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Zhu J, Zhang K, Xiong H, Xie Y, Li R, Wu X, Yang Y, Wu H, Hao Z, Sun X, Chen J. H 2O 2 Significantly Affects Larix kaempferi × Larix olgensis Somatic Embryogenesis. Int J Mol Sci 2024; 25:669. [PMID: 38203839 PMCID: PMC10779820 DOI: 10.3390/ijms25010669] [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: 12/03/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Larch is widely distributed throughout the world and is an important species for timber supply and the extraction of industrial raw materials. In recent years, the hybrid breeding of Larix kaempferi and Larix olgensis has shown obvious heterosis in quick-growth, stress resistance and wood properties. However, its growth and development cycle is too long to meet general production needs. In order to shorten the breeding cycle, we have for the first time successfully established and optimized a somatic embryogenesis system for Larix kaempferi × Larix olgensis. We found that the highest rate of embryonal-suspensor mass (ESM) induction was observed when late cotyledonary embryos were used as explants. The induced ESMs were subjected to stable proliferation, after which abscisic acid (ABA) and polyethylene glycol (PEG) were added to successfully induce somatic embryos. Treatment with PEG and ABA was of great importance to somatic embryo formation and complemented each other's effect. ABA assisted embryo growth, whereas PEG facilitated the formation of proembryo-like structures. On top of this, we studied in more detail the relationship between redox homeostasis and the efficiency of somatic embryogenesis (frequency of ESM induction). During subculture, we observed the gradual formation of three distinct types of ESM. The Type I ESM is readily able to form somatic embryos. In contrast to type I, the type III ESM suffers from severe browning, contains a higher level of hydrogen peroxide (H2O2) and demonstrates a decreased ability to form somatic embryos. External treatment with H2O2 decreased the somatic embryogenesis efficiency of Type I and type III ESMs, or the higher the exogenous H2O2 content, the lower the resulting somatic embryogenesis efficiency. We found that treatment with the H2O2 scavenger DMTU (dimethylthiourea) could significantly increase the somatic embryogenesis efficiency of the type III ESM, as a result of a decline in endogenous H2O2 content. Overall, these findings have contributed to setting up a successful somatic embryogenesis system for larch production.
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Affiliation(s)
- Junjie Zhu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (J.Z.); (H.X.); (R.L.); (X.W.); (Y.Y.); (H.W.); (Z.H.)
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Kaikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (K.Z.); (Y.X.)
| | - Huiru Xiong
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (J.Z.); (H.X.); (R.L.); (X.W.); (Y.Y.); (H.W.); (Z.H.)
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Yunhui Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (K.Z.); (Y.X.)
| | - Rui Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (J.Z.); (H.X.); (R.L.); (X.W.); (Y.Y.); (H.W.); (Z.H.)
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Xinru Wu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (J.Z.); (H.X.); (R.L.); (X.W.); (Y.Y.); (H.W.); (Z.H.)
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Yun Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (J.Z.); (H.X.); (R.L.); (X.W.); (Y.Y.); (H.W.); (Z.H.)
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Hua Wu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (J.Z.); (H.X.); (R.L.); (X.W.); (Y.Y.); (H.W.); (Z.H.)
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (J.Z.); (H.X.); (R.L.); (X.W.); (Y.Y.); (H.W.); (Z.H.)
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaomei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (K.Z.); (Y.X.)
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (J.Z.); (H.X.); (R.L.); (X.W.); (Y.Y.); (H.W.); (Z.H.)
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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He J, Sun ML, Li DW, Zhu LH, Ye JR, Huang L. A real-time PCR for detection of pathogens of anthracnose on Chinese fir using TaqMan probe targeting ApMat gene. PEST MANAGEMENT SCIENCE 2023; 79:980-988. [PMID: 36310118 DOI: 10.1002/ps.7260] [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: 07/03/2022] [Revised: 10/13/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Anthracnose is one of the most widespread and destructive diseases on Chinese fir. Colletotrichum cangyuanense, Colletotrichum fructicola, Colletotrichum gloeosporioides, and Colletotrichum siamense are the causal agents of anthracnose on Chinese fir. A rapid and accurate diagnosis of different pathogens is critical for the disease management. RESULTS Phylogenetic tree and sequence similarity analysis showed that the single-locus ApMat provides superior phylogenetic information and is an appropriate target to distinguish C. cangyuanense, C. fructicola, C. gloeosporioides, and C. siamense. The real-time PCR assays with the primer sets of MQ-F/R, 1#C-F/R, YK-F/R, and WZ-F/R, and corresponding TaqMan probes of MQ-P, 1#C-P, YK-P, and WZ-P were specific for C. cangyuanense, C. fructicola, C. gloeosporioides, and C. siamense, respectively. The sensitivity tests showed that the lowest amount of gDNA that the PCRs can detect was 1 ng of genomic DNA. The validity of the assays was confirmed by directly detecting the pathogens from both the fungal culture and infected Chinese fir. CONCLUSION These results demonstrated the potential of the TaqMan real-time PCR targeting the ApMat gene to provide rapid, specific, and reliable molecular detection of C. fructicola, C. gloeosporioides, C. siamense, and C. cangyuanense, respectively. The data also provided a reference solution for the identification of species within Colletotrichum gloeosporioides species complex (CGSC), which share similar morphological characteristics. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Jiao He
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Mei-Ling Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - De-Wei Li
- The Connecticut Agricultural Experiment Station Valley Laboratory, Windsor, CT, USA
| | - Li-Hua Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jian-Ren Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lin Huang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Further Mining and Characterization of miRNA Resource in Chinese Fir (Cunninghamia lanceolata). Genes (Basel) 2022; 13:genes13112137. [DOI: 10.3390/genes13112137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
In this study, we aimed to expand the current miRNA data bank of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) regarding its potential value for further genetic and genomic use in this species. High-throughput small RNA sequencing successfully captured 140 miRNAs from a Chinese fir selfing family harboring vigor and depressed progeny. Strikingly, 75.7% (n = 106) of these miRNAs have not been documented previously, and most (n = 105) of them belong to the novel set with 6858 putative target genes. The new datasets were then integrated with the previous information to gain insight into miRNA genetic architecture in Chinese fir. Collectively, a relatively high proportion (62%, n = 110) of novel miRNAs were found. Furthermore, we identified one MIR536 family that has not been previously documented in this species and four overlapped miRNA families (MIR159, MIR164, MIR171_1, and MIR396) from new datasets. Regarding the stability, we calculated the secondary structure free energy and found a relatively low R2 value (R2 < 0.22) between low minimal folding free energy (MFE) of pre-miRNAs and MFE of its corresponding mature miRNAs in most datasets. When in view of the conservation aspect, the phylogenetic trees showed that MIR536 and MIR159 sequences were highly conserved in gymnosperms.
