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Chen S, Guo D, Deng Z, Tang Q, Li C, Xiao Y, Zhong L, Chen B. Integration analysis of transcriptome and proteome profiles brings new insights of somatic embryogenesis of two eucalyptus species. BMC PLANT BIOLOGY 2024; 24:561. [PMID: 38877454 PMCID: PMC11179386 DOI: 10.1186/s12870-024-05271-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Somatic embryogenesis (SE) is recognized as a promising technology for plant vegetative propagation. Although previous studies have identified some key regulators involved in the SE process in plant, our knowledge about the molecular changes in the SE process and key regulators associated with high embryogenic potential is still poor, especially in the important fiber and energy source tree - eucalyptus. RESULTS In this study, we analyzed the transcriptome and proteome profiles of E. camaldulensis (with high embryogenic potential) and E. grandis x urophylla (with low embryogenic potential) in SE process: callus induction and development. A total of 12,121 differentially expressed genes (DEGs) and 3,922 differentially expressed proteins (DEPs) were identified in the SE of the two eucalyptus species. Integration analysis identified 1,353 (131 to 546) DEGs/DEPs shared by the two eucalyptus species in the SE process, including 142, 13 and 186 DEGs/DEPs commonly upregulated in the callus induction, maturation and development, respectively. Further, we found that the trihelix transcription factor ASR3 isoform X2 was commonly upregulated in the callus induction of the two eucalyptus species. The SOX30 and WRKY40 TFs were specifically upregulated in the callus induction of E. camaldulensis. Three TFs (bHLH62, bHLH35 isoform X2, RAP2-1) were specifically downregulated in the callus induction of E. grandis x urophylla. WGCNA identified 125 and 26 genes/proteins with high correlation (Pearson correlation > 0.8 or < -0.8) with ASR3 TF in the SE of E. camaldulensis and E. grandis x urophylla, respectively. The potential target gene expression patterns of ASR3 TF were then validated using qRT-PCR in the material. CONCLUSIONS This is the first time to integrate multiple omics technologies to study the SE of eucalyptus. The findings will enhance our understanding of molecular regulation mechanisms of SE in eucalyptus. The output will also benefit the eucalyptus breeding program.
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Affiliation(s)
- Shengkan Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Dongqiang Guo
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Ziyu Deng
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Qinglan Tang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Changrong Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China.
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Yanxia Z, Jianping J, Yanfen H, Qingsong D, Kunhua W. Comparative transcriptome analysis of the effects of friction and exogenous gibberellin on germination in Abrus cantoniensis. PLANT SIGNALING & BEHAVIOR 2022; 17:2149113. [PMID: 36448597 PMCID: PMC9721420 DOI: 10.1080/15592324.2022.2149113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
The seeds of Abrus cantoniensis (A. cantonensis) have dormancy characteristics with very low germination under natural conditions. In general, its seed dormancy could be broken by friction or soaking with exogenous gibberellins (GA3). To date, the molecular mechanism underlying the effects of GA3 and friction on its seed germination is unclear. In this study, we tested the effects of different treatments, including soaking in sterile water (G1), friction (G2), soaking in GA3 (G3), combined treatment of friction, and GA3 (G4)) on seed germination. Then, we have investigated the seed transcriptome profiles corresponding to the different treatments by RNA sequencing. The results showed that seed germination was significantly increased by combined treatment with friction and GA3. RNA-Seq analysis generated 84.80 gigabases (Gb) of sequences. 82,996 out of 121,776 unigenes were annotated. Comparative transcriptome analysis observed that 1,130, 1,097, and 708 unigenes were deferentially expressed in G1 vs. G2, G1 vs. G3, and G1 vs. G4 groups, respectively. Additionally, 20 putatively candidate genes related to seed germination, including CYP78A5, Bg7s, GA-20-ox, rd22, MYB4, LEA, CHS, and STH-2, and other potential candidates with abundant expression were identified. Our findings provide first insights into gene expression profiles and physiological response for friction combined with GA3 on A. cantoniensis seed germination.
