-02461-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/24/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species. RESULTS We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species. CONCLUSION Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
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Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, 556011 Guizhou Province China
| | - Fei Nie
- Biological institute of Guizhou Province, Guiyang City, 556000 Guizhou Province China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong Province China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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19
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Deng Y, Li Y, Sun H. Selection of reference genes for RT-qPCR normalization in blueberry (Vaccinium corymbosum × angustifolium) under various abiotic stresses. FEBS Open Bio 2020; 10:1418-1435. [PMID: 32438500 PMCID: PMC7396441 DOI: 10.1002/2211-5463.12903] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 11/06/2022] Open
Abstract
As a small fruit rich in anthocyanins, blueberry (Vaccinium corymbosum × angustifolium) has become a focus of research in recent years for identifying genes related to anthocyanin transport and stress resistance mechanisms based on transcriptome sequencing. However, the lack of validated, stably expressed reference genes greatly limits the functional study of blueberry genes. Therefore, in this study, we selected 14 candidate reference genes from a blueberry transcriptome database and used three algorithms (geNorm, NormFinder and BestKeeper) to evaluate the expression stability of these genes in various organs at different fruit developmental stages under five abiotic stress conditions. EF1α, EIF and TBP were observed to be the most stable and were thus chosen as reference genes for quantitative real-time PCR. Measurement of the relative expression of VcMATE1 (European Nucleotide Archive accession number KF875433) in blueberry further verified the reliability of these reference genes, which may have great utility for determining the accuracy of gene expression analyses in future research on blueberry.
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Affiliation(s)
- Yu Deng
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Yadong Li
- Engineering Center of Genetic Breeding and Innovative Utilization of Small Fruits of Jilin Province, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Haiyue Sun
- Engineering Center of Genetic Breeding and Innovative Utilization of Small Fruits of Jilin Province, College of Horticulture, Jilin Agricultural University, Changchun, China
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An H, Zhang J, Xu F, Jiang S, Zhang X. Transcriptomic profiling and discovery of key genes involved in adventitious root formation from green cuttings of highbush blueberry (Vaccinium corymbosum L.). BMC PLANT BIOLOGY 2020; 20:182. [PMID: 32334538 PMCID: PMC7183619 DOI: 10.1186/s12870-020-02398-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/15/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Propagation of cuttings is frequently used in various plant species, including blueberry, which shows special root characteristics that may hinder adventitious root (AR) formation. AR formation is influenced by various factors, and auxin is considered to play a central role; however, little is known of the related regulatory mechanisms. In this study, a comparative transcriptome analysis of green cuttings treated with or without indole-butyric acid (IBA) was performed via RNA_seq to identify candidate genes associated with IBA-induced AR formation. RESULTS Rooting phenotypes, especially the rooting rate, were significantly promoted by exogenous auxin in the IBA application. Blueberry AR formation was an auxin-induced process, during which adventitious root primordium initiation (rpi) began at 14 days after cutting (DAC), root primordium (rp) was developed at 21 DAC, mature AR was observed at 28 DAC and finally outgrowth from the stem occurred at 35 DAC. Higher IAA levels and lower ABA and zeatin contents might facilitate AR formation and development. A time series transcriptome analysis identified 14,970 differentially expressed genes (DEGs) during AR formation, of which there were 7467 upregulated and 7503 downregulated genes. Of these, approximately 35 candidate DEGs involved in the auxin-induced pathway and AR formation were further identified, including 10 auxin respective genes (ARFs and SAURs), 13 transcription factors (LOB domain-containing protein (LBDs)), 6 auxin transporters (AUX22, LAX3/5 and PIN-like 6 (PIL6s)) and 6 rooting-associated genes (root meristem growth factor 9 (RGF9), lateral root primordium 1 (LRP1s), and dormancy-associated protein homologue 3 (DRMH3)). All these identified DEGs were highly upregulated in certain stages during AR formation, indicating their potential roles in blueberry AR formation. CONCLUSIONS The transcriptome profiling results indicated candidate genes or major regulatory factors that influence adventitious root formation in blueberry and provided a comprehensive understanding of the rooting mechanism underlying the auxin-induced AR formation from blueberry green cuttings.
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Affiliation(s)
- Haishan An
- Forestry and Pomology Research Insitute, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China
| | - Jiaying Zhang
- Forestry and Pomology Research Insitute, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China
| | - Fangjie Xu
- Forestry and Pomology Research Insitute, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China
| | - Shuang Jiang
- Forestry and Pomology Research Insitute, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China.
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China.
| | - Xueying Zhang
- Forestry and Pomology Research Insitute, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China.
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Jinqi Road No. 1000, Fengxian District, Shanghai, 201403, China.
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21
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Gao J, Li WB, Liu HF, Chen FB. Identification of differential expression genes related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots using comparative RNA-Seq method. PLoS One 2020; 15:e0231729. [PMID: 32330148 PMCID: PMC7182184 DOI: 10.1371/journal.pone.0231729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/30/2020] [Indexed: 01/13/2023] Open
Abstract
Radish (Raphanus sativus L.), is an important root vegetable crop grown worldwide, and it contains phyto-anthocyanins. However, only limited studies have been conducted to elucidate the molecular mechanisms underlying anthocyanin biosynthesis in the different color variants of the radish fleshy root. In this study, Illumina paired-end RNA-sequencing was employed to characterize the transcriptomic changes in seven different types of radish fleshy roots. Approximately, 126 co-modulated differentially expressed genes were obtained, and most DEGs were more likely to participate in anthocyanin biosynthesis, including two transcription factors RsMYB_9 and RsERF070, and four functional genes RsBRICK1, RsBRI1-like2, RsCOX1, and RsCRK10. In addition, some related genes such as RsCHS, RsCHI, RsANS, RsMT2-4, RsUF3GT, glutathione S-transferase F12, RsUFGT78D2-like and RsUDGT-75C1-like significantly contributed to the regulatory mechanism of anthocyanin biosynthesis in the radish cultivars. Furthermore, gene ontology analysis revealed that the anthocyanin-containing compound biosynthetic process, anthocyanin-containing compound metabolic process, and significantly enriched pathways of the co-modulated DEGs were overrepresented in these cultivars. These results will expand our understanding of the complex molecular mechanism underlying anthocyanin synthesis-related genes in radish.
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Affiliation(s)
- Jian Gao
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China
| | - Wen-Bo Li
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China
| | - Hong-Fang Liu
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China
- Green Intelligence Environmental School, Yangtze Normal University, Fuling, China
| | - Fa-Bo Chen
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, China
- * E-mail:
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Thole V, Bassard JE, Ramírez-González R, Trick M, Ghasemi Afshar B, Breitel D, Hill L, Foito A, Shepherd L, Freitag S, Nunes dos Santos C, Menezes R, Bañados P, Naesby M, Wang L, Sorokin A, Tikhonova O, Shelenga T, Stewart D, Vain P, Martin C. RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics. BMC Genomics 2019; 20:995. [PMID: 31856735 PMCID: PMC6924045 DOI: 10.1186/s12864-019-6183-2] [Citation(s) in RCA: 20] [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: 05/02/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds. RESULTS To access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae. RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database (http://jicbio.nbi.ac.uk/berries) and were used, as a proof of concept, via its BLAST portal (http://jicbio.nbi.ac.uk/berries/blast.html) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry (Rubus genevieri) and cultivated red raspberry (Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana. Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser (http://www.bachberryexp.com) in R. genevieri and R. idaeus cv. Prestige. CONCLUSIONS We report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.