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Liao YCZ, Sun JW, Li DW, Nong ML, Zhu LH. First Report of Top Blight of Cunninghamia lanceolata Caused by Diaporthe unshiuensis and Diaporthe hongkongensis in China. PLANT DISEASE 2022; 107:962. [PMID: 35876759 DOI: 10.1094/pdis-06-22-1467-pdn] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cunninghamia lanceolata (Lamb.) Hook. is an important conifer species widely planted in southern China. A top blight, with an incidence of 20% (40/200 seedlings), occurred on 1-year-old seedlings of C. lanceolata in a nursery, Luzhai, Guangxi, China in August 2021. The disease mainly occurred on shoot tips. The infected needles and shoots appeared brown to brownish red. White conidial tendrils oozed from pycnidia under wet-weather conditions. Lesion margins from fresh samples were cut into small pieces (n=100), which were sterilized according to Mao et al., and placed on potato dextrose agar (PDA) at 25°C. Three isolates (GXJ2, GXJ4, and GXJ6) were obtained and deposited in The China Forestry Culture Collection Center (CFCC 55717, CFCC 55716, and CFCC 55722). The colony of GXJ2 on PDA was white, with sparse aerial mycelia, and became grey with time. The α conidia were fusiform, hyaline, and aseptate, 6.7±0.6 μm × 2.6±0.2 μm (n=30). The β conidia were filiform, hyaline, and curved, 30.4±2.1 μm × 1.4±0.1 μm (n=30). Colonies of GXJ4 and GXJ6 were white, with moderate aerial mycelia, which collapsed at the center, and the collapsed parts were iron-gray. The α conidia were 7.8±0.8 μm × 2.5±0.2 μm (n=30). The β conidia were absent. Morphological characters of 3 isolates matched those of Diaporthe spp.. The partial sequences of ITS, EF1-α, CAL, β-tub, and HIS genes were amplified with primers ITS1/ITS4, EF1-728F/EF1-986R and CAL228F/CAL737R, βt2a/βt2b and CYLH3F/H3-1b according to Gomes et al. 2013, respectively. The sequences for the five genes of each of 3 isolates were deposited in GenBank (Accession Nos. see Supplementary Table 1). BLAST results showed that the ITS, EF1-α, β-tub, HIS, and CAL sequences of GXJ2 were highly similar (>99%) with sequences of Diaporthe unshiuensis, while sequences of GXJ4 and GXJ6 were highly similar (>99%) to those of D. hongkongensis (Supplementary Table 1). Phylogenetic analyses using concatenated sequences placed GXJ2 in the clade of D. unshiuensis, while GXJ4 and GXJ6 in the clade of D. hongkongensis. Based on the phylogeny and morphology, GXJ2 was identified as D. unshiuensis, GXJ4 and GXJ6 as D. hongkongensis. Pathogenicity tests were performed on nine 1-year-old seedlings of C. lanceolata, and 10 needles at shoot tip per seedling were slightly wounded and inoculated with 5-mm mycelial plugs from one of 3 isolates. Three control seedlings were treated with PDA plugs. Each plant was covered with a plastic bag after inoculation and kept in an air-conditioned nursery at 25°C/16°C (day/night). The symptoms appeared 5-8 days after inoculation and were similar to those observed in the nursery. D. unshiuensis and D. hongkongensis were re-isolated from the inoculated seedlings and were confirmed based on morphology and ITS sequences. The controls were symptomless, and no fungus was isolated from them. D. unshiuensis was first reported as an endophyte on the fruit of Citrus unshiu, and caused peach constriction canker, shoot blight of kiwifruit. D. hongkongensis was first described from fruit of Dichroa febrifuga and caused shoot canker of pear, shoot blight and leaf spot of kiwifruit, and fruit rot of peach. This is the first report of D. unshiuensis and D. hongkongensis causing the top blight of C. lanceolata. This study provides a basis for controlling this newly emerging disease in the nursery.
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Affiliation(s)
- Yang-Chun-Zi Liao
- Nanjing Forestry University, 159 Longpan Road, Nanjing, Nanjing, United States, 210037;
| | - Jian-Wei Sun
- Nanjing Forestry University, No. 159 Longpan Road, Nanjing, China, 210037;
| | - De-Wei Li
- The Connecticut Agricultural Experiment Station, Valley Laboratory, 153 Cook Hill Road, Windsor, Connecticut, United States, 06095;
| | - Mei-Ling Nong
- State-owned Huangmian Forestry Farm of Guangxi, Luzhai, Guangxi, ChinaLuzhai, China, 545600;
| | - Li-Hua Zhu
- Nanjing Forestry University, College of Forestry, No. 159 Longpan Road, Nanjing, Jiangsu, China, 210037;
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Eliášová K, Konrádová H, Dobrev PI, Motyka V, Lomenech AM, Fischerová L, Lelu-Walter MA, Vondráková Z, Teyssier C. Desiccation as a Post-maturation Treatment Helps Complete Maturation of Norway Spruce Somatic Embryos: Carbohydrates, Phytohormones and Proteomic Status. FRONTIERS IN PLANT SCIENCE 2022; 13:823617. [PMID: 35237290 PMCID: PMC8882965 DOI: 10.3389/fpls.2022.823617] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/04/2022] [Indexed: 06/12/2023]
Abstract
Exposure of Norway spruce (Picea abies) somatic embryos and those of many other conifers to post-maturation desiccation treatment significantly improves their germination. An integration analysis was conducted to understand the underlying processes induced during the desiccation phase at the molecular level. Carbohydrate, protein and phytohormone assays associated with histological and proteomic studies were performed for the evaluation of markers and actors in this phase. Multivariate comparison of mature somatic embryos with mature desiccated somatic embryos and/or zygotic embryos provided new insights into the processes involved during the desiccation step of somatic embryogenesis. Desiccated embryos were characterized by reduced levels of starch and soluble carbohydrates but elevated levels of raffinose family oligosaccharides. Desiccation treatment decreased the content of abscisic acid and its derivatives but increased total auxins and cytokinins. The content of phytohormones in dry zygotic embryos was lower than in somatic embryos, but their profile was mostly analogous, apart from differences in cytokinin profiles. The biological processes "Acquisition of desiccation tolerance", "Response to stimulus", "Response to stress" and "Stored energy" were activated in both the desiccated somatic embryos and zygotic embryos when compared to the proteome of mature somatic embryos before desiccation. Based on the specific biochemical changes of important constituents (abscisic acid, raffinose, stachyose, LEA proteins and cruciferins) induced by the desiccation treatment and observed similarities between somatic and zygotic P. abies embryos, we concluded that the somatic embryos approximated to a state of desiccation tolerance. This physiological change could be responsible for the reorientation of Norway spruce somatic embryos toward a stage suitable for germination.
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Affiliation(s)
- Kateřina Eliášová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Hana Konrádová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Petre I. Dobrev
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Václav Motyka
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | - Lucie Fischerová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | - Zuzana Vondráková
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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Current Proteomic and Metabolomic Knowledge of Zygotic and Somatic Embryogenesis in Plants. Int J Mol Sci 2021; 22:ijms222111807. [PMID: 34769239 PMCID: PMC8583726 DOI: 10.3390/ijms222111807] [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: 09/28/2021] [Revised: 10/13/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Embryogenesis is the primary developmental program in plants. The mechanisms that underlie the regulation of embryogenesis are an essential research subject given its potential contribution to mass in vitro propagation of profitable plant species. Somatic embryogenesis (SE) refers to the use of in vitro techniques to mimic the sexual reproduction program known as zygotic embryogenesis (ZE). In this review, we synthesize the current state of research on proteomic and metabolomic studies of SE and ZE in angiosperms (monocots and dicots) and gymnosperms. The most striking finding was the small number of studies addressing ZE. Meanwhile, the research effort focused on SE has been substantial but disjointed. Together, these research gaps may explain why the embryogenic induction stage and the maturation of the somatic embryo continue to be bottlenecks for efficient and large-scale regeneration of plants. Comprehensive and integrative studies of both SE and ZE are needed to provide the molecular foundation of plant embryogenesis, information which is needed to rationally guide experimental strategies to solve SE drawbacks in each species.
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Kawanami T, Kawanami-Iwao H, Takata T, Ishigaki Y, Tomosugi N, Takegami T, Yanagisawa H, Fujimoto S, Sakai T, Fujita Y, Yamada K, Mizuta S, Kawabata H, Fukushima T, Hirose Y, Masaki Y. Comprehensive analysis of protein-expression changes specific to immunoglobulin G4-related disease. Clin Chim Acta 2021; 523:45-57. [PMID: 34453919 DOI: 10.1016/j.cca.2021.08.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/30/2021] [Accepted: 08/20/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Immunoglobulin 4 (IgG4)-related disease (IgG4-RD) is a lymphoproliferative disorder characterized by elevated serum IgG4 levels and tissue infiltration of IgG4-positive plasma cells. We analyzed the serum proteins, whose levels varied based on the disease state and treatment. MATERIALS AND METHODS Serum proteins from patients with IgG4-related disease and healthy subjects were resolved using two-dimensional electrophoresis, silver-stained, and scanned. Alternatively, the proteins were labeled with Cy2, Cy3, and Cy5 before electrophoresis. The proteins, whose expression differed significantly between patients and healthy individuals, and between before and after steroid treatment, were identified and validated using enzyme-linked immunosorbent assays. RESULTS Pre-treatment sera from patients with IgG4-related disease was characterized by increased levels of immunoglobulins such as IgG1, IgG4; inflammatory factors such as α-1 antitrypsin (A1AT); and proteins associated with immune system regulation such as clusterin and leucine-rich α-2-glycoprotein (LRG-1). The serum levels of A1AT, LRG-1 and clusterin, during treatment with prednisolone for up to 12 months revealed that LRG-1 levels were halved after 1 month of treatment, comparable to those in healthy subjects; LRG-1 levels remained normal until the end of treatment. CONCLUSION LRG-1 could serve as a novel biomarker of IgG4-related diseases.