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Affiliation(s)
- Zhu Yanxia
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jiang Jianping
- Guangxi Key Laboratory of High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Huang Yanfen
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Dong Qingsong
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Wei Kunhua
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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Khoso MA, Hussain A, Ritonga FN, Ali Q, Channa MM, Alshegaihi RM, Meng Q, Ali M, Zaman W, Brohi RD, Liu F, Manghwar H. WRKY transcription factors (TFs): Molecular switches to regulate drought, temperature, and salinity stresses in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1039329. [PMID: 36426143 PMCID: PMC9679293 DOI: 10.3389/fpls.2022.1039329] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 06/01/2023]
Abstract
The WRKY transcription factor (TF) belongs to one of the major plant protein superfamilies. The WRKY TF gene family plays an important role in the regulation of transcriptional reprogramming associated with plant stress responses. Change in the expression patterns of WRKY genes or the modifications in their action; participate in the elaboration of numerous signaling pathways and regulatory networks. WRKY proteins contribute to plant growth, for example, gamete formation, seed germination, post-germination growth, stem elongation, root hair growth, leaf senescence, flowering time, and plant height. Moreover, they play a key role in many types of environmental signals, including drought, temperature, salinity, cold, and biotic stresses. This review summarizes the current progress made in unraveling the functions of numerous WRKY TFs under drought, salinity, temperature, and cold stresses as well as their role in plant growth and development.
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Affiliation(s)
- Muneer Ahmed Khoso
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
- Department of Life Science, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Amjad Hussain
- College of Plant Science and Technology, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | | | - Qurban Ali
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | | | - Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Qinglin Meng
- Department of Biology and Food Engineering, Bozhou University, Bozhou, China
| | - Musrat Ali
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad Pakistan, Islamabad, Pakistan
| | - Wajid Zaman
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Rahim Dad Brohi
- Department of Animal Reproduction/Theriogenology, Faculty of Veterinary Science, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Pakistan
| | - Fen Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
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Ceriotti LF, Gatica-Soria L, Sanchez-Puerta MV. Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes. PLANT MOLECULAR BIOLOGY 2022; 109:673-688. [PMID: 35359176 DOI: 10.1007/s11103-022-01266-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.
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Affiliation(s)
- Luis F Ceriotti
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Leonardo Gatica-Soria
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
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Comparative Proteomic Analysis Provides New Insights into the Development of Haustorium in Taxillus chinensis (DC.) Danser. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9567647. [PMID: 35941969 PMCID: PMC9356245 DOI: 10.1155/2022/9567647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/09/2022] [Indexed: 11/28/2022]
Abstract
Taxillus chinensis is an important medicinal and parasitic plant that attacks other plants for living. The development of haustorium is a critical process, imperative for successful parasitic invasion. To reveal the mechanisms underlying haustorium development, we performed an iTRAQ-based proteomics analysis which led to the identification of several differentially abundant proteins (DAPs) in fresh seeds (CK), baby (FB), and adult haustoria (FD). A total of 563 and 785 DAPs were identified and quantified in the early and later developmental stages, respectively. Pathway enrichment analysis revealed that the DAPs are mainly associated with metabolic pathways, ribosome, phenylpropanoid biosynthesis, and photosynthesis. In addition, DAPs associated with the phytohormone signaling pathway changed markedly. Furthermore, we evaluated the content of various phytohormones during different stages of haustoria development. These results indicated that phytohormones are very important for haustorium development. qRT-PCR results validated that the mRNA expression levels were consistent with the expression of proteins, suggesting that our results are reliable. This is the first report on haustoria proteomes in the parasitic plant, Taxillus chinensis, to the best of our knowledge. Our findings will enhance our understanding of the molecular mechanism of haustoria development.
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A De Novo Transcriptome Analysis Identifies Cold-Responsive Genes in the Seeds of Taxillus chinensis (DC.) Danser. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9247169. [PMID: 35845948 PMCID: PMC9279050 DOI: 10.1155/2022/9247169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/30/2022] [Accepted: 06/20/2022] [Indexed: 12/03/2022]
Abstract
Taxillus chinensis (DC.) Danser, a parasitic plant of the Loranthaceae family, grows by attacking other plants. It has a long history of being used in Chinese medicine to treat multiple chronic diseases. We previously observed that T. chinensis seeds are sensitive to cold. In this study, we performed transcriptome sequencing for T. chinensis seeds treated by cold (0°C) for 0 h, 12 h, 24 h, and 36 h. TRINITY assembled 257,870 transcripts from 223,512 genes. The GC content and N50 were calculated as 42.29% and 1,368, respectively. Then, we identified 42,183 CDSs and 35,268 likely proteins in the assembled transcriptome, which contained 1,622 signal peptides and 6,795 transmembrane domains. Next, we identified 17,217 genes (FPKM > 5) and 2,333 differentially expressed genes (DEGs) in T. chinensis seeds under cold stress. The MAPK pathway, as an early cold response, was significantly enriched by the DEGs in the T. chinensis seeds after 24 h of cold treatment. Known cold-responsive genes encoding abscisic acid-associated, aquaporin, C-repeat binding factor (CBF), cold-regulated protein, heat shock protein, protein kinase, ribosomal protein, transcription factor (TF), zinc finger protein, and ubiquitin were deregulated in the T. chinensis seeds under cold stress. Notably, the upregulation of CBF gene might be the consequences of the downregulation of MYB and GATA TFs. Additionally, we identified that genes encoding CDC20, YLS9, EXORDIUM, and AUX1 and wound-responsive family protein might be related to novel mechanisms of T. chinensis seeds exposed to cold. This study is first to report the differential transcriptional induction in T. chinensis seeds under cold stress. It will improve our understanding of parasitic plants in response to cold and provide a valuable resource for future studies.