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Affiliation(s)
- Vera Thole
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jean-Etienne Bassard
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark
- Present address: Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 Rue General Zimmer, 67084 Strasbourg, France
| | | | - Martin Trick
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bijan Ghasemi Afshar
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Dario Breitel
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present address: Tropic Biosciences UK LTD, Norwich Research Park, Norwich, NR4 7UG UK
| | - Lionel Hill
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | | | - Sabine Freitag
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - Cláudia Nunes dos Santos
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Rua Câmara Pestana 6, 1150-082 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Regina Menezes
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Rua Câmara Pestana 6, 1150-082 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Pilar Bañados
- Facultad De Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna Ote, 4860 Macul, Chile
| | | | - Liangsheng Wang
- Institute of Botany, The Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Artem Sorokin
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Olga Tikhonova
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Tatiana Shelenga
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Derek Stewart
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Philippe Vain
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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Qi X, Ogden EL, Die JV, Ehlenfeldt MK, Polashock JJ, Darwish O, Alkharouf N, Rowland LJ. Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations. BMC PLANT BIOLOGY 2019; 19:460. [PMID: 31711416 PMCID: PMC6844065 DOI: 10.1186/s12870-019-2073-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/14/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Blueberry is of high economic value. Most blueberry varieties selected for the fresh market have an appealing light blue coating or "bloom" on the fruit due to the presence of a visible heavy epicuticular wax layer. This waxy layer also serves as natural defense against fruit desiccation and deterioration. RESULTS In this study, we attempted to identify gene(s) whose expression is related to the protective waxy coating on blueberry fruit utilizing two unique germplasm populations that segregate for the waxy layer. We bulked RNA from waxy and non-waxy blueberry progenies from the two northern-adapted rabbiteye hybrid breeding populations ('Nocturne' x T 300 and 'Nocturne' x US 1212), and generated 316.85 million RNA-seq reads. We de novo assembled this data set integrated with other publicly available RNA-seq data and trimmed the assembly into a 91,861 blueberry unigene collection. All unigenes were functionally annotated, resulting in 79 genes potentially related to wax accumulation. We compared the expression pattern of waxy and non-waxy progenies using edgeR and identified overall 1125 genes in the T 300 population and 2864 genes in the US 1212 population with at least a two-fold expression difference. After validating differential expression of several genes by RT-qPCR experiments, a candidate gene, FatB, which encodes acyl-[acyl-carrier-protein] hydrolase, emerged whose expression was closely linked to the segregation of the waxy coating in our populations. This gene was expressed at more than a five-fold higher level in waxy than non-waxy plants of both populations. We amplified and sequenced the cDNA for this gene from three waxy plants of each population, but were unable to amplify the cDNA from three non-waxy plants that were tested from each population. We aligned the Vaccinium deduced FATB protein sequence to FATB protein sequences from other plant species. Within the PF01643 domain, which gives FATB its catalytic function, 80.08% of the amino acids were identical or had conservative replacements between the blueberry and the Cucumis melo sequence (XP_008467164). We then amplified and sequenced a large portion of the FatB gene itself from waxy and non-waxy individuals of both populations. Alignment of the cDNA and gDNA sequences revealed that the blueberry FatB gene consists of six exons and five introns. Although we did not sequence through two very large introns, a comparison of the exon sequences found no significant sequence differences between the waxy and non-waxy plants. This suggests that another gene, which regulates or somehow affects FatB expression, must be segregating in the populations. CONCLUSIONS This study is helping to achieve a greater understanding of epicuticular wax biosynthesis in blueberry. In addition, the blueberry unigene collection should facilitate functional annotation of the coming chromosomal level blueberry genome.
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Affiliation(s)
- Xinpeng Qi
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
| | - Elizabeth L. Ogden
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
| | - Jose V. Die
- Departmento de Genetica, University of Córdoba Campus Rabanales, Blg. C5, 14071 Córdoba, Spain
| | - Mark K. Ehlenfeldt
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, at Rutgers University P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019 USA
| | - James J. Polashock
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, at Rutgers University P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019 USA
| | - Omar Darwish
- Department of Mathematics and Computer Science, Texas Woman’s University, Denton, TX 76204 USA
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252 USA
| | - L. Jeannine Rowland
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
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De novo transcriptome sequencing of radish (Raphanus sativus L.) fleshy roots: analysis of major genes involved in the anthocyanin synthesis pathway. BMC Mol Cell Biol 2019; 20:45. [PMID: 31646986 PMCID: PMC6813128 DOI: 10.1186/s12860-019-0228-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 09/20/2019] [Indexed: 01/07/2023] Open
Abstract
Background The HongXin radish (Raphanus sativus L.), which contains the natural red pigment (red radish pigment), is grown in the Fuling district of Chongqing City. However, the molecular mechanisms underlying anthocyanin synthesis for the formation of natural red pigment in the fleshy roots of HongXin radish are not well studied. Results De novo transcriptome of HX-1 radish, as well as that of the advanced inbred lines HX-2 and HX-3 were characterized using next generation sequencing (NGS) technology. In total, approximately 66.22 million paired-end reads comprising 34, 927 unigenes (N50 = 1, 621 bp) were obtained. Based on sequence similarity search with known proteins, total of 30, 127 (about 86.26%) unigenes were identified. Additionally, functional annotation and classification of these unigenes indicated that most of the unigenes were predominantly enriched in the metabolic process-related terms, especially for the biosynthetic pathways of secondary metabolites. Moreover, majority of the anthocyanin biosynthesis-related genes (ABRGs) involved in the regulation of anthocyanin biosynthesis were identified by targeted search for their annotation. Subsequently, the expression of 15 putative ABRGs involved in the anthocyanin synthesis-related pathways were validated using quantitative real-time polymerase chain reaction (qRT-PCR). Of those, RsPAL2, RsCHS-B2, RsDFR1, RsDFR2, RsFLS, RsMT3 and RsUFGT73B2-like were identified significantly associated with anthocyanin biosynthesis. Especially for RsDFR1, RsDFR2 and RsFLS, of those, RsDFR1 and RsDFR2 were highest enriched in the HX-3 and WG-3, but RsFLS were down-regulated in HX-3 and WG-3. We proposed that the transcripts of RsDFR1, RsDFR2 and RsFLS might be act as key regulators in anthocyanin biosynthesis pathway. Conclusions The assembled radish transcript sequences were analysed to identify the key ABRGs involved in the regulation of anthocyanin biosynthesis. Additionally, the expression patterns of candidate ABRGs involved in the anthocyanin biosynthetic pathway were validated by qRT-PCR. We proposed that the transcripts of RsDFR1, RsDFR2 and RsFLS might be acted as key regulators in anthocyanin biosynthesis pathway. This study will enhance our understanding of the biosynthesis and metabolism of anthocyanin in radish.
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25
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Transcriptional regulation of abscisic acid biosynthesis and signal transduction, and anthocyanin biosynthesis in 'Bluecrop' highbush blueberry fruit during ripening. PLoS One 2019; 14:e0220015. [PMID: 31318958 PMCID: PMC6638965 DOI: 10.1371/journal.pone.0220015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/05/2019] [Indexed: 11/19/2022] Open
Abstract
Highbush blueberry (Vaccinium corymbosum) fruit accumulate high levels of anthocyanins during ripening, which might be controlled by abscisic acid (ABA), a signal molecule in non-climacteric fruits. For an integrated view of the ripening process from ABA to anthocyanin biosynthesis, we analyzed the transcriptomes of ‘Bluecrop’ highbush blueberry fruit using RNA-Seq at three ripening stages, categorized based on fruit skin coloration: pale green at ca. 30 days after full bloom (DAFB), reddish purple at ca. 40 DAFB, and dark purple at ca. 50 DAFB. Mapping the trimmed reads against the reference sequences yielded 25,766 transcripts. Of these, 143 transcripts were annotated to encode five ABA biosynthesis enzymes, four ABA signal transduction regulators, four ABA-responsive transcription factors, and 12 anthocyanin biosynthesis enzymes. The analysis of differentially expressed genes between the ripening stages revealed that 11 transcripts, including those encoding nine-cis-epoxycarotenoid dioxygenase, SQUAMOSA-class MADS box transcription factor, and flavonoid 3′,5′-hydroxylase, were significantly up-regulated throughout the entire ripening stages. In fruit treated with 1 g L−1 ABA, at least nine transcripts of these 11 transcripts as well as one transcript encoding flavonoid 3′-hydroxylase were up-regulated, presumably promoting anthocyanin accumulation and fruit skin coloration. These results will provide fundamental information demonstrating that ABA biosynthesis and signal transduction, and anthocyanin biosynthesis are closely associated with anthocyanin accumulation and skin coloration in highbush blueberry fruit during ripening.