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Affiliation(s)
- Takafumi Kawanami
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan.
| | - Haruka Kawanami-Iwao
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Takanobu Takata
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Yasuhito Ishigaki
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Naohisa Tomosugi
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Tsutomu Takegami
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Hiroto Yanagisawa
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Shino Fujimoto
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Tomoyuki Sakai
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Yoshimasa Fujita
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Kazunori Yamada
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Shuichi Mizuta
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Hiroshi Kawabata
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan; Department of Hematology, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa Mukaihata-cho, Fushimi-ku, Kyoto, Japan
| | - Toshihiro Fukushima
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Yuko Hirose
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Yasufumi Masaki
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
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Bian JY, Fang YL, Song Q, Sun ML, Yang JY, Ju YW, Li DW, Huang L. The Fungal Endophyte Epicoccum dendrobii as a Potential Biocontrol Agent Against Colletotrichum gloeosporioides. PHYTOPATHOLOGY 2021; 111:293-303. [PMID: 32748735 DOI: 10.1094/phyto-05-20-0170-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthracnose caused by Colletotrichum gloeosporioides is one of most serious fungal diseases on Chinese fir (Cunninghamia lanceolata). Eight fungal endophytes were isolated from a young heathy branch of Chinese fir and screened against the pathogen in vitro. One isolate, designated as SMEL1 and subsequently identified as Epicoccum dendrobii based on morphological and phylogenetic analyses, suppressed mycelial growth of Colletotrichum gloeosporioides on dual-culture plates. Additionally, E. dendrobii metabolites significantly decreased the biomass of Colletotrichum gloeosporioides. E. dendrobii was able to enter the internal tissues of the host plant via stomatal cells. Metabolites of E. dendrobii significantly inhibited conidial germination and appressorium formation, which at least partly explained why the endophyte significantly inhibited lesion development caused by Colletotrichum gloeosporioides on various host plants. We further confirmed that some components with antifungal activity could be extracted from E. dendrobii using ethyl acetate as an organic solvent. To our knowledge, this is the first report of E. dendrobii as a potential biocontrol agent against a fungal phytopathogen.
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Affiliation(s)
- Jin-Yue Bian
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yu-Lan Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Qing Song
- SUST Think Tank for Urban Development, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Mei-Ling Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ji-Yun Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yun-Wei Ju
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - De-Wei Li
- Connecticut Agricultural Experiment Station Valley Laboratory, Windsor, CT 06095, U.S.A
| | - Lin Huang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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Wang D, Hao Z, Long X, Wang Z, Zheng X, Ye D, Peng Y, Wu W, Hu X, Wang G, Zheng R, Shi J, Chen J. The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development. BMC PLANT BIOLOGY 2020; 20:508. [PMID: 33153428 PMCID: PMC7643283 DOI: 10.1186/s12870-020-02634-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/30/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Cunninghamia lanceolata (Chinese fir), a member of the conifer family Cupressaceae, is one of the most popular cultivated trees for wood production in China. Continuous research is being performed to improve C. lanceolata breeding values. Given the high rate of seed abortion (one of the reasons being the failure of ovule and pollen development) in C. lanceolata, the proper formation of female/male cones could theoretically increase the number of offspring in future generations. MIKC MADS-box genes are well-known for their roles in the flower/cone development and comprise the typical/atypical floral development model for both angiosperms and gymnosperms. RESULTS We performed a transcriptomic analysis to find genes differentially expressed between female and male cones at a single, carefully determined developmental stage, focusing on the MIKC MADS-box genes. We finally obtained 47 unique MIKC MADS-box genes from C. lanceolata and divided these genes into separate branches. 27 out of the 47 MIKC MADS-box genes showed differential expression between female and male cones, and most of them were not expressed in leaves. Out of these 27 genes, most B-class genes (AP3/PI) were up-regulated in the male cone, while TM8 genes were up-regulated in the female cone. Then, with no obvious overall preference for AG (class C + D) genes in female/male cones, it seems likely that these genes are involved in the development of both cones. Finally, a small number of genes such as GGM7, SVP, AGL15, that were specifically expressed in female/male cones, making them candidate genes for sex-specific cone development. CONCLUSIONS Our study identified a number of MIKC MADS-box genes showing differential expression between female and male cones in C. lanceolata, illustrating a potential link of these genes with C. lanceolata cone development. On the basis of this, we postulated a possible cone development model for C. lanceolata. The gene expression library showing differential expression between female and male cones shown here, can be used to discover unknown regulatory networks related to sex-specific cone development in the future.
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Affiliation(s)
- Dandan Wang
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhaodong Hao
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaofei Long
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Xueyan Zheng
- National Germplasm Bank of Chinese fir at Fujian Yangkou Forest Farm, Shunchang, 353211, China
| | - Daiquan Ye
- National Germplasm Bank of Chinese fir at Fujian Yangkou Forest Farm, Shunchang, 353211, China
| | - Ye Peng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Weihuang Wu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Renhua Zheng
- Fujian Academy of Forestry, Fuzhou, 350012, China
| | - Jisen Shi
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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10
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UAV-Based High-Throughput Approach for Fast Growing Cunninghamia lanceolata (Lamb.) Cultivar Screening by Machine Learning. FORESTS 2019. [DOI: 10.3390/f10090815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Obtaining accurate measurements of tree height and diameter at breast height (DBH) in forests to evaluate the growth rate of cultivars is still a significant challenge, even when using light detection and ranging (LiDAR) and three-dimensional (3-D) modeling. As an alternative, we provide a novel high-throughput strategy for predicting the biomass of forests in the field by vegetation indices. This study proposes an integrated pipeline methodology to measure the biomass of different tree cultivars in plantation forests with high crown density, which combines unmanned aerial vehicles (UAVs), hyperspectral image sensors, and data processing algorithms using machine learning. Using a planation of Cunninghamia lanceolate, which is commonly known as Chinese fir, in Fujian, China, images were collected while using a hyperspectral camera. Vegetation indices and modeling were processed in Python using decision trees, random forests, support vector machine, and eXtreme Gradient Boosting (XGBoost) third-party libraries. The tree height and DBH of 2880 samples were manually measured and clustered into three groups—“Fast”, “median”, and “normal” growth groups—and 19 vegetation indices from 12,000 pixels were abstracted as the input of features for the modeling. After modeling and cross-validation, the classifier that was generated by random forests had the best prediction accuracy when compared to other algorithms (75%). This framework can be applied to other tree species to make management and business decisions.
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11
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Huang L, Kim KT, Yang JY, Song H, Choi G, Jeon J, Cheong K, Ko J, Xu H, Lee YH. A High-Quality Draft Genome Sequence of Colletotrichum gloeosporioides sensu stricto SMCG1#C, a Causal Agent of Anthracnose on Cunninghamia lanceolata in China. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:139-141. [PMID: 30019989 DOI: 10.1094/mpmi-05-18-0144-a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Colletotrichum has a broad host range and causes major yield losses of crops. The fungus Colletotrichum gloeosporioides is associated with anthracnose on Chinese fir. In this study, we present a high-quality draft genome sequence of C. gloeosporioides sensu stricto SMCG1#C, providing a reference genomic data for further research on anthracnose of Chinese fir and other hosts.