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Zhang Y, Li J, Li C, Chen S, Tang Q, Xiao Y, Zhong L, Chen Y, Chen B. Gene expression programs during callus development in tissue culture of two Eucalyptus species. BMC PLANT BIOLOGY 2022; 22:1. [PMID: 34979920 PMCID: PMC8722213 DOI: 10.1186/s12870-021-03391-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/09/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Eucalyptus is a highly diverse genus of the Myrtaceae family and widely planted in the world for timber and pulp production. Tissue culture induced callus has become a common tool for Eucalyptus breeding, however, our knowledge about the genes related to the callus maturation and shoot regeneration is still poor. RESULTS We set up an experiment to monitor the callus induction and callus development of two Eucalyptus species - E. camaldulensis (high embryogenic potential) and E. grandis x urophylla (low embryogenic potential). Then, we performed transcriptome sequencing for primary callus, mature callus, shoot regeneration stage callus and senescence callus. We identified 707 upregulated and 694 downregulated genes during the maturation process of the two Eucalyptus species and most of them were involved in the signaling pathways like plant hormone and MAPK. Next, we identified 135 and 142 genes that might play important roles during the callus development of E. camaldulensis and E. grandis x urophylla, respectively. Further, we found 15 DEGs shared by these two Eucalyptus species during the callus development, including Eucgr.D00640 (stem-specific protein TSJT1), Eucgr.B00171 (BTB/POZ and TAZ domain-containing protein 1), Eucgr.C00948 (zinc finger CCCH domain-containing protein 20), Eucgr.K01667 (stomatal closure-related actinbinding protein 3), Eucgr.C00663 (glutaredoxin-C10) and Eucgr.C00419 (UPF0481 protein At3g47200). Interestingly, the expression patterns of these genes displayed "N" shape in the samples. Further, we found 51 genes that were dysregulated during the callus development of E. camaldulensis but without changes in E. grandis x urophylla, such as Eucgr.B02127 (GRF1-interacting factor 1), Eucgr.C00947 (transcription factor MYB36), Eucgr.B02752 (laccase-7), Eucgr.B03985 (transcription factor MYB108), Eucgr.D00536 (GDSL esterase/lipase At5g45920) and Eucgr.B02347 (scarecrow-like protein 34). These 51 genes might be associated with the high propagation ability of Eucalyptus and 22 might be induced after the dedifferentiation. Last, we performed WGCNA to identify the co-expressed genes during the callus development of Eucalyptus and qRT-PCR experiment to validate the gene expression patterns. CONCLUSIONS This is the first time to globally study the gene profiles during the callus development of Eucalyptus. The results will improve our understanding of gene regulation and molecular mechanisms in the callus maturation and shoot regeneration.