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Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS, Nie F. Transcriptome analysis and annotation: SNPs identified from single copy annotated unigenes of three polyploid blueberry crops. PLoS One 2019; 14:e0216299. [PMID: 31034501 PMCID: PMC6488077 DOI: 10.1371/journal.pone.0216299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/17/2019] [Indexed: 02/03/2023] Open
Abstract
Blueberry is a kind of new rising popular perennial fruit with high healthful quality. It is of utmost importance to develop new blueberry varieties for different climatic zones to satisfy the demand of people in the world. Molecular marker assisted breeding is believed to be an ideal method for the development of new blueberry varieties for its shorter breeding cycle than the conventional breeding. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers are widely used molecular tools for marker assisted breeding, which could be detected at large scale by the transcriptome sequencing. Here, we sequenced the leaves transcriptome of 19 rabbiteye (Vaccinium ashei Reade), 13 southern highbush (Vaccinium. corymbosum L × native southern Vaccinium Spp) and 22 cultivars of northern highbush blueberry (Vaccinium corymbosum L) by using next generation sequencing technologies. A total of 80.825 Gb clean data with an average of about 12.525 million reads per cultivar were obtained. We assembled 58,968, 55,973 and 53,887 unigenes by using the clean data from rabbiteye, southern highbush and northern highbush blueberry cultivars, respectively. Among these unigenes, 3599, 3495 and 3513 unigenes were detected as candidate resistance genes in three blueberry crops. Moreover, we identified more than 8756, 9020, and 9198 SSR markers from these unigenes, and 7665, 4861, 13,063 SNPs from the annotated single copy unigenes, respectively. The results will be helpful for the molecular genetics and association analysis of blueberry and the basic molecular information of pest and disease resistance of blueberry, and would also offer huge number of molecular tools for the marker assisted breeding to produce blueberry cultivars with different adaptive characteristics.
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Affiliation(s)
- Yunsheng Wang
- College of Life and Health Science, Kaili University, Kaili City, Guizhou Province, China
- * E-mail: (YW); (FN)
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| | - Fei Nie
- Biological Institute of Guizhou Province, Guiyang City, Guizhou Province, China
- * E-mail: (YW); (FN)
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Li Y, Meng F, Deng X, Wang X, Feng Y, Zhang W, Pan L, Zhang X. Comparative Transcriptome Analysis of the Pinewood Nematode Bursaphelenchus xylophilus Reveals the Molecular Mechanism Underlying Its Defense Response to Host-Derived α-pinene. Int J Mol Sci 2019; 20:E911. [PMID: 30791528 PMCID: PMC6412324 DOI: 10.3390/ijms20040911] [Citation(s) in RCA: 20] [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: 01/17/2019] [Revised: 02/10/2019] [Accepted: 02/16/2019] [Indexed: 12/20/2022] Open
Abstract
Bursaphelenchus xylophilus is fatal to the pine trees around the world. The production of the pine tree secondary metabolite gradually increases in response to a B. xylophilus infestation, via a stress reaction mechanism(s). α-pinene is needed to combat the early stages of B. xylophilus infection and colonization, and to counter its pathogenesis. Therefore, research is needed to characterize the underlying molecular response(s) of B. xylophilus to resist α-pinene. We examined the effects of different concentrations of α-pinene on the mortality and reproduction rate of B. xylophilus in vitro. The molecular response by which B. xylophilus resists α-pinene was examined via comparative transcriptomics of the nematode. Notably, B. xylophilus genes involved in detoxification, transport, and receptor activities were differentially expressed in response to two different concentrations of α-pinene compared with control. Our results contribute to our understanding of the molecular mechanisms by which B. xylophilus responds to monoterpenes in general, and the pathogenesis of B. xylophilus.
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Affiliation(s)
- Yongxia Li
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Fanli Meng
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Xun Deng
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China.
| | - Xuan Wang
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Yuqian Feng
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Wei Zhang
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Long Pan
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Xingyao Zhang
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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Wang Y, Ji S, Dai H, Kong X, Hao J, Wang S, Zhou X, Zhao Y, Wei B, Cheng S, Zhou Q. Changes in Membrane Lipid Metabolism Accompany Pitting in Blueberry During Refrigeration and Subsequent Storage at Room Temperature. FRONTIERS IN PLANT SCIENCE 2019; 10:829. [PMID: 31316535 PMCID: PMC6610484 DOI: 10.3389/fpls.2019.00829] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 06/07/2019] [Indexed: 05/14/2023]
Abstract
Low-temperature storage is the primary postharvest method employed to maintain fruit quality and commercial value. However, pitting can develop during refrigeration, especially during the shelf life. In this study, a membrane lipidomic approach was employed to analyze the potential relationship between pitting and membrane lipid metabolism during post-cold-storage shelf life. We also determined the changes in ultrastructure and water distribution by low-field nuclear magnetic resonance (LF-NMR) and assessed the permeability of membrane, membrane lipid peroxidation, proline and malondialdehyde contents, and the activity and gene expression of phospholipase D and lipoxygenase, which are involved in membrane lipid metabolism. The results indicated that the changes in blueberry phospholipids during storage could be caused by cold stress. Furthermore, dehydration is a manifestation of chilling injury. Finally, the significant increase in electrolyte leakage, content of malondialdehyde and proline, and activity of phospholipase D and lipoxygenase in chilled blueberry also indicated that membrane lipid metabolism plays an important role in cold stress response.
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Ma L, Sun Z, Zeng Y, Luo M, Yang J. Molecular Mechanism and Health Role of Functional Ingredients in Blueberry for Chronic Disease in Human Beings. Int J Mol Sci 2018; 19:E2785. [PMID: 30223619 PMCID: PMC6164568 DOI: 10.3390/ijms19092785] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/08/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Functional ingredients in blueberry have the best health benefits. To obtain a better understanding of the health role of blueberry in chronic disease, we conducted systematic preventive strategies for functional ingredients in blueberry, based on comprehensive databases, especially PubMed, ISI Web of Science, and CNKI for the period 2008⁻2018. Blueberry is rich in flavonoids (mainly anthocyanidins), polyphenols (procyanidin), phenolic acids, pyruvic acid, chlorogenic acid, and others, which have anticancer, anti-obesity, prevent degenerative diseases, anti-inflammation, protective properties for vision and liver, prevent heart diseases, antidiabetes, improve brain function, protective lung properties, strong bones, enhance immunity, prevent cardiovascular diseases, and improve cognitive decline. The anthocyanins and polyphenols in blueberry are major functional ingredients for preventive chronic disease. These results support findings that blueberry may be one of the best functional fruits, and further reveals the mechanisms of anthocyanins and polyphenols in the health role of blueberry for chronic disease. This paper may be used as scientific evidence for developing functional foods, nutraceuticals, and novel drugs of blueberry for preventive chronic diseases.
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Affiliation(s)
- Luyao Ma
- Economics and Management College, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory for Forest Resources Conservation and Utilisation in the Southwest Mountains of China, Southwest Forestry University, Ministry of Education, Kunming 650224, China.
| | - Zhenghai Sun
- Economics and Management College, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory for Forest Resources Conservation and Utilisation in the Southwest Mountains of China, Southwest Forestry University, Ministry of Education, Kunming 650224, China.
| | - Yawen Zeng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.
| | - Mingcan Luo
- Key Laboratory for Forest Resources Conservation and Utilisation in the Southwest Mountains of China, Southwest Forestry University, Ministry of Education, Kunming 650224, China.
| | - Jiazhen Yang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.
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Plunkett BJ, Espley RV, Dare AP, Warren BAW, Grierson ERP, Cordiner S, Turner JL, Allan AC, Albert NW, Davies KM, Schwinn KE. MYBA From Blueberry ( Vaccinium Section Cyanococcus) Is a Subgroup 6 Type R2R3MYB Transcription Factor That Activates Anthocyanin Production. FRONTIERS IN PLANT SCIENCE 2018; 9:1300. [PMID: 30254656 PMCID: PMC6141686 DOI: 10.3389/fpls.2018.01300] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/17/2018] [Indexed: 05/09/2023]
Abstract
The Vaccinium genus in the family Ericaceae comprises many species, including the fruit-bearing blueberry, bilberry, cranberry, huckleberry, and lingonberry. Commercially, the most important are the blueberries (Vaccinium section Cyanococcus), such as Vaccinium corymbosum (northern highbush blueberry), Vaccinium virgatum (rabbiteye blueberry), and Vaccinium angustifolium (lowbush blueberry). The rising popularity of blueberries can partly be attributed to their "superfood" status, with an increasing body of evidence around human health benefits resulting from the fruit metabolites, particularly products of the phenylpropanoid pathway such as anthocyanins. Activation of anthocyanin production by R2R3-MYB transcription factors (TFs) has been characterized in many species, but despite recent studies on blueberry, cranberry, and bilberry, no MYB anthocyanin regulators have been reported for Vaccinium. Indeed, there has been conjecture that at least in bilberry, MYB TFs divergent to the usual type are involved. We report identification of MYBA from blueberry, and show through sequence analysis and functional studies that it is homologous to known anthocyanin-promoting R2R3-MYBs of subgroup 6 of the MYB superfamily. In transient assays, MYBA complemented an anthocyanin MYB mutant of Antirrhinum majus and, together with a heterologous bHLH anthocyanin regulator, activated anthocyanin production in Nicotiana benthamiana. Furthermore anthocyanin accumulation and anthocyanin structural gene expression (assayed by qPCR and RNA-seq analyses) correlated with MYBA expression, and MYBA was able to transactivate the DFR promoter from blueberry and other species. The RNA-seq data also revealed a range of other candidate genes involved in the regulation of anthocyanin production in blueberry fruit. The identification of MYBA will help to resolve the regulatory mechanism for anthocyanin pigmentation in the Vaccinium genus. The sequence information should also prove useful in developing tools for the accelerated breeding of new Vaccinium cultivars.