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Affiliation(s)
- Lin Huang
- 1 Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ki-Tae Kim
- 2 Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Ji-Yun Yang
- 1 Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Hyeunjeong Song
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
| | - Gobong Choi
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
| | - Jongbum Jeon
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
| | - Kyeongchae Cheong
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
| | - Jaeho Ko
- 2 Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Haibin Xu
- 4 College of Biology and the Environment, Nanjing Forestry University; and
| | - Yong-Hwan Lee
- 2 Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
- 5 Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University
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12
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Debez A, Belghith I, Pich A, Taamalli W, Abdelly C, Braun HP. High salinity impacts germination of the halophyte Cakile maritima but primes seeds for rapid germination upon stress release. PHYSIOLOGIA PLANTARUM 2018; 164:134-144. [PMID: 29220080 DOI: 10.1111/ppl.12679] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
Seed germination recovery aptitude is an adaptive trait of overriding significance for the successful establishment and dispersal of extremophile plants in their native ecosystems. Cakile maritima is an annual halophyte frequent on Mediterranean coasts, which produces transiently dormant seeds under high salinity, that germinate fast when soil salinity is lowered by rainfall. Here, we report ecophysiological and proteomic data about (1) the effect of high salt (200 mM NaCl) on the early developmental stages (germination and seedling) and (2) the seed germination recovery capacity of this species. Upon salt exposure, seed germination was severely inhibited and delayed and seedling length was restricted. Interestingly, non-germinated seeds remained viable, showing high germination percentage and faster germination than the control seeds after their transfer onto distilled water. The plant phenotypic plasticity during germination was better highlighted by the proteomic data. Salt exposure triggered (1) a marked slower degradation of seed storage reserves and (2) a significant lower abundance of proteins involved in several biological processes (primary metabolism, energy, stress-response, folding and stability). Yet, these proteins showed strong increased abundance early after stress release, thereby sustaining the faster seed storage proteins mobilization under recovery conditions compared to the control. Overall, as part of the plant survival strategy, C. maritima seems to avoid germination and establishment under high salinity. However, this harsh condition may have a priming-like effect, boosting seed germination and vigor under post-stress conditions, sustained by active metabolic machinery.
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Affiliation(s)
- Ahmed Debez
- Laboratoire des Plantes Extrêmophiles (LPE), Centre de Biotechnologie de Borj-Cedria (CBBC), Hammam-Lif, 2050, Tunisia
- Abteilung Pflanzenproteomik, Institut für Pflanzengenetik, Leibniz Universität Hannover, D-30419, Hannover, Germany
| | - Ikram Belghith
- Laboratoire des Plantes Extrêmophiles (LPE), Centre de Biotechnologie de Borj-Cedria (CBBC), Hammam-Lif, 2050, Tunisia
- Abteilung Pflanzenproteomik, Institut für Pflanzengenetik, Leibniz Universität Hannover, D-30419, Hannover, Germany
| | - Andreas Pich
- Institut für Toxikologie, Medizinische Hochschule Hannover, D-30625, Hannover, Germany
| | - Wael Taamalli
- Laboratoire de Biotechnologie de l'Olivier (LBO), Centre de Biotechnologie de Borj-Cedria (CBBC), Hammam-Lif, 2050, Tunisia
| | - Chedly Abdelly
- Laboratoire des Plantes Extrêmophiles (LPE), Centre de Biotechnologie de Borj-Cedria (CBBC), Hammam-Lif, 2050, Tunisia
| | - Hans-Peter Braun
- Abteilung Pflanzenproteomik, Institut für Pflanzengenetik, Leibniz Universität Hannover, D-30419, Hannover, Germany
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13
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Huang L, Zhu YN, Yang JY, Li DW, Li Y, Bian LM, Ye JR. Shoot Blight on Chinese Fir (Cunninghamia lanceolata) is Caused by Bipolaris oryzae. PLANT DISEASE 2018; 102:500-506. [PMID: 30673483 DOI: 10.1094/pdis-07-17-1032-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chinese fir (Cunninghamia lanceolata) is a significant timber species that has been broadly cultivated in southern China. A shoot blight disease on Chinese fir seedlings was discovered in Fujian, China and a fungus was then consistently associated with the symptoms. This fungus was determined to be causing this disease, among others by fulfilling Koch's postulates. Based on morphological characteristics and multilocus phylogenetic analyses with the sequences of the internal transcribed spacer, partial glyceraldehyde-3-phosphate dehydrogenase gene, partial translation elongation factor 1-α gene, and partial 28S large subunit ribosomal RNA gene, the fungus was identified as Bipolaris oryzae. These characteristics and phylogenetic analyses clearly support that this pathogen is different from B. sacchari, which was, until now, considered to be the causal agent of a similar blight on Chinese fir in Guangdong, China. The fungus was also shown to be strongly pathogenic to rice, one of the most susceptible hosts to B. oryzae. Crop rotation involving rice is often carried out with Chinese fir in southern China, a practice that most likely increases the risk of shoot blight on C. lanceolata. To our knowledge, shoot blight caused by B. oryzae is reported for the first time in a gymnosperm species.
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Affiliation(s)
- Lin Huang
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ya-Nan Zhu
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ji-Yun Yang
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - De-Wei Li
- The Connecticut Agricultural Experiment Station Valley Laboratory, Windsor 06095; and Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University
| | - Yong Li
- Yangkou State Forest Farm, Nanping, Fujian 353211, China
| | - Li-Ming Bian
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University
| | - Jian-Ren Ye
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University
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14
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Zhou X, Zheng R, Liu G, Xu Y, Zhou Y, Laux T, Zhen Y, Harding SA, Shi J, Chen J. Desiccation Treatment and Endogenous IAA Levels Are Key Factors Influencing High Frequency Somatic Embryogenesis in Cunninghamia lanceolata (Lamb.) Hook. FRONTIERS IN PLANT SCIENCE 2017; 8:2054. [PMID: 29259612 PMCID: PMC5723420 DOI: 10.3389/fpls.2017.02054] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/16/2017] [Indexed: 05/12/2023]
Abstract
Cunninghamia lanceolata (Lamb.) Hook (Chinese fir) is an important tree, commercially and ecologically, in southern China. The traditional regenerating methods are based on organogenesis and cutting propagation. Here, we report the development of a high-frequency somatic embryogenesis (SE) regeneration system synchronized via a liquid culture from immature zygotic embryos. Following synchronization, PEM II cell aggregates were developmentally equivalent in appearance to cleaved zygotic embryos. Embryo and suspensor growth and subsequent occurrence of the apical and then the cotyledonary meristems were similar for zygotic and SE embryo development. However, SE proembryos exhibited a more reddish coloration than zygotic proembryos, and SE embryos were smaller than zygotic embryos. Mature somatic embryos gave rise to plantlets on hormone-free medium. For juvenile explants, low concentrations of endogenous indole-3-acetic acid in initial explants correlated with improved proembryogenic mass formation, and high SE competency. Analysis of karyotypes and microsatellites detected no major genetic variation in the plants regenerated via SE, and suggest a potential in the further development of this system as a reliable methodology for true-to-type seedling production. Treatment with polyethylene glycol (PEG) and abscisic acid (ABA) were of great importance to proembryo formation and complemented each other. ABA assisted the growth of embryonal masses, whereas PEG facilitated the organization of the proembryo-like structures. SOMATIC EMBRYOGENESIS RECEPTOR KINASE SERK) and the WUSCHEL homeobox (WOX) transcription factor served as molecular markers during early embryogenesis. Our results show that ClSERKs are conserved and redundantly expressed during SE. SERK and WOX transcript levels were highest during development of the proembryos and lowest in developed embryos. ClWOX13 expression correlates with the critical transition from proembryogenic masses to proembryos. Both SERK and WOX expression reveal their applicability in Chinese fir as markers of early embryogenesis. Overall, the findings provided evidence for the potential of this system in high fidelity Chinese fir seedlings production. Also, SE modification strategies were demonstrated and could be applied in other conifer species on the basis of our hormonal, morphological and molecular analyses.