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Affiliation(s)
- Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Changrong Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Shengkan Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Qinglan Tang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Yingying Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
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Fu J, Wan L, Song L, He L, Jiang N, Long H, Huo J, Ji X, Hu F, Wei S, Pan L. OUP accepted manuscript. Genome Biol Evol 2022; 14:6575330. [PMID: 35482027 PMCID: PMC9113316 DOI: 10.1093/gbe/evac060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
| | | | - Lisha Song
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Lili He
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Ni Jiang
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Hairong Long
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Juan Huo
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Xiaowen Ji
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Fengyun Hu
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
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Li D, Li Y, Qian J, Liu X, Xu H, Zhang G, Ren J, Wang L, Zhang L, Yu H. Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds. FRONTIERS IN PLANT SCIENCE 2021; 12:717563. [PMID: 34616414 PMCID: PMC8488369 DOI: 10.3389/fpls.2021.717563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Chinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of this species are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. However, little is known about the underlying molecular mechanism of desiccation sensitivity of Q. variabilis seeds. In this study, the seeds were desiccated with silica gel for certain days as different treatments from 0 (Control) to 15 days (T15) with a gradient of 1 day. According to the seed germination percentage, four key stages (Control, T2, T4, and T11) were found. Then the transcriptomic profiles of these four stages were compared. A total of 4,405, 4,441, and 5,907 differentially expressed genes (DEGs) were identified in T2 vs. Control, T4 vs. Control, and T11 vs. Control, respectively. Among them, 2,219 DEGs were overlapped in the three comparison groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were enriched into 124 pathways, such as "Plant hormone signal transduction" and "Glycerophospholipid metabolism". DEGs related to hormone biosynthesis and signal transduction (ZEP, YUC, PYR, ABI5, ERF1B, etc.), stress response proteins (LEA D-29, HSP70, etc.), and phospholipase D (PLD1) were detected during desiccation. These genes and their interactions may determine the desiccation sensitivity of seeds. In addition, group specific DEGs were also identified in T2 vs. Control (PP2C62, UNE12, etc.), T4 vs. Control (WRKY1-like, WAK10, etc.), and T11 vs. Control (IBH1, bZIP44, etc.), respectively. Finally, a possible work model was proposed to show the molecular regulation mechanism of desiccation sensitivity in Q. variabilis seeds. This is the first report on the molecular regulation mechanism of desiccation sensitivity of Q. variabilis seeds using RNA-Seq. The findings could make a great contribution to seed storage and long-term conservation of recalcitrant seeds in the future.
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Affiliation(s)
- Dongxing Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yingchao Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jialian Qian
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaojuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Huihui Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Guowei Zhang
- Hongya Mountain State-Owned Forest Farm of Hebei, Yixian, China
| | - Junjie Ren
- Hongya Mountain State-Owned Forest Farm of Hebei, Yixian, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Haiyan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Qin Z, Li J, Zhang Y, Xiao Y, Zhang X, Zhong L, Liu H, Chen B. Genome-wide identification of microRNAs involved in the somatic embryogenesis of Eucalyptus. G3-GENES GENOMES GENETICS 2021; 11:6163290. [PMID: 33693674 PMCID: PMC8049409 DOI: 10.1093/g3journal/jkab070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 11/13/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (18-24 nt) and function in many biological processes in plants. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis (SE) of Eucalyptus is still poor. Here we reported, for the first time, the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus species and identified miRNAs involved in SE of Eucalyptus. Stem and tissue culture-induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla and were used as differentiated and dedifferentiated samples, respectively. Small RNA sequencing generated 304.2 million clean reads for the Eucalyptus samples (n = 3) and identified 888 miRNA precursors (197 known and 691 novel) for Eucalyptus. These miRNAs were mainly distributed in chromosomes Chr03, Chr05, and Chr08 and can produce 46 miRNA clusters. Then, we identified 327 and 343 differentially expressed miRNAs (DEmiRs) in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. DEmiRs shared by the two Eucalyptus species might be involved in the development of embryonic callus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399, and MIR482. Notably, we identified 81 upregulated and 67 downregulated miRNAs specific to E. camaldulensis, which might be associated with the high embryogenic potential. Target prediction and functional analysis showed that they might be involved in longevity regulating and plant hormone signal transduction pathways. Further, using the gene expression profiles, we observed the negative regulation of miRNA-target pairs, such as MIR160~ARF18, MIR396~GRF6, MIR166~ATHB15/HD-ZIP, and MIR156/MIR157~SPL1. Interestingly, transcription factors such as WRKY, MYB, GAMYB, TCP4, and PIL1 were found to be regulated by the DEmiRs. The genes encoding PIL1 and RPS21C, regulated by upregulated miRNAs (e.g., egd-N-miR63-5p, egd-N-miR63-5p, and MIR169,) were downregulated exclusively in the dedifferentiation of E. camaldulensis. This is the first time to study the miRNA regulation in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, it will improve our understanding of miRNA regulation during the somatic embryogenesis of Eucalyptus and benefit the Eucalyptus breeding program.