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Affiliation(s)
- Blue J. Plunkett
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Richard V. Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Andrew P. Dare
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ben A. W. Warren
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ella R. P. Grierson
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Sarah Cordiner
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Janice L. Turner
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Kevin M. Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Kathy E. Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
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Hwang JE, Kim YJ, Shin MH, Hyun HJ, Bohnert HJ, Park HC. A comprehensive analysis of the Korean fir (Abies koreana) genes expressed under heat stress using transcriptome analysis. Sci Rep 2018; 8:10233. [PMID: 29980711 PMCID: PMC6035224 DOI: 10.1038/s41598-018-28552-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 06/22/2018] [Indexed: 11/09/2022] Open
Abstract
Korean fir (Abies koreana), a rare species endemic to South Korea, is sensitive to climate change. Here, we used next-generation massively parallel sequencing technology and de novo transcriptome assembly to gain a comprehensive overview of the Korean fir transcriptome under heat stress. Sequencing control and heat-treated samples of Korean fir, we obtained more than 194,872,650 clean reads from each sample. After de novo assembly and quantitative assessment, 42,056 unigenes were generated with an average length of 908 bp. In total, 6,401 differentially expressed genes were detected, of which 2,958 were up-regulated and 3,443 down-regulated, between the heat-treated and control samples. A gene ontology analysis of these unigenes revealed heat-stress-related terms, such as "response to stimulus". Further, in depth analysis revealed 204 transcription factors and 189 Hsps as differentially expressed. Finally, 12 regulated candidate genes associated with heat stress were examined using quantitative real-time PCR (qRT-PCR). In this study, we present the first comprehensive characterisation of Korean fir subjected to heat stress using transcriptome analysis. It provides an important resource for future studies of Korean fir with the objective of identifying heat stress tolerant lines.
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Affiliation(s)
- Jung Eun Hwang
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Yun Jeong Kim
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Myung Hwan Shin
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Hwa Ja Hyun
- National Institute Forest Science Warm Temperate and Subtropical Forest Research Center, Jeju, Republic of Korea
| | - Hans J Bohnert
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hyeong Cheol Park
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea.
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Lin Y, Wang Y, Li B, Tan H, Li D, Li L, Liu X, Han J, Meng X. Comparative transcriptome analysis of genes involved in anthocyanin synthesis in blueberry. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:561-572. [PMID: 29727860 DOI: 10.1016/j.plaphy.2018.04.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/10/2018] [Accepted: 04/25/2018] [Indexed: 05/09/2023]
Abstract
Blueberry (Vaccinium, family Ericaceae) is well known for its strong antioxidant properties and abundant active ingredients including anthocyanins, flavonols, and proanthocyanidins. In this study, variations in anthocyanin and phenolic compounds content in Bluecrop and Northblue blueberry cultivar fruits were studied, and comparative transcriptome analysis was performed to analyze differences in the molecular mechanisms of anthocyanin biosynthesis. A total of 13 799 unique genes were identified by differential expression analysis, and further subjected to GO classification and pathway enrichment. Nine differentially expressed genes (DEGs), including CHI, DFR, F3'H, FLS, CHS, OMT, UGT, ANS and F3H, were selected to validate the differential expression data using quantitative real-time PCR. The obtained qRT-PCR expression results were consistent with the RNA-Seq results. The expression levels of 9 candidate genes involved in flavonoid biosynthesis and metabolism were concurrent with the anthocyanin content. The developmental stage appeared to affect the expression of genes related to flavonoid biosynthesis to a greater extent than the tissue or cultivar type. This study provides an abundant data resource that will further our understanding of the molecular mechanisms of anthocyanin biosynthesis in blueberries.
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Affiliation(s)
- Yang Lin
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yuehua Wang
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Bin Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Hui Tan
- Faculty of Health Sciences, Hokkaido Universty, Sapporo, Japan
| | - Dongnan Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Li Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xuan Liu
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Jichen Han
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Xianjun Meng
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China.
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Identification of Blueberry miRNAs and Their Targets Based on High-Throughput Sequencing and Degradome Analyses. Int J Mol Sci 2018; 19:ijms19040983. [PMID: 29587414 PMCID: PMC5979386 DOI: 10.3390/ijms19040983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/24/2018] [Accepted: 03/02/2018] [Indexed: 01/06/2023] Open
Abstract
miRNAs are important regulators of plant gene expression. To better characterize their functions, we applied high-throughput sequencing and degradome analyses to investigate three blueberry (Vaccinium ashei) tissues. A total of 127 known and 101 novel miRNAs were identified. Moreover, 141 targets for 42 known and 19 novel miRNAs were experimentally validated by degradome sequencing. A functional analysis of these miRNA targets revealed they were associated with diverse biological activities and several pathways, e.g., anthocyanin biosynthesis and cytokinin signal transduction. The data presented herein expand our understanding of the regulation of blueberry miRNAs during floral and fruit development stages. They may also provide new insights into the roles of miRNAs during anthocyanin biosynthesis in blueberry fruits.
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Alam Z, Roncal J, Peña-Castillo L. Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea. BMC Genomics 2018; 19:4. [PMID: 29291734 PMCID: PMC5748963 DOI: 10.1186/s12864-017-4396-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022] Open
Abstract
Background Lingonberry (Vaccinium vitis-idaea L.), one of the least studied fruit crops in the Ericaceae family, has a dramatically increased worldwide demand due to its numerous health benefits. Genetic markers can facilitate the selection of berries with desirable climatic adaptations, agronomic and nutritious characteristics to improve cultivation programs. However, no genomic resources are available for this species. Results We used Genotyping-by-Sequencing (GBS) to analyze the genetic variation of 56 lingonberry samples from across Newfoundland and Labrador, Canada. To elucidate a potential adaptation to environmental conditions we searched for genotype-environment associations by applying three distinct approaches to screen the identified single nucleotide polymorphisms (SNPs) for correlation with six environmental variables. We also searched for an association between the identified SNPs and two phenotypic traits: the total phenolic content (TPC) and antioxidant capacity (AC) of fruit. We identified 1586 high-quality putative SNPs using the UNEAK pipeline available in TASSEL. We found 132 SNPs likely associated with at least one of the environmental or phenotypic variables. To obtain insights on the function of the genomic sequences containing the SNPs likely to be associated with the environmental or phenotypic variables, we performed a sequence-based functional annotation and identified homologous protein-coding sequences with functional roles related to abiotic stress response, pathogen defense, RNA metabolism, and, most interestingly, phenolic compound biosynthesis. Conclusions The putative SNPs discovered are the first genomic resource for lingonberry. This resource might prove useful in high-density quantitative trait locus analysis, and association mapping. The identified candidate genes containing the SNPs need further studies on their potential role in local adaptation of lingonberry. Altogether, the present study provides new resources that can be used to breed for desirable traits in lingonberry. Electronic supplementary material The online version of this article (10.1186/s12864-017-4396-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zobayer Alam
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada
| | - Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.,Department of Computer Science, Memorial University of Newfoundland, St. John's, NL, A1B 3X5, Canada
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Zhu H, Liu J, Wen Q, Chen M, Wang B, Zhang Q, Xue Z. De novo sequencing and analysis of the transcriptome during the browning of fresh-cut Luffa cylindrica 'Fusi-3' fruits. PLoS One 2017; 12:e0187117. [PMID: 29145430 PMCID: PMC5690621 DOI: 10.1371/journal.pone.0187117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/13/2017] [Indexed: 11/19/2022] Open
Abstract
Fresh-cut luffa (Luffa cylindrica) fruits commonly undergo browning. However, little is known about the molecular mechanisms regulating this process. We used the RNA-seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut fruits from luffa cultivar 'Fusi-3'. Over 90 million high-quality reads were assembled into 58,073 Unigenes, and 60.86% of these were annotated based on sequences in four public databases. We detected 35,282 Unigenes with significant hits to sequences in the NCBInr database, and 24,427 Unigenes encoded proteins with sequences that were similar to those of known proteins in the Swiss-Prot database. Additionally, 20,546 and 13,021 Unigenes were similar to existing sequences in the Eukaryotic Orthologous Groups of proteins and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Furthermore, 27,301 Unigenes were differentially expressed during the browning of fresh-cut luffa fruits (i.e., after 1-6 h). Moreover, 11 genes from five gene families (i.e., PPO, PAL, POD, CAT, and SOD) identified as potentially associated with enzymatic browning as well as four WRKY transcription factors were observed to be differentially regulated in fresh-cut luffa fruits. With the assistance of rapid amplification of cDNA ends technology, we obtained the full-length sequences of the 15 Unigenes. We also confirmed these Unigenes were expressed by quantitative real-time polymerase chain reaction analysis. This study provides a comprehensive transcriptome sequence resource, and may facilitate further studies aimed at identifying genes affecting luffa fruit browning for the exploitation of the underlying mechanism.