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Affiliation(s)
- Xiaohong Zhou
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Renhua Zheng
- The Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, State Forestry Administration Engineering Research Center of Chinese Fir, Fujian Academy of Forestry, Fuzhou, China
| | - Guangxin Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yang Xu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Yanwei Zhou
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Thomas Laux
- Centre for Biological Signaling Studies, Faculty of Biology, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Yan Zhen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Scott A. Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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15
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Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
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Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
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16
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Cao D, Xu H, Zhao Y, Deng X, Liu Y, Soppe WJJ, Lin J. Transcriptome and Degradome Sequencing Reveals Dormancy Mechanisms of Cunninghamia lanceolata Seeds. PLANT PHYSIOLOGY 2016; 172:2347-2362. [PMID: 27760880 PMCID: PMC5129703 DOI: 10.1104/pp.16.00384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 10/14/2016] [Indexed: 05/05/2023]
Abstract
Seeds with physiological dormancy usually experience primary and secondary dormancy in the nature; however, little is known about the differential regulation of primary and secondary dormancy. We combined multiple approaches to investigate cytological changes, hormonal levels, and gene expression dynamics in Cunninghamia lanceolata seeds during primary dormancy release and secondary dormancy induction. Light microscopy and transmission electron microscopy revealed that protein bodies in the embryo cells coalesced during primary dormancy release and then separated during secondary dormancy induction. Transcriptomic profiling demonstrated that expression of genes negatively regulating gibberellic acid (GA) sensitivity reduced specifically during primary dormancy release, whereas the expression of genes positively regulating abscisic acid (ABA) biosynthesis increased during secondary dormancy induction. Parallel analysis of RNA ends revealed uncapped transcripts for ∼55% of all unigenes. A negative correlation between fold changes in expression levels of uncapped versus capped mRNAs was observed during primary dormancy release. However, this correlation was loose during secondary dormancy induction. Our analyses suggest that the reversible changes in cytology and gene expression during dormancy release and induction are related to ABA/GA balance. Moreover, mRNA degradation functions as a critical posttranscriptional regulator during primary dormancy release. These findings provide a mechanistic framework for understanding physiological dormancy in seeds.
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Affiliation(s)
- Dechang Cao
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Huimin Xu
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Yuanyuan Zhao
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Xin Deng
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Yongxiu Liu
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Wim J J Soppe
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Jinxing Lin
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.);
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.);
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
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17
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Bao W, Qu Y, Shan X, Wan Y. Screening and Validation of Housekeeping Genes of the Root and Cotyledon of Cunninghamia lanceolata under Abiotic Stresses by Using Quantitative Real-Time PCR. Int J Mol Sci 2016; 17:ijms17081198. [PMID: 27483238 PMCID: PMC5000596 DOI: 10.3390/ijms17081198] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/10/2016] [Accepted: 07/15/2016] [Indexed: 12/25/2022] Open
Abstract
Cunninghamia lanceolata (Chinese fir) is a fast-growing and commercially important conifer of the Cupressaceae family. Due to the unavailability of complete genome sequences and relatively poor genetic background information of the Chinese fir, it is necessary to identify and analyze the expression levels of suitable housekeeping genes (HKGs) as internal reference for precise analysis. Based on the results of database analysis and transcriptome sequencing, we have chosen five candidate HKGs (Actin, GAPDH, EF1a, 18S rRNA, and UBQ) with conservative sequences in the Chinese fir and related species for quantitative analysis. The expression levels of these HKGs in roots and cotyledons under five different abiotic stresses in different time intervals were measured by qRT-PCR. The data were statistically analyzed using the following algorithms: NormFinder, BestKeeper, and geNorm. Finally, RankAggreg was applied to merge the sequences generated from three programs and rank these according to consensus sequences. The expression levels of these HKGs showed variable stabilities under different abiotic stresses. Among these, Actin was the most stable internal control in root, and GAPDH was the most stable housekeeping gene in cotyledon. We have also described an experimental procedure for selecting HKGs based on the de novo sequencing database of other non-model plants.
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Affiliation(s)
- Wenlong Bao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
| | - Yanli Qu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
| | - Xiaoyi Shan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
| | - Yinglang Wan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
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Zheng W, Chen J, Hao Z, Shi J. Comparative Analysis of the Chloroplast Genomic Information of Cunninghamia lanceolata (Lamb.) Hook with Sibling Species from the Genera Cryptomeria D. Don, Taiwania Hayata, and Calocedrus Kurz. Int J Mol Sci 2016; 17:ijms17071084. [PMID: 27399686 PMCID: PMC4964460 DOI: 10.3390/ijms17071084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/01/2016] [Accepted: 06/23/2016] [Indexed: 11/18/2022] Open
Abstract
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an important coniferous tree species for timber production, which accounts for ~40% of log supply from plantations in southern China. Chloroplast genetic engineering is an exciting field to engineer several valuable tree traits. In this study, we revisited the published complete Chinese fir (NC_021437) and four other coniferous species chloroplast genome sequence in Taxodiaceae. Comparison of their chloroplast genomes revealed three unique inversions found in the downstream of the gene clusters and evolutionary divergence were found, although overall the chloroplast genomic structure of the Cupressaceae linage was conserved. We also investigated the phylogenetic position of Chinese fir among conifers by examining gene functions, selection forces, substitution rates, and the full chloroplast genome sequence. Consistent with previous molecular systematics analysis, the results provided a well-supported phylogeny framework for the Cupressaceae that strongly confirms the “basal” position of Cunninghamia lanceolata. The structure of the Cunninghamia lanceolata chloroplast genome showed a partial lack of one IR copy, rearrangements clearly occurred and slight evolutionary divergence appeared among the cp genome of C. lanceolata, Taiwania cryptomerioides, Taiwania flousiana, Calocedrus formosana and Cryptomeria japonica. The information from sequence divergence and length variation of genes could be further considered for bioengineering research.
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Affiliation(s)
- Weiwei Zheng
- Collaborative Innovation Center of Sustainable Forestry in Southern China; Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China.
- College of Electronics and Information Science, Fujian Jiangxia University, Fuzhou 350108, China.
| | - Jinhui Chen
- Collaborative Innovation Center of Sustainable Forestry in Southern China; Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China.
| | - Zhaodong Hao
- Collaborative Innovation Center of Sustainable Forestry in Southern China; Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China.
| | - Jisen Shi
- Collaborative Innovation Center of Sustainable Forestry in Southern China; Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China.
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19
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Zhang Y, Han X, Sang J, He X, Liu M, Qiao G, Zhuo R, He G, Hu J. Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases. PeerJ 2016; 4:e2097. [PMID: 27330860 PMCID: PMC4906661 DOI: 10.7717/peerj.2097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/10/2016] [Indexed: 12/23/2022] Open
Abstract
Background.Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results. We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome. Conclusion. Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications.
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Affiliation(s)
- Yunxing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
- Institute of Architectural and Artistic Design, Henan Polytechnic University, Jiaozuo, Henan, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Jian Sang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Xuelian He
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Mingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Guiping He
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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20
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Label-free proteome profiling reveals developmental-dependent patterns in young barley grains. J Proteomics 2016; 143:106-121. [DOI: 10.1016/j.jprot.2016.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/16/2016] [Accepted: 04/11/2016] [Indexed: 12/17/2022]
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21
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Yu Y, Zhu D, Ma C, Cao H, Wang Y, Xu Y, Zhang W, Yan Y. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.01.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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22
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Xu H, Cao D, Chen Y, Wei D, Wang Y, Stevenson RA, Zhu Y, Lin J. Gene expression and proteomic analysis of shoot apical meristem transition from dormancy to activation in Cunninghamia lanceolata (Lamb.) Hook. Sci Rep 2016; 6:19938. [PMID: 26832850 PMCID: PMC4735791 DOI: 10.1038/srep19938] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/21/2015] [Indexed: 11/17/2022] Open
Abstract
In contrast to annual plants, in perennial plants, the shoot apical meristem (SAM) can undergo seasonal transitions between dormancy and activity; understanding this transition is crucial for understanding growth in perennial plants. However, little is known about the molecular mechanisms of SAM development in trees. Here, light and transmission electron microscopy revealed that evident changes in starch granules, lipid bodies, and cell walls thickness of the SAM in C. lanceolata during the transition from dormancy to activation. HPLC-ESI-MS/MS analysis showed that levels of indole-3-acetic acid (IAA) increased and levels of abscisic acid (ABA) decreased from dormant to active stage. Examination of 20 genes and 132 differentially expressed proteins revealed that the expression of genes and proteins potentially involved in cell division and expansion significantly increased in the active stage, whereas those related to the abscisic acid insensitive 3(ABI3), the cytoskeleton and energy metabolism decreased in the dormant stage. These findings provide new insights into the complex mechanism of gene and protein expression and their relation to cytological and physiological changes of SAM in this coniferous species.