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Affiliation(s)
- Zihai Qin
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Xiaoning Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Hailong Liu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
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Manna M, Thakur T, Chirom O, Mandlik R, Deshmukh R, Salvi P. Transcription factors as key molecular target to strengthen the drought stress tolerance in plants. PHYSIOLOGIA PLANTARUM 2021; 172:847-868. [PMID: 33180329 DOI: 10.1111/ppl.13268] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 05/03/2023]
Abstract
Amid apprehension of global climate change, crop plants are inevitably confronted with a myriad of abiotic stress factors during their growth that inflicts a serious threat to their development and overall productivity. These abiotic stresses comprise extreme temperature, pH, high saline soil, and drought stress. Among different abiotic stresses, drought is considered the most calamitous stressor with its serious impact on the crops' yield stability. The development of climate-resilient crops that withstands reduced water availability is a major focus of the scientific fraternity to ensure the food security of the sharply increasing population. Numerous studies aim to recognize the key regulators of molecular and biochemical processes associated with drought stress tolerance response. A few potential candidates are now considered as promising targets for crop improvement. Transcription factors act as a key regulatory switch controlling the gene expression of diverse biological processes and, eventually, the metabolic processes. Understanding the role and regulation of the transcription factors will facilitate the crop improvement strategies intending to develop and deliver agronomically-superior crops. Therefore, in this review, we have emphasized the molecular avenues of the transcription factors that can be exploited to engineer drought tolerance potential in crop plants. We have discussed the molecular role of several transcription factors, such as basic leucine zipper (bZIP), dehydration responsive element binding (DREB), DNA binding with one finger (DOF), heat shock factor (HSF), MYB, NAC, TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP), and WRKY. We have also highlighted candidate transcription factors that can be used for the development of drought-tolerant crops.
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Affiliation(s)
- Mrinalini Manna
- National Institute of Plant Genome Research, New Delhi, India
| | - Tanika Thakur
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Oceania Chirom
- National Institute of Plant Genome Research, New Delhi, India
| | - Rushil Mandlik
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Rupesh Deshmukh
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Prafull Salvi
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
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Identification of MicroRNAs in Taxillus chinensis (DC.) Danser Seeds under Cold Stress. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5585884. [PMID: 34159194 PMCID: PMC8188600 DOI: 10.1155/2021/5585884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/18/2021] [Indexed: 12/16/2022]
Abstract
Taxillus chinensis (DC.) Danser, a parasitic plant that belongs to the Loranthaceae family, has a long history of being used in the Chinese medicine. We observed that the loranthus seeds were sensitive to temperature and could lose viability below 0°C quickly. Thus, we performed small RNA sequencing to study the microRNA (miRNA) regulation in the loranthus seeds under cold stress. In total, we identified 600 miRNAs, for the first time, in the loranthus seeds under cold stress. Then, we detected 224, 229, and 223 miRNAs (TPM > 1) in A0 (control), A1 (cold treatment for 12 h at 0°C), and A2 (cold treatment for 36 h at 0°C), respectively. We next identified 103 differentially expressed miRNAs (DEmiRs) in the loranthus seeds in response to cold. Notably, miR408 was upregulated during the cold treatment, which can regulate genes encoding phytocyanin family proteins and phytophenol oxidases. Some DEmiRs were specific to A1 and may function in early response to cold, such as gma-miR393b-3p, miR946, ath-miR779.2-3p, miR398, and miR9662. It is interesting that ICE3, IAA13, and multiple transcription factors (e.g., WRKY and CRF4 and TCP4) regulated by the DEmiRs have been reported to respond cold in other plants. We further identified 4, 3, and 4 DEmiRs involved in the pathways “responding to cold,” “responding to abiotic stimulus,” and “seed development/germination,” respectively. qRT-PCR was used to confirm the expression changes of DEmiRs and their targets in the loranthus seeds during the cold treatment. This is the first time to study cold-responsive miRNAs in loranthus, and our findings provide a valuable resource for future studies.