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Affiliation(s)
- Haisheng Zhu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Jianting Liu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Qingfang Wen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Mindong Chen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Bin Wang
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Qianrong Zhang
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Zhuzheng Xue
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
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Zhao W, Shi M, Ye XQ, Li F, Wang XW, Chen XX. Comparative transcriptome analysis of venom glands from Cotesia vestalis and Diadromus collaris, two endoparasitoids of the host Plutella xylostella. Sci Rep 2017; 7:1298. [PMID: 28465546 PMCID: PMC5431001 DOI: 10.1038/s41598-017-01383-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/29/2017] [Indexed: 11/09/2022] Open
Abstract
Venoms secreted by the venom gland (VG) of parasitoid wasp help ensure successful parasitism by host immune suppression and developmental regulation. Cotesia vestalis, a larval endoparasitoid, and Diadromus collaris, a pupal endoparasitoid, parasitize the diamondback moth (DBM), Plutella xylostella. To explore and compare the venom components of two endoparasitoids, we sequenced transcriptomes of the VGs and wasp bodies without VGs (BWVGs) of the two endoparasitoids. Statistically enriched GO terms and KEGG pathways of the two VGs compared to respective whole-body background were similar and reflected active protein biosynthesis activities in the two VGs. 1,595 VG specific genes of the D. collaris VG and 1,461 VG specific genes of the C. vestalis VG were identified by comparative transcript profiling. A total of 444 and 513 genes encoding potential secretory proteins were identified and defined as putative venom genes in D. collaris VG and C. vestalis VG, respectively. The putative venom genes of the two wasps showed no significant similarity or convergence. More venom genes were predicted in D. collaris VG than C. vestalis VG, especially hydrolase-coding genes. Differences in the types and quantities of putative venom genes shed light on different venom functions.
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Affiliation(s)
- Wei Zhao
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Min Shi
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xi-Qian Ye
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Fei Li
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xiao-Wei Wang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xue-Xin Chen
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
- State Key Lab of Rice Biology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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Li L, Zhang H, Liu Z, Cui X, Zhang T, Li Y, Zhang L. Comparative transcriptome sequencing and de novo analysis of Vaccinium corymbosum during fruit and color development. BMC PLANT BIOLOGY 2016; 16:223. [PMID: 27729032 PMCID: PMC5059916 DOI: 10.1186/s12870-016-0866-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/05/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Blueberry is an economically important fruit crop in Ericaceae family. The substantial quantities of flavonoids in blueberry have been implicated in a broad range of health benefits. However, the information regarding fruit development and flavonoid metabolites based on the transcriptome level is still limited. In the present study, the transcriptome and gene expression profiling over berry development, especially during color development were initiated. RESULTS A total of approximately 13.67 Gbp of data were obtained and assembled into 186,962 transcripts and 80,836 unigenes from three stages of blueberry fruit and color development. A large number of simple sequence repeats (SSRs) and candidate genes, which are potentially involved in plant development, metabolic and hormone pathways, were identified. A total of 6429 sequences containing 8796 SSRs were characterized from 15,457 unigenes and 1763 unigenes contained more than one SSR. The expression profiles of key genes involved in anthocyanin biosynthesis were also studied. In addition, a comparison between our dataset and other published results was carried out. CONCLUSIONS Our high quality reads produced in this study are an important advancement and provide a new resource for the interpretation of high-throughput data for blueberry species whether regarding sequencing data depth or species extension. The use of this transcriptome data will serve as a valuable public information database for the studies of blueberry genome and would greatly boost the research of fruit and color development, flavonoid metabolisms and regulation and breeding of more healthful blueberries.
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Affiliation(s)
- Lingli Li
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing, 100083 P. R. China
- Present address: College of Forestry, Northwest A&F University, Yangling, Shanxi 712100 P. R. China
| | - Hehua Zhang
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing, 100083 P. R. China
| | - Zhongshuai Liu
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing, 100083 P. R. China
| | - Xiaoyue Cui
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing, 100083 P. R. China
| | - Tong Zhang
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing, 100083 P. R. China
| | - Yanfang Li
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing, 100083 P. R. China
| | - Lingyun Zhang
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing, 100083 P. R. China
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Transcript Profile of Flowering Regulatory Genes in VcFT-Overexpressing Blueberry Plants. PLoS One 2016; 11:e0156993. [PMID: 27271296 PMCID: PMC4896415 DOI: 10.1371/journal.pone.0156993] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
In order to identify genetic components in flowering pathways of highbush blueberry (Vaccinium corymbosum L.), a transcriptome reference composed of 254,396 transcripts and 179,853 gene contigs was developed by assembly of 72.7 million reads using Trinity. Using this transcriptome reference and a query of flowering pathway genes of herbaceous plants, we identified potential flowering pathway genes/transcripts of blueberry. Transcriptome analysis of flowering pathway genes was then conducted on leaf tissue samples of transgenic blueberry cv. Aurora (‘VcFT-Aurora’), which overexpresses a blueberry FLOWERING LOCUS T-like gene (VcFT). Sixty-one blueberry transcripts of 40 genes showed high similarities to 33 known flowering-related genes of herbaceous plants, of which 17 down-regulated and 16 up-regulated genes were identified in ‘VcFT-Aurora’. All down-regulated genes encoded transcription factors/enzymes upstream in the signaling pathway containing VcFT. A blueberry CONSTANS-LIKE 5-like (VcCOL5) gene was down-regulated and associated with five other differentially expressed (DE) genes in the photoperiod-mediated flowering pathway. Three down-regulated genes, i.e., a MADS-AFFECTING FLOWERING 2-like gene (VcMAF2), a MADS-AFFECTING FLOWERING 5-like gene (VcMAF5), and a VERNALIZATION1-like gene (VcVRN1), may function as integrators in place of FLOWERING LOCUS C (FLC) in the vernalization pathway. Because no CONSTAN1-like or FLOWERING LOCUS C-like genes were found in blueberry, VcCOL5 and VcMAF2/VcMAF5 or VRN1 might be the major integrator(s) in the photoperiod- and vernalization-mediated flowering pathway, respectively. The major down-stream genes of VcFT, i.e., SUPPRESSOR of Overexpression of Constans 1-like (VcSOC1), LEAFY-like (VcLFY), APETALA1-like (VcAP1), CAULIFLOWER 1-like (VcCAL1), and FRUITFULL-like (VcFUL) genes were present and showed high similarity to their orthologues in herbaceous plants. Moreover, overexpression of VcFT promoted expression of all of these VcFT downstream genes. These results suggest that VcFT’s down-stream genes appear conserved in blueberry.