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Affiliation(s)
- Huimin Xu
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Dechang Cao
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yanmei Chen
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Dongmei Wei
- School of Life Science, Taizhou University, Zhejiang 318000, China
| | - Yanwei Wang
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Rebecca Ann Stevenson
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
| | - Yingfang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
| | - Jinxing Lin
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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23
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Trontin JF, Klimaszewska K, Morel A, Hargreaves C, Lelu-Walter MA. Molecular Aspects of Conifer Zygotic and Somatic Embryo Development: A Review of Genome-Wide Approaches and Recent Insights. Methods Mol Biol 2016; 1359:167-207. [PMID: 26619863 DOI: 10.1007/978-1-4939-3061-6_8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome-wide profiling (transcriptomics, proteomics, metabolomics) is providing unprecedented opportunities to unravel the complexity of coordinated gene expression during embryo development in trees, especially conifer species harboring "giga-genome." This knowledge should be critical for the efficient delivery of improved varieties through seeds and/or somatic embryos in fluctuating markets and to cope with climate change. We reviewed "omics" as well as targeted gene expression studies during both somatic and zygotic embryo development in conifers and tentatively puzzled over the critical processes and genes involved at the specific developmental and transition stages. Current limitations to the interpretation of these large datasets are going to be lifted through the ongoing development of comprehensive genome resources in conifers. Nevertheless omics already confirmed that master regulators (e.g., transcription and epigenetic factors) play central roles. As in model angiosperms, the molecular regulation from early to late embryogenesis may mainly arise from spatiotemporal modulation of auxin-, gibberellin-, and abscisic acid-mediated responses. Omics also showed the potential for the development of tools to assess the progress of embryo development or to build genotype-independent, predictive models of embryogenesis-specific characteristics.
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Affiliation(s)
- Jean-François Trontin
- FCBA, Pôle Biotechnologie et Sylviculture Avancée, Campus Forêt-Bois de Pierroton, 71 Route d'Arcachon, Cestas, 33610, France.
| | - Krystyna Klimaszewska
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., 10380, Stn. Sainte-Foy, QC, Canada, G1V 4C7
| | - Alexandre Morel
- INRA, UR 0588 Unité Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, CS 4001, Ardon, Orléans Cedex 2, 45075, France
| | | | - Marie-Anne Lelu-Walter
- INRA, UR 0588 Unité Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, CS 4001, Ardon, Orléans Cedex 2, 45075, France
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24
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Assessing 62 Chinese Fir (Cunninghamia lanceolata) Breeding Parents in a 12-Year Grafted Clone Test. FORESTS 2015. [DOI: 10.3390/f6103799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Wang WQ, Liu SJ, Song SQ, Møller IM. Proteomics of seed development, desiccation tolerance, germination and vigor. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 86:1-15. [PMID: 25461695 DOI: 10.1016/j.plaphy.2014.11.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/03/2014] [Indexed: 05/19/2023]
Abstract
Proteomics, the large-scale study of the total complement of proteins in a given sample, has been applied to all aspects of seed biology mainly using model species such as Arabidopsis or important agricultural crops such as corn and rice. Proteins extracted from the sample have typically been separated and quantified by 2-dimensional polyacrylamide gel electrophoresis followed by liquid chromatography and mass spectrometry to identify the proteins in the gel spots. In this way, qualitative and quantitative changes in the proteome during seed development, desiccation tolerance, germination, dormancy release, vigor alteration and responses to environmental factors have all been studied. Many proteins or biological processes potentially important for each seed process have been highlighted by these studies, which greatly expands our knowledge of seed biology. Proteins that have been identified to be particularly important for at least two of the seed processes are involved in detoxification of reactive oxygen species, the cytoskeleton, glycolysis, protein biosynthesis, post-translational modifications, methionine metabolism, and late embryogenesis-abundant (LEA) proteins. It will be useful for molecular biologists and molecular plant breeders to identify and study genes encoding particularly interesting target proteins with the aim to improve the yield, stress tolerance or other critical properties of our crop species.
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Affiliation(s)
- Wei-Qing Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China.
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark.
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26
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Morel A, Trontin JF, Corbineau F, Lomenech AM, Beaufour M, Reymond I, Le Metté C, Ader K, Harvengt L, Cadene M, Label P, Teyssier C, Lelu-Walter MA. Cotyledonary somatic embryos of Pinus pinaster Ait. most closely resemble fresh, maturing cotyledonary zygotic embryos: biological, carbohydrate and proteomic analyses. PLANTA 2014; 240:1075-95. [PMID: 25115559 DOI: 10.1007/s00425-014-2125-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/07/2014] [Indexed: 05/22/2023]
Abstract
Cotyledonary somatic embryos (SEs) of maritime pine are routinely matured for 12 weeks before being germinated and converted to plantlets. Although regeneration success is highly dependent on SEs quality, the date of harvesting is currently determined mainly on the basis of morphological features. This empirical method does not provide any accurate information about embryo quality with respect to storage compounds (proteins, carbohydrates). We first analyzed SEs matured for 10, 12 and 14 weeks by carrying out biological (dry weight, water content) and biochemical measurements (total protein and carbohydrate contents). No difference could be found between collection dates, suggesting that harvesting SEs after 12 weeks is appropriate. Cotyledonary SEs were then compared to various stages, from fresh to fully desiccated, in the development of cotyledonary zygotic embryos (ZEs). We identified profiles that were similar using hierarchical ascendant cluster analysis (HCA). Fresh and dehydrated ZEs could be distinguished, and SEs clustered with fresh ZEs. Both types of embryo exhibited similar carbohydrate and protein contents and signatures. This high level of similarity (94.5 %) was further supported by proteome profiling. Highly expressed proteins included storage, stress-related, late embryogenesis abundant and energy metabolism proteins. By comparing overexpressed proteins in developing and cotyledonary SEs or ZEs, some (23 proteins) could be identified as candidate biomarkers for the late, cotyledonary stage. This is the first report of useful generic protein markers for monitoring embryo development in maritime pine. Our results also suggest that improvements of SEs quality may be achieved if the current maturation conditions are refined.
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Affiliation(s)
- Alexandre Morel
- INRA, UR 0588 Unité Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, CS 4001, Ardon, 45075, Orléans Cedex 2, France
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27
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Wang Y, Wang N, Hao H, Guo Y, Zhen Y, Shi J, Wu R. A computational algorithm for functional clustering of proteome dynamics during development. Curr Genomics 2014; 15:237-43. [PMID: 24955031 PMCID: PMC4064563 DOI: 10.2174/1389202915666140407212147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 03/27/2013] [Accepted: 04/05/2014] [Indexed: 12/29/2022] Open
Abstract
Phenotypic traits, such as seed development, are a consequence of complex biochemical interactions among genes, proteins and metabolites, but the underlying mechanisms that operate in a coordinated and sequential manner remain elusive. Here, we address this issue by developing a computational algorithm to monitor proteome changes during the course of trait development. The algorithm is built within the mixture-model framework in which each mixture component is modeled by a specific group of proteins that display a similar temporal pattern of expression in trait development. A nonparametric approach based on Legendre orthogonal polynomials was used to fit dynamic changes of protein expression, increasing the power and flexibility of protein clustering. By analyzing a dataset of proteomic dynamics during early embryogenesis of the Chinese fir, the algorithm has successfully identified several distinct types of proteins that coordinate with each other to determine seed development in this forest tree commercially and environmentally important to China. The algorithm will find its immediate applications for the characterization of mechanistic underpinnings for any other biological processes in which protein abundance plays a key role.