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Bao W, Ao D, Wang L, Ling Z, Chen M, Bai Y, Wuyun TN, Chen J, Zhang S, Li F. Dynamic transcriptome analysis identifies genes related to fatty acid biosynthesis in the seeds of Prunus pedunculata Pall. BMC PLANT BIOLOGY 2021; 21:152. [PMID: 33761884 PMCID: PMC7992973 DOI: 10.1186/s12870-021-02921-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Prunus pedunculata Pall, the deciduous shrub of Amygdalus subgenus in Rosaceae, is a new kind of desert oil-bearing tree. It has a long story of being planted in the West and North of China for sand fixation and desert control. In addition, the seeds of P. pedunculata are rich of oil, especially the monounsaturated fatty acid and polyunsaturated fatty acid. However, little is known about the molecular mechanisms of oil accumulation during the seed development of P. pedunculata. RESULTS The seeds of P. pedunculata from three independent plants at 10, 18, 24, 31, 39, 45, 59 and 73 days after flowering (DAF) were obtained and the oil compositions were evaluated. It showed that oleic acid was the dominant type of oil content in the mature seeds (from 32.724% at 10DAF to 72.06% at 73DAF). Next, transcriptome sequencing for the developing seeds produced 988.795 million high quality reads and TRINITY assembled 326,271 genes for the first transcriptome for P. pedunculata. After the assembled transcriptome was evaluated by BUSCO with 85.9% completeness, we identified 195,342, 109,850 and 121,897 P. pedunculata genes aligned to NR, GO and KEGG pathway databases, respectively. Then, we predicted 23,229 likely proteins from the assembled transcriptome and identified 1917 signal peptides and 5512 transmembrane related proteins. In the developing seeds we detected 91,362 genes (average FPKM > 5) and correlation analysis indicated three possible development stages - early (10 ~ 24DAF), middle (31 ~ 45DAF) and late (59 ~ 73DAF). We next analyzed the differentially expressed genes (DEGs) in the developing seeds. Interestingly, compared to 10DAF the number of DEGs was increased from 4406 in 18DAF to 27,623 in 73DAF. Based on the gene annotation, we identified 753, 33, 8 and 645 DEGs related to the fatty acid biosynthesis, lipid biosynthesis, oil body and transcription factors. Notably, GPAT, DGD1, LACS2, UBC and RINO were highly expressed at the early development stage, ω6-FAD, SAD, ACP, ACCA and AHG1 were highly expressed at the middle development stage, and LACS6, DGD1, ACAT1, AGPAT, WSD1, EGY2 and oleosin genes were highly expressed at the late development stage. CONCLUSIONS This is the first time to study the developing seed transcriptome of P. pedunculata and our findings will provide a valuable resource for future studies. More importantly, it will improve our understanding of molecular mechanisms of oil accumulation in P. pedunculata.
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Affiliation(s)
- Wenquan Bao
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dun Ao
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lin Wang
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, 450003, China.
| | - Zhihao Ling
- Chengdu Jiyu Technology, Chengdu, 610213, Sichuan, China
| | - Maoshan Chen
- Australian Center for Blood Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Yue Bai
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Ta-Na Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Junxing Chen
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Shuning Zhang
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Fengming Li
- Inner Mongolia Agricultural University, Hohhot, 010018, China
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Hormonal and transcriptional analyses provides new insights into the molecular mechanisms underlying root thickening and isoflavonoid biosynthesis in Callerya speciosa (Champ. ex Benth.) Schot. Sci Rep 2021; 11:9. [PMID: 33420059 PMCID: PMC7794344 DOI: 10.1038/s41598-020-76633-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/27/2020] [Indexed: 01/26/2023] Open
Abstract
Callerya speciosa (Champ. ex Benth.) Schot is a traditional Chinese medicine characterized by tuberous roots as the main organ of isoflavonoid accumulation. Root thickening and isoflavonoid accumulation are two major factors for yield and quality of C. speciosa. However, the underlying mechanisms of root thickening and isoflavonoid biosynthesis have not yet been elucidated. Here, integrated morphological, hormonal and transcriptomic analyses of C. speciosa tuberous roots at four different ages (6, 12, 18, 30 months after germination) were performed. The growth cycle of C. speciosa could be divided into three stages: initiation, rapid-thickening and stable-thickening stage, which cued by the activity of vascular cambia. Endogenous changes in phytohormones were associated with developmental changes during root thickening. Jasmonic acid might be linked to the initial development of tuberous roots. Abscisic acid seemed to be essential for tuber maturation, whereas IAA, cis-zeatin and gibberellin 3 were considered essential for rapid thickening of tuberous roots. A total of 4337 differentially expressed genes (DEGs) were identified during root thickening, including 15 DEGs participated in isoflavonoid biosynthesis, and 153 DEGs involved in starch/sucrose metabolism, hormonal signaling, transcriptional regulation and cell wall metabolism. A hypothetical model of genetic regulation associated with root thickening and isoflavonoid biosynthesis in C. speciosa is proposed, which will help in understanding the underlying mechanisms of tuberous root formation and isoflavonoid biosynthesis.