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Karppinen K, Zoratti L, Nguyenquynh N, Häggman H, Jaakola L. On the Developmental and Environmental Regulation of Secondary Metabolism in Vaccinium spp. Berries. FRONTIERS IN PLANT SCIENCE 2016; 7:655. [PMID: 27242856 PMCID: PMC4870239 DOI: 10.3389/fpls.2016.00655] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/28/2016] [Indexed: 05/24/2023]
Abstract
Secondary metabolites have important defense and signaling roles, and they contribute to the overall quality of developing and ripening fruits. Blueberries, bilberries, cranberries, and other Vaccinium berries are fleshy berry fruits recognized for the high levels of bioactive compounds, especially anthocyanin pigments. Besides anthocyanins and other products of the phenylpropanoid and flavonoid pathways, these berries also contain other metabolites of interest, such as carotenoid derivatives, vitamins and flavor compounds. Recently, new information has been achieved on the mechanisms related with developmental, environmental, and genetic factors involved in the regulation of secondary metabolism in Vaccinium fruits. Especially light conditions and temperature are demonstrated to have a prominent role on the composition of phenolic compounds. The present review focuses on the studies on mechanisms associated with the regulation of key secondary metabolites, mainly phenolic compounds, in Vaccinium berries. The advances in the research concerning biosynthesis of phenolic compounds in Vaccinium species, including specific studies with mutant genotypes in addition to controlled and field experiments on the genotype × environment (G×E) interaction, are discussed. The recently published Vaccinium transcriptome and genome databases provide new tools for the studies on the metabolic routes.
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Affiliation(s)
- Katja Karppinen
- Genetics and Physiology Unit, University of Oulu, OuluFinland
- Climate laboratory Holt, Department of Arctic and Marine Biology, UiT the Arctic University of Norway, TromsøNorway
| | - Laura Zoratti
- Genetics and Physiology Unit, University of Oulu, OuluFinland
| | - Nga Nguyenquynh
- Genetics and Physiology Unit, University of Oulu, OuluFinland
| | - Hely Häggman
- Genetics and Physiology Unit, University of Oulu, OuluFinland
| | - Laura Jaakola
- Climate laboratory Holt, Department of Arctic and Marine Biology, UiT the Arctic University of Norway, TromsøNorway
- NIBIO, Norwegian Institute of Bioeconomy Research, ÅsNorway
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Qiu Z, Wang X, Gao J, Guo Y, Huang Z, Du Y. The Tomato Hoffman's Anthocyaninless Gene Encodes a bHLH Transcription Factor Involved in Anthocyanin Biosynthesis That Is Developmentally Regulated and Induced by Low Temperatures. PLoS One 2016; 11:e0151067. [PMID: 26943362 PMCID: PMC4778906 DOI: 10.1371/journal.pone.0151067] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 02/23/2016] [Indexed: 12/28/2022] Open
Abstract
Anthocyanin pigments play many roles in plants, including providing protection against biotic and abiotic stresses. Many of the genes that mediate anthocyanin accumulation have been identified through studies of flowers and fruits; however, the mechanisms of genes involved in anthocyanin regulation in seedlings under low-temperature stimulus are less well understood. Genetic characterization of a tomato inbred line, FMTT271, which showed no anthocyanin pigmentation, revealed a mutation in a bHLH transcription factor (TF) gene, which corresponds to the ah (Hoffman's anthocyaninless) locus, and so the gene in FMTT271 at that locus was named ah. Overexpression of the wild type allele of AH in FMTT271 resulted in greater anthocyanin accumulation and increased expression of several genes in the anthocyanin biosynthetic pathway. The expression of AH and anthocyanin accumulation in seedlings was shown to be developmentally regulated and induced by low-temperature stress. Additionally, transcriptome analyses of hypocotyls and leaves from the near-isogenic lines seedlings revealed that AH not only influences the expression of anthocyanin biosynthetic genes, but also genes associated with responses to abiotic stress. Furthermore, the ah mutation was shown to cause accumulation of reactive oxidative species and the constitutive activation of defense responses under cold conditions. These results suggest that AH regulates anthocyanin biosynthesis, thereby playing a protective role, and that this function is particularly important in young seedlings that are particularly vulnerable to abiotic stresses.
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Affiliation(s)
- Zhengkun Qiu
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xiaoxuan Wang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Jianchang Gao
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Yanmei Guo
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Zejun Huang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Yongchen Du
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
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Casimiro-Soriguer I, Narbona E, Buide ML, del Valle JC, Whittall JB. Transcriptome and Biochemical Analysis of a Flower Color Polymorphism in Silene littorea (Caryophyllaceae). FRONTIERS IN PLANT SCIENCE 2016; 7:204. [PMID: 26973662 PMCID: PMC4770042 DOI: 10.3389/fpls.2016.00204] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/06/2016] [Indexed: 05/23/2023]
Abstract
Flower color polymorphisms are widely used as model traits from genetics to ecology, yet determining the biochemical and molecular basis can be challenging. Anthocyanin-based flower color variations can be caused by at least 12 structural and three regulatory genes in the anthocyanin biosynthetic pathway (ABP). We use mRNA-Seq to simultaneously sequence and estimate expression of these candidate genes in nine samples of Silene littorea representing three color morphs (dark pink, light pink and white) across three developmental stages in hopes of identifying the cause of flower color variation. We identified 29 putative paralogs for the 15 candidate genes in the ABP. We assembled complete coding sequences for 16 structural loci and nine of ten regulatory loci. Among these 29 putative paralogs, we identified 622 SNPs, yet only nine synonymous SNPs in Ans had allele frequencies that differentiated pigmented petals (dark pink and light pink) from white petals. These Ans allele frequency differences were further investigated with an expanded sequencing survey of 38 individuals, yet no SNPs consistently differentiated the color morphs. We also found one locus, F3h1, with strong differential expression between pigmented and white samples (>42x). This may be caused by decreased expression of Myb1a in white petal buds. Myb1a in S. littorea is a regulatory locus closely related to Subgroup 7 Mybs known to regulate F3h and other loci in the first half of the ABP in model species. We then compare the mRNA-Seq results with petal biochemistry which revealed cyanidin as the primary anthocyanin and five flavonoid intermediates. Concentrations of three of the flavonoid intermediates were significantly lower in white petals than in pigmented petals (rutin, quercetin and isovitexin). The biochemistry results for rutin, quercetin, luteolin and apigenin are consistent with the transcriptome results suggesting a blockage at F3h, possibly caused by downregulation of Myb1a.
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Affiliation(s)
- Inés Casimiro-Soriguer
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
- Department of Plant Biology and Ecology, University of SevilleSeville, Spain
| | - Eduardo Narbona
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - M. L. Buide
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - José C. del Valle
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - Justen B. Whittall
- Department of Biology, Santa Clara University, College of Arts and SciencesSanta Clara, CA, USA
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Castro JC, Maddox JD, Cobos M, Requena D, Zimic M, Bombarely A, Imán SA, Cerdeira LA, Medina AE. De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. BMC Genomics 2015; 16:997. [PMID: 26602763 PMCID: PMC4658800 DOI: 10.1186/s12864-015-2225-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/17/2015] [Indexed: 01/13/2023] Open
Abstract
Background Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. Results In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. Conclusions This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2225-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan C Castro
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú. .,Círculo de Investigación en Plantas con Efecto en Salud (FONDECYT N° 010-2014), Lima, Perú.
| | - J Dylan Maddox
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum of Natural History, Chicago, IL, USA.
| | - Marianela Cobos
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Av. Abelardo Quiñones km 2.5, San Juan Bautista, Iquitos, Perú.