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Affiliation(s)
- Yaqun Wang
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
| | - Ningtao Wang
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
| | - Han Hao
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
| | - Yunqian Guo
- Center for Computational Biology, Beijing Forestry University, Beijing 100083, China
| | - Yan Zhen
- Key Laboratory of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing 210037, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing 210037, China
| | - Rongling Wu
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
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28
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Teyssier C, Maury S, Beaufour M, Grondin C, Delaunay A, Le Metté C, Ader K, Cadene M, Label P, Lelu-Walter MA. In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses. PHYSIOLOGIA PLANTARUM 2014; 150:271-91. [PMID: 23789891 DOI: 10.1111/ppl.12081] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/08/2013] [Accepted: 05/28/2013] [Indexed: 05/22/2023]
Abstract
A global DNA methylation and proteomics approach was used to investigate somatic embryo maturation in hybrid larch. Each developmental step during somatic embryogenesis was associated with a distinct and significantly different global DNA methylation level: from 45.8% mC for undifferentiated somatic embryos (1-week proliferation) to 61.5% mC for immature somatic embryos (1-week maturation), while maturation was associated with a decrease in DNA methylation to 53.4% for mature cotyledonary somatic embryos (8-weeks maturation). The presence of 5-azacytidine (hypo-methylating agent) or hydroxyurea (hyper-methylating agent) in the maturation medium altered the global DNA methylation status of the embryogenic cultures, and significantly reduced both their relative growth rate and embryogenic potential, suggesting an important role for DNA methylation in embryogenesis. Maturation was also assessed by examining changes in the total protein profile. Storage proteins, identified as legumin- and vicilin-like, appeared at the precotyledonary stage. In the proteomic study, total soluble proteins were extracted from embryos after 1 and 8 weeks of maturation, and separated by two-dimensional gel electrophoresis. There were 147 spots which showed significant differences between the stages of maturation; they were found to be involved mainly in primary metabolism and the stabilization of the resulting metabolites. This indicated that the somatic embryo was still metabolically active at 8 weeks of maturation. This is the first report of analyses of global DNA methylation (including the effects of hyper- and hypo-treatments) and proteome during somatic embryogenesis in hybrid larch, and thus provides novel insights into maturation of conifer somatic embryos.
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Affiliation(s)
- Caroline Teyssier
- INRA, UR 0588, Research Unit for Breeding, Genetics and Physiology of Forest Trees, Orléans, F-45075, France
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29
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Zi J, Zhang J, Wang Q, Zhou B, Zhong J, Zhang C, Qiu X, Wen B, Zhang S, Fu X, Lin L, Liu S. Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis. PLoS One 2013; 8:e74229. [PMID: 24058531 PMCID: PMC3776822 DOI: 10.1371/journal.pone.0074229] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/28/2013] [Indexed: 11/19/2022] Open
Abstract
Embryogenesis is the initial step in a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation.
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Affiliation(s)
- Jin Zi
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jiyuan Zhang
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Quanhui Wang
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Baojin Zhou
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Junyan Zhong
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | | | - Xuemei Qiu
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Bo Wen
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Shenyan Zhang
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiqin Fu
- Hunan Hybrid Rice Research Center, Changsha, China
| | - Liang Lin
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- * E-mail: (LL); (SL)
| | - Siqi Liu
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (LL); (SL)
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30
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Wang Z, Chen J, Liu W, Luo Z, Wang P, Zhang Y, Zheng R, Shi J. Transcriptome characteristics and six alternative expressed genes positively correlated with the phase transition of annual cambial activities in Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook). PLoS One 2013; 8:e71562. [PMID: 23951189 PMCID: PMC3741379 DOI: 10.1371/journal.pone.0071562] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 07/01/2013] [Indexed: 11/24/2022] Open
Abstract
Background The molecular mechanisms that govern cambial activity in angiosperms are well established, but little is known about these molecular mechanisms in gymnosperms. Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), a diploid (2n = 2x = 22) gymnosperm, is one of the most important industrial and commercial timber species in China. Here, we performed transcriptome sequencing to identify the repertoire of genes expressed in cambium tissue of Chinese fir. Methodology/Principal Findings Based on previous studies, the four stage-specific cambial tissues of Chinese fir were defined using transmission electron microscopy (TEM). In total, 20 million sequencing reads (3.6 Gb) were obtained using Illumina sequencing from Chinese fir cambium tissue collected at active growth stage, with a mean length of 131 bp and a N50 of 90 bp. SOAPdenovo software was used to assemble 62,895 unigenes. These unigenes were further functionally annotated by comparing their sequences to public protein databases. Expression analysis revealed that the altered expression of six homologous genes (ClWOX1, ClWOX4, ClCLV1-like, ClCLV-like, ClCLE12, and ClPIN1-like) correlated positively with changes in cambial activities; moreover, these six genes might be directly involved in cambial function in Chinese fir. Further, the full-length cDNAs and DNAs for ClWOX1 and ClWOX4 were cloned and analyzed. Conclusions In this study, a large number of tissue/stage-specific unigene sequences were generated from the active growth stage of Chinese fir cambium. Transcriptome sequencing of Chinese fir not only provides extensive genetic resources for understanding the molecular mechanisms underlying cambial activities in Chinese fir, but also is expected to be an important foundation for future genetic studies of Chinese fir. This study indicates that ClWOX1 and ClWOX4 could be possible reverse genetic target genes for revealing the molecular mechanisms of cambial activities in Chinese fir.
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Affiliation(s)
- Zhanjun Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Weidong Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Zhanshou Luo
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Pengkai Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Yanjuan Zhang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
| | - Renhua Zheng
- Fujian Academies of Forestry, Southern Mountain Timber Forest Cultivation Lab, the Ministry of Forestry, Fuzhou, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China
- * E-mail:
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TAKATA TAKANOBU, ISHIGAKI YASUHITO, SHIMASAKI TAKEO, TSUCHIDA HIDEYUKI, MOTOO YOSHIHARU, HAYASHI AKIO, TOMOSUGI NAOHISA. Characterization of proteins secreted by pancreatic cancer cells with anticancer drug treatment in vitro. Oncol Rep 2012; 28:1968-76. [PMID: 22961650 PMCID: PMC3583485 DOI: 10.3892/or.2012.2020] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/23/2012] [Indexed: 12/25/2022] Open
Abstract
Pancreatic cancer is one of the most lethal cancers, with an incidence equaling mortality. It is a heterogeneous group of neoplasms in which pancreatic ductal adenocarcinoma is most common. Pancreatic cancer cannot be cured even if detected early. When treatment is initiated, a suitable method of administration of anticancer drugs must be chosen. Anticancer drugs kill tumor cells. However, side effects including initiation are problematic in anticancer drug therapy. Improved methods for the diagnosis of side effects of pancreatic cancer by using sensitive and specific tumor markers are highly desirable. Therefore, efficient strategies for biomarker discovery are urgently needed. Here, we present an approach based on direct experimental access to proteins released by PANC-1 human pancreatic cancer cells in vitro. A two-dimensional (2-D) map and catalog of this subproteome, herein termed the secretome, were established comprising more than 1,000 proteins observed by '2-D difference in-gel electrophoresis analysis using cyanine dye'. We investigated 22 spots that were 1.20-fold upregulated and 31 spots that were 0.66-fold downregulated by gemcitabine chloride treatment. Proteins in these spots were identified by nano-high-performance liquid chromatography electrospray ionization time of flight mass spectrometry/mass spectrometry. Most secretome constituents were nominally cellular proteins. By mass spectrometry screening, 14-3-3 protein sigma (14-3-3 σ), protein S100-A8, protein S100-A9, galectin-7, lactotransferrin (lactoferrin, LF) precursor, serotransferrin (transferrin) precursor, and vitamin D binding protein precursor were identified. Western blotting confirmed the presence of 14-3-3 σ and LF. We found that upregulation of 14-3-3 σ was associated with apoptosis, and downregulation of LF was found to suppress tumorigenesis.
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Affiliation(s)
- TAKANOBU TAKATA
- Medical Research Institute, Kanazawa Medical University, Uchinada
| | | | - TAKEO SHIMASAKI
- Medical Research Institute, Kanazawa Medical University, Uchinada
- Department of Medical Oncology, Kanazawa Medical University, Takakura, Hachioji 192-8510
| | - HIDEYUKI TSUCHIDA
- Department of Advanced Medicine, Kanazawa Medical University, Takakura, Hachioji 192-8510
| | - YOSHIHARU MOTOO
- Medical Research Institute, Kanazawa Medical University, Uchinada
- Department of Medical Oncology, Kanazawa Medical University, Takakura, Hachioji 192-8510
| | - AKIO HAYASHI
- Agilent Technologies Japan, Ltd., Takakura, Hachioji 192-8510
| | - NAOHISA TOMOSUGI
- Medical Research Institute, Kanazawa Medical University, Uchinada
- Department of Nephrology, Kanazawa Medical University, Uchinada, Japan
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Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Giri AP, Gupta VS. Proteome profiling of flax (Linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development. J Proteome Res 2012; 11:6264-76. [PMID: 23153172 DOI: 10.1021/pr300984r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Flax (Linum usitatissimum L.) seeds are an important source of food and feed due to the presence of various health promoting compounds, making it a nutritionally and economically important plant. An in-depth analysis of the proteome of developing flax seed is expected to provide significant information with respect to the regulation and accumulation of such storage compounds. Therefore, a proteomic analysis of seven seed developmental stages (4, 8, 12, 16, 22, 30, and 48 days after anthesis) in a flax variety, NL-97 was carried out using a combination of 1D-SDS-PAGE and LC-MSE methods. A total 1716 proteins were identified and their functional annotation revealed that a majority of them were involved in primary metabolism, protein destination, storage and energy. Three carbon assimilatory pathways appeared to operate in flax seeds. Reverse transcription quantitative PCR of selected 19 genes was carried out to understand their roles during seed development. Besides storage proteins, methionine synthase, RuBisCO and S-adenosylmethionine synthetase were highly expressed transcripts, highlighting their importance in flax seed development. Further, the identified proteins were mapped onto developmental seed specific expressed sequence tag (EST) libraries of flax to obtain transcriptional evidence and 81% of them had detectable expression at the mRNA level. This study provides new insights into the complex seed developmental processes operating in flax.
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Affiliation(s)
- Vitthal T Barvkar
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
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33
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Debez A, Braun HP, Pich A, Taamalli W, Koyro HW, Abdelly C, Huchzermeyer B. Proteomic and physiological responses of the halophyte Cakile maritima to moderate salinity at the germinative and vegetative stages. J Proteomics 2012; 75:5667-94. [DOI: 10.1016/j.jprot.2012.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 08/09/2012] [Accepted: 08/14/2012] [Indexed: 01/29/2023]
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Wan LC, Wang F, Guo X, Lu S, Qiu Z, Zhao Y, Zhang H, Lin J. Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing. BMC PLANT BIOLOGY 2012; 12:146. [PMID: 22894611 PMCID: PMC3462689 DOI: 10.1186/1471-2229-12-146] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 07/05/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date. RESULTS To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated. CONCLUSIONS We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution.
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MESH Headings
- Base Sequence
- Conserved Sequence
- Cunninghamia/genetics
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Gene Library
- Genes, Plant
- High-Throughput Nucleotide Sequencing
- Molecular Sequence Annotation
- Molecular Sequence Data
- RNA, Plant/genetics
- RNA, Plant/isolation & purification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/isolation & purification
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/isolation & purification
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, RNA
- Transcriptome
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Affiliation(s)
- Li-Chuan Wan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Feng Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangqian Guo
- Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shanfa Lu
- Medicinal Plant Cultivation Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haidian District, Beijing, 100193, China
| | - Zongbo Qiu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanyuan Zhao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jinxing Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Zhen Y, Zhao ZZ, Zheng RH, Shi J. Proteomic analysis of early seed development in Pinus massoniana L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 54:97-104. [PMID: 22391127 DOI: 10.1016/j.plaphy.2012.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 02/06/2012] [Indexed: 05/13/2023]
Abstract
Understanding seed development is important for large-scale propagation and germplasm conservation for the Masson pine. We undertook a proteomic analysis of Masson pine seeds during the early stages of embryogenesis. Two-dimensional difference gel electrophoresis (2D DIGE) was used to quantify the differences in protein expression during early seed development. Using electrospray ionization mass spectrometry/mass spectrometry, we identified proteins from 43 gel spots that had been excised from preparative "pick" gels. Proteins involved in carbon metabolism were identified and were predominantly expressed at higher levels during the cleavage polyembryony and columnar embryo stages. Functional annotation of one seed protein revealed it involvement in programmed cell death and translation of selective mRNAs, which may play an important role in subordinate embryo elimination and suspensor degeneration in polyembryonic seed gymnosperms. Other identified proteins were associated with protein folding, nitrogen metabolism, disease/defense response, and protein storage, synthesis and stabilization. The comprehensive protein expression profiles generated by this study will provide new insights into the complex developmental process of seed development in Masson pine.
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Affiliation(s)
- Yan Zhen
- Key Laboratory of Forest Genetics and Biotechnology, Nanjing Forestry University, Ministry of Education, Nanjing 210037, People's Republic of China
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Nogueira FCS, Palmisano G, Soares EL, Shah M, Soares AA, Roepstorff P, Campos FAP, Domont GB. Proteomic profile of the nucellus of castor bean (Ricinus communis L.) seeds during development. J Proteomics 2012; 75:1933-9. [PMID: 22266101 DOI: 10.1016/j.jprot.2012.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 12/28/2011] [Accepted: 01/04/2012] [Indexed: 11/16/2022]
Abstract
In this study, we performed a proteomic analysis of nucellus from two developmental stages of Ricinus communis seeds by a GeLC-MS/MS approach, using of a high resolution orbitrap mass spectrometer, which resulted in the identification of a total of 766 proteins that were grouped into 553 protein groups. The distribution of the identified proteins in stages III and IV into different Gene Ontology categories was similar, with a remarkable abundance of proteins associated with the protein synthesis machinery of cells, as well as several classes of proteins involved in protein degradation, particularly of peptidases associated with programmed cell death. Consistent with the role of the nucellus in mediating nutrient transfer from maternal tissues to the endosperm and embryo, a significant proportion of the identified proteins are related to amino acid metabolism, but none of the identified proteins are known to have a role as storage proteins. Moreover for the first time, ricin isoforms were identified in tissues other than seed endosperm. Results are discussed in the context of the spatial and temporal distribution of the identified proteins within the nucellar cell layers.
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Affiliation(s)
- Fábio C S Nogueira
- Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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37
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Abril N, Gion JM, Kerner R, Müller-Starck G, Cerrillo RMN, Plomion C, Renaut J, Valledor L, Jorrin-Novo JV. Proteomics research on forest trees, the most recalcitrant and orphan plant species. PHYTOCHEMISTRY 2011; 72:1219-42. [PMID: 21353265 DOI: 10.1016/j.phytochem.2011.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 12/27/2010] [Accepted: 01/06/2011] [Indexed: 05/06/2023]
Abstract
The contribution of proteomics to the knowledge of forest tree (the most recalcitrant and almost forgotten plant species) biology is being reviewed and discussed, based on the author's own research work and papers published up to November 2010. This review is organized in four introductory sections starting with the definition of forest trees (1), the description of the environmental and economic importance (2) and its derived current priorities and research lines for breeding and conservation (3) including forest tree genomics (4). These precede the main body of this review: a general overview to proteomics (5) for introducing the forest tree proteomics section (6). Proteomics, defined as scientific discipline or experimental approach, it will be discussed both from a conceptual and methodological point of view, commenting on realities, challenges and limitations. Proteomics research in woody plants is limited to a reduced number of genera, including Pinus, Picea, Populus, Eucalyptus, and Fagus, mainly using first-generation approaches, e.g., those based on two-dimensional electrophoresis coupled to mass spectrometry. This area joins the own limitations of the technique and the difficulty and recalcitrance of the plant species as an experimental system. Furthermore, it contributes to a deeper knowledge of some biological processes, namely growth, development, organogenesis, and responses to stresses, as it is also used in the characterization and cataloguing of natural populations and biodiversity (proteotyping) and in assisting breeding programmes.
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Affiliation(s)
- Nieves Abril
- Dpt. of Biochemistry and Molecular Biology, ETSIAM, University of Cordoba, Campus de Rabanales, Ed. Severo Ochoa, Cordoba, Spain
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38
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Seed proteomics. J Proteomics 2011; 74:389-400. [DOI: 10.1016/j.jprot.2010.12.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/08/2010] [Accepted: 12/10/2010] [Indexed: 12/29/2022]
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39
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Arruda SCC, Barbosa HDS, Azevedo RA, Arruda MAZ. Two-dimensional difference gel electrophoresis applied for analytical proteomics: fundamentals and applications to the study of plant proteomics. Analyst 2011; 136:4119-26. [DOI: 10.1039/c1an15513j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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