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | | | - Sixto A Imán
- Área de Conservación de Recursos Fitogenéticos, Instituto Nacional de Innovación Agraria (INIA), Calle San Roque 209, Iquitos, Perú.
| | - Luis A Cerdeira
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
| | - Andersson E Medina
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
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Sun H, Liu Y, Gai Y, Geng J, Chen L, Liu H, Kang L, Tian Y, Li Y. De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation. BMC Genomics 2015; 16:652. [PMID: 26330221 PMCID: PMC4556307 DOI: 10.1186/s12864-015-1842-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 08/14/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cranberries (Vaccinium macrocarpon Ait.), renowned for their excellent health benefits, are an important berry crop. Here, we performed transcriptome sequencing of one cranberry cultivar, from fruits at two different developmental stages, on the Illumina HiSeq 2000 platform. Our main goals were to identify putative genes for major metabolic pathways of bioactive compounds and compare the expression patterns between white fruit (W) and red fruit (R) in cranberry. RESULTS In this study, two cDNA libraries of W and R were constructed. Approximately 119 million raw sequencing reads were generated and assembled de novo, yielding 57,331 high quality unigenes with an average length of 739 bp. Using BLASTx, 38,460 unigenes were identified as putative homologs of annotated sequences in public protein databases, including NCBI NR, NT, Swiss-Prot, KEGG, COG and GO. Of these, 21,898 unigenes mapped to 128 KEGG pathways, with the metabolic pathways, secondary metabolites, glycerophospholipid metabolism, ether lipid metabolism, starch and sucrose metabolism, purine metabolism, and pyrimidine metabolism being well represented. Among them, many candidate genes were involved in flavonoid biosynthesis, transport and regulation. Furthermore, digital gene expression (DEG) analysis identified 3,257 unigenes that were differentially expressed between the two fruit developmental stages. In addition, 14,473 simple sequence repeats (SSRs) were detected. CONCLUSIONS Our results present comprehensive gene expression information about the cranberry fruit transcriptome that could facilitate our understanding of the molecular mechanisms of fruit development in cranberries. Although it will be necessary to validate the functions carried out by these genes, these results could be used to improve the quality of breeding programs for the cranberry and related species.
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Affiliation(s)
- Haiyue Sun
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Yushan Liu
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Yuzhuo Gai
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Jinman Geng
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Li Chen
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Hongdi Liu
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Limin Kang
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Youwen Tian
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
| | - Yadong Li
- College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China.
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Primetta AK, Karppinen K, Riihinen KR, Jaakola L. Metabolic and molecular analyses of white mutant Vaccinium berries show down-regulation of MYBPA1-type R2R3 MYB regulatory factor. PLANTA 2015; 242:631-43. [PMID: 26168981 DOI: 10.1007/s00425-015-2363-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/30/2015] [Indexed: 05/06/2023]
Abstract
MYBPA1-type R2R3 MYB transcription factor shows down-regulation in white mutant berries of Vaccinium uliginosum deficient in anthocyanins but not proanthocyanidins suggesting a role in the regulation of anthocyanin biosynthesis. Berries of the genus Vaccinium are among the best natural sources of flavonoids. In this study, the expression of structural and regulatory flavonoid biosynthetic genes and the accumulation of flavonoids in white mutant and blue-colored wild-type bog bilberry (V. uliginosum) fruits were measured at different stages of berry development. In contrast to high contents of anthocyanins in ripe blue-colored berries, only traces were detected by HPLC-ESI-MS in ripe white mutant berries. However, similar profile and high levels of flavonol glycosides and proanthocyanidins were quantified in both ripe white and ripe wild-type berries. Analysis with qRT-PCR showed strong down-regulation of structural genes chalcone synthase (VuCHS), dihydroflavonol 4-reductase (VuDFR) and anthocyanidin synthase (VuANS) as well as MYBPA1-type transcription factor VuMYBPA1 in white berries during ripening compared to wild-type berries. The profiles of transcript accumulation of chalcone isomerase (VuCHI), anthocyanidin reductase (VuANR), leucoanthocyanidin reductase (VuLAR) and flavonoid 3'5' hydroxylase (VuF3'5'H) were more similar between the white and the wild-type berries during fruit development, while expression of UDP-glucose: flavonoid 3-O-glucosyltransferase (VuUFGT) showed similar trend but fourfold lower level in white mutant. VuMYBPA1, the R2R3 MYB family member, is a homologue of VmMYB2 of V. myrtillus and VcMYBPA1 of V. corymbosum and belongs to MYBPA1-type MYB family which members are shown in some species to be related with proanthocyanidin biosynthesis in fruits. Our results combined with earlier data of the role of VmMYB2 in white mutant berries of V. myrtillus suggest that the regulation of anthocyanin biosynthesis in Vaccinium species could differ from other species studied.
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Affiliation(s)
- Anja K Primetta
- Department of Environmental Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
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Zoratti L, Jaakola L, Häggman H, Giongo L. Modification of Sunlight Radiation through Colored Photo-Selective Nets Affects Anthocyanin Profile in Vaccinium spp. Berries. PLoS One 2015; 10:e0135935. [PMID: 26288240 PMCID: PMC4545418 DOI: 10.1371/journal.pone.0135935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/28/2015] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES In recent years, the interest on the effects of the specific wavelengths of the light spectrum on growth and metabolism of plants has been increasing markedly. The present study covers the effect of modified sunlight conditions on the accumulation of anthocyanin pigments in two Vaccinium species: the European wild bilberry (V. myrtillus L.) and the cultivated highbush blueberry (V. corymbosum L.). METHODS The two Vaccinium species were grown in the same test field in the Alps of Trentino (Northern Italy) under modified light environment. The modification of sunlight radiation was carried out in field, through the use of colored photo-selective nets throughout the berry ripening during two consecutive growing seasons. The anthocyanin profile was then assessed in berries at ripeness. RESULTS The results indicated that the light responses of the two Vaccinium species studied were different. Although both studied species are shade-adapted plants, 90% shading of sunlight radiation was beneficial only for bilberry plants, which accumulated the highest content of anthocyanins in both seasons. The same condition, instead, was not favorable for blueberries, whose maturation was delayed for at least two weeks, and anthocyanin accumulation was significantly decreased compared to berries grown under sunlight conditions. Moreover, the growing season had strong influence on the anthocyanin accumulation in both species, in relation to temperature flow and sunlight spectra composition during the berry ripening period. CONCLUSIONS Our results suggest that the use of colored photo-selective nets may be a complementary agricultural practice for cultivation of Vaccinium species. However, further studies are needed to analyze the effect of the light spectra modifications to other nutritional properties, and to elucidate the molecular mechanisms behind the detected differences between the two relative Vaccinium species.
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Affiliation(s)
- Laura Zoratti
- Genetics and Physiology Unit, University of Oulu, Oulu, Finland
- Genomics and Biology of Fruit Crop Department, Research and Innovation Center, Edmund Mach Foundation, S. Michele all'Adige, Trento, Italy
| | - Laura Jaakola
- Climate laboratory, Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian Institute of Bioeconomy Research, NIBIO Holt, Tromsø, Norway
| | - Hely Häggman
- Genetics and Physiology Unit, University of Oulu, Oulu, Finland
| | - Lara Giongo
- Genomics and Biology of Fruit Crop Department, Research and Innovation Center, Edmund Mach Foundation, S. Michele all'Adige, Trento, Italy
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Zhang D, Lu K, Jiang G, Liu W, Dong Z, Tian H, Li X. A global transcriptional analysis of Megalobrama amblycephala revealing the molecular determinants of diet-induced hepatic steatosis. Gene 2015; 570:255-63. [PMID: 26074088 DOI: 10.1016/j.gene.2015.06.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/19/2015] [Accepted: 06/09/2015] [Indexed: 02/07/2023]
Abstract
Blunt snout bream (Megalobrama amblycephala), a prevalent species in China's intensive polyculture systems, is highly susceptible to hepatic steatosis, resulting in considerable losses to the fish farming industry. Due to a lack of genomic resources, the molecular mechanisms of lipid metabolism in M. amblycephala are poorly understood. Here, a hepatic cDNA library was generated from equal amounts of mRNAs isolated from M. amblycephala fed normal-fat and high-fat diets. Sequencing of this library using the Illumina/Solexa platform produced approximately 51.87 million clean reads, which were assembled into 48,439 unigenes with an average length of 596 bp and an N50 value of 800 bp. These unigenes were searched against the nucleotide (NT), non-redundant (NR), Swiss-Prot, Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases using the BLASTn or BLASTx algorithms (E-value ≤ 10(-5)). A total of 8602 unigenes and 22,155 unigenes were functionally classified into 25 COG categories and 259 KEGG pathways, respectively. Furthermore, 22,072 unigenes were grouped into 62 sub-categories belonging to three main Gene Ontology (GO) terms. Using a digital gene expression analysis and the M. amblycephala transcriptome as a reference, 477 genes (134 up-regulated and 343 down-regulated) were identified as differentially expressed in fish fed a high-fat diet versus a normal-fat diet. KEGG and GO functional enrichment analyses of the differentially expressed unigenes were performed and 12 candidate genes related to lipid metabolism were identified. This study provides a global survey of hepatic transcriptome profiles and identifies candidate genes that may be related to lipid metabolism in M. amblycephala. These findings will facilitate further investigations of the mechanisms underlying hepatic steatosis in M. amblycephala.
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Affiliation(s)
- Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Kangle Lu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenbin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Hongyan Tian
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Liu JP, Xia ZQ, Tian XY, Li YJ. Transcriptome sequencing and analysis of rubber tree (Hevea brasiliensis Muell.) to discover putative genes associated with tapping panel dryness (TPD). BMC Genomics 2015; 16:398. [PMID: 25994052 PMCID: PMC4438507 DOI: 10.1186/s12864-015-1562-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/21/2015] [Indexed: 01/13/2023] Open
Abstract
Background Tapping panel dryness (TPD) involves in the partial or complete cessation of latex flow thus seriously affect latex production in rubber tree (Hevea brasiliensis). Numerous studies have been conducted to define its origin and nature, but the molecular nature and mechanism of TPD occurrence remains unknown. This study is committed to de novo sequencing and comparative analysis of the transcriptomes of healthy (H) and TPD-affected (T) rubber trees to identify the genes and pathways related to the TPD. Results Total raw reads of 34,632,012 and 35,913,020 bp were obtained from H and T library, respectively using Illumina Hiseq 2000 sequencing technology. De novo assemblies yielded 141,456 and 169,285 contigs, and 96,070 and 112,243 unigenes from H and T library, respectively. Among 73597 genes, 22577 genes were identified as differential expressed genes between H and T library via comparative transcript profiling. A majority of genes involved in natural rubber biosynthesis and jasmonate synthesis with most potential relevance in TPD occurrence were found to be differentially expressed. Conclusions In TPD-affected trees, the expression of most genes related to the latex biosynthesis and jasmonate synthesis was severely inhibited and is probably the direct cause of the TPD. These new de novo transcriptome data sets provide a significant resource for the discovery of genes related to TPD and improve our understanding of the occurrence and maintainace of TPD. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1562-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jin-Ping Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agronomy, Hainan University, Haikou, Hainan Province, 570228, P. R China.
| | - Zhi-Qiang Xia
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan Province, 571101, P. R China.
| | - Xiao-Yan Tian
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agronomy, Hainan University, Haikou, Hainan Province, 570228, P. R China.
| | - Yi-Jian Li
- Service Center of Science and Technology, Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan Province, 571737, P. R China.
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Wu ZG, Jiang W, Mantri N, Bao XQ, Chen SL, Tao ZM. Transciptome analysis reveals flavonoid biosynthesis regulation and simple sequence repeats in yam (Dioscorea alata L.) tubers. BMC Genomics 2015; 16:346. [PMID: 25924983 PMCID: PMC4415240 DOI: 10.1186/s12864-015-1547-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/17/2015] [Indexed: 01/06/2023] Open
Abstract
Background Yam (Dioscorea alata L.) is an important tuber crop and purple pigmented elite cultivar has recently become popular because of associated health benefits. Identifying candidate genes responsible for flavonoid biosynthesis pathway (FBP) will facilitate understanding the molecular mechanism of controlling pigment formation in yam tubers. Here, we used Illumina sequencing to characterize the transcriptome of tubers from elite purple-flesh cultivar (DP) and conventional white-flesh cultivar (DW) of yam. In this process, we also designed high quality molecular markers to assist molecular breeding for tuber trait improvement. Results A total of 125,123 unigenes were identified from the DP and DW cDNA libraries, of which about 49.5% (60,020 unigenes) were annotated by BLASTX analysis using the publicly available protein database. These unigenes were further annotated functionally and subject to biochemical pathway analysis. 511 genes were identified to be more than 2-fold (FDR < 0.05) differentially expressed between the two yam cultivars, of which 288 genes were up-regulated and 223 genes were down-regulated in the DP tubers. Transcriptome analysis detected 61 unigenes encoding multiple well-known enzymes in the FBP. Furthermore, the unigenes encoding chalcone isomerase (CHS), flavanone 3-hydroxylase (F3H), flavonoid 3′-monooxygenase (F3’H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX), and flavonol 3-O-glucosyltransferase (UF3GT) were found to be significantly up-regulated in the DP, implying that these genes were potentially associated with tuber color formation in this elite cultivar. The expression of these genes was further confirmed by qRT-PCR. Finally, 11,793 SSRs were successfully identified with these unigenes and 6,082 SSR markers were developed using Primer 3. Conclusions This study provides the first comprehensive transcriptomic dataset for yam tubers, which will significantly contribute to genomic research of this and other related species. Some key genes associated with purple-flesh trait were successfully identified, thus providing valuable information about molecular process of regulating pigment accumulation in elite yam tubers. In the future, this information might be directly used to genetically manipulate the conventional white-fleshed tuber cultivars to enable them to produce purple flesh. In addition, our SSR marker sets will facilitate identification of QTLs for various tuber traits in yam breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1547-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhi-Gang Wu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China.
| | - Wu Jiang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China.
| | - Nitin Mantri
- School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, VIC, Australia.
| | - Xiao-Qing Bao
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China. .,School of pharmacy, Wenzhou Medical University, Wenzhou, 325035, P.R. China.
| | - Song-Lin Chen
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China. .,School of pharmacy, Wenzhou Medical University, Wenzhou, 325035, P.R. China.
| | - Zheng-Ming Tao
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, P.R. China.
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Wei C, Tao X, Li M, He B, Yan L, Tan X, Zhang Y. De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification. Mol Genet Genomics 2015; 290:1873-84. [PMID: 25877516 DOI: 10.1007/s00438-015-1034-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 03/23/2015] [Indexed: 01/14/2023]
Abstract
Ipomoea nil is widely used as an ornamental plant due to its abundance of flower color, but the limited transcriptome and genomic data hinder research on it. Using illumina platform, transcriptome profiling of I. nil was performed through high-throughput sequencing, which was proven to be a rapid and cost-effective means to characterize gene content. Our goal is to use the resulting information to facilitate the relevant research on flowering and flower color formation in I. nil. In total, 268 million unique illumina RNA-Seq reads were produced and used in the transcriptome assembly. These reads were assembled into 220,117 contigs, of which 137,307 contigs were annotated using the GO and KEGG database. Based on the result of functional annotations, a total of 89,781 contigs were assigned 455,335 GO term annotations. Meanwhile, 17,418 contigs were identified with pathway annotation and they were functionally assigned to 144 KEGG pathways. Our transcriptome revealed at least 55 contigs as probably flowering-related genes in I. nil, and we also identified 25 contigs that encode key enzymes in the phenylpropanoid biosynthesis pathway. Based on the analysis relating to gene expression profiles, in the phenylpropanoid biosynthesis pathway of I. nil, the repression of lignin biosynthesis might lead to the redirection of the metabolic flux into anthocyanin biosynthesis. This may be the most likely reason that I. nil has high anthocyanins content, especially in its flowers. Additionally, 15,537 simple sequence repeats (SSRs) were detected using the MISA software, and these SSRs will undoubtedly benefit future breeding work. Moreover, the information uncovered in this study will also serve as a valuable resource for understanding the flowering and flower color formation mechanisms in I. nil.
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Affiliation(s)
- Changhe Wei
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Ming Li
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, China
| | - Bin He
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Lang Yan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Xuemei Tan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Yizheng Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
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Wei H, Chen X, Zong X, Shu H, Gao D, Liu Q. Comparative transcriptome analysis of genes involved in anthocyanin biosynthesis in the red and yellow fruits of sweet cherry (Prunus avium L.). PLoS One 2015; 10:e0121164. [PMID: 25799516 PMCID: PMC4370391 DOI: 10.1371/journal.pone.0121164] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/28/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry. METHODOLOGY/PRINCIPAL FINDINGS In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR). CONCLUSIONS/SIGNIFICANCE The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into the molecular mechanisms underlying anthocyanin biosynthesis. These results will provide a platform for further functional genomic research on this fruit crop.
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Affiliation(s)
- Hairong Wei
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai’an, Shandong 271000, China
| | - Xin Chen
- Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai’an, Shandong 271000, China
| | - Xiaojuan Zong
- Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai’an, Shandong 271000, China
| | - Huairui Shu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Dongsheng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Qingzhong Liu
- Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai’an, Shandong 271000, China
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