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Xiao Y, Li J, Zhang Y, Zhang X, Liu H, Qin Z, Chen B. Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus. BMC Genomics 2020; 21:803. [PMID: 33208105 PMCID: PMC7672952 DOI: 10.1186/s12864-020-07214-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/08/2020] [Indexed: 01/11/2023] Open
Abstract
Background Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE. Results We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9229 and 8989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2687 up-regulated and 2581 down-regulated genes shared. Next, we identified 2003 up-regulated and 1958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07214-5.
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Affiliation(s)
- Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Xiaoning Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Hailong Liu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Zihai Qin
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China.
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De novo Transcriptome Reveals Gene Changes in the Development of the Endosperm Chalazal Haustorium in Taxillus chinensis (DC.) Danser. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7871918. [PMID: 32149138 PMCID: PMC7053452 DOI: 10.1155/2020/7871918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/26/2019] [Indexed: 01/25/2023]
Abstract
Loranthus (Taxillus chinensis) is a facultative, hemiparasite and stem parasitic plant that attacks other plants for living. Transcriptome sequencing and bioinformatics analysis were applied in this study to identify the gene expression profiles of fresh seeds (CK), baby (FB), and adult haustoria tissues (FD). We assembled 160,571 loranthus genes, of which 64,926, 35,417, and 47,249 were aligned to NR, GO, and KEGG pathway databases, respectively. We identified 14,295, 15,921, and 16,402 genes in CK, FB, and FD, respectively. We next identified 5,480 differentially expressed genes (DEGs) in the process, of which 258, 174, 81, and 94 were encoding ribosomal proteins (RP), transcription factors (TF), ubiquitin, and disease resistance proteins, respectively. Some DEGs were identified to be upregulated along with the haustoria development (e.g., 68 RP and 26 ubiquitin genes). Notably, 36 RP DEGs peak at FB; 10 ER, 5 WRKY, 6 bHLH, and 4 MYB TF genes upregulated only in FD. Further, we identified 4 out of 32 microRNA genes dysregulated in the loranthus haustoria development. This is the first haustoria transcriptome of loranthus, and our findings will improve our understanding of the molecular mechanism of haustoria.
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De Novo Transcriptome Identifies Olfactory Genes in Diachasmimorpha longicaudata (Ashmead). Genes (Basel) 2020; 11:genes11020144. [PMID: 32013248 PMCID: PMC7074194 DOI: 10.3390/genes11020144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 01/01/2023] Open
Abstract
Diachasmimoorpha longicaudata (Ashmead, D. longicaudata) (Hymenoptera: Braconidae) is a solitary species of parasitoid wasp and widely used in integrated pest management (IPM) programs as a biological control agent in order to suppress tephritid fruit flies of economic importance. Although many studies have investigated the behaviors in the detection of their hosts, little is known of the molecular information of their chemosensory system. We assembled the first transcriptome of D. longgicaudata using transcriptome sequencing and identified 162,621 unigenes for the Ashmead insects in response to fruit flies fed with different fruits (guava, mango, and carambola). We annotated these transcripts on both the gene and protein levels by aligning them to databases (e.g., NR, NT, KEGG, GO, PFAM, UniProt/SwissProt) and prediction software (e.g., SignalP, RNAMMER, TMHMM Sever). CPC2 and MIREAP were used to predict the potential noncoding RNAs and microRNAs, respectively. Based on these annotations, we found 43, 69, 60, 689, 26 and 14 transcripts encoding odorant-binding protein (OBP), chemosensory proteins (CSPs), gustatory receptor (GR), odorant receptor (OR), odorant ionotropic receptor (IR), and sensory neuron membrane protein (SNMP), respectively. Sequence analysis identified the conserved six Cys in OBP sequences and phylogenetic analysis further supported the identification of OBPs and CSPs. Furthermore, 9 OBPs, 13 CSPs, 3 GRs, 4IRs, 25 ORs, and 4 SNMPs were differentially expressed in the insects in response to fruit flies with different scents. These results support that the olfactory genes of the parasitoid wasps were specifically expressed in response to their hosts with different scents. Our findings improve our understanding of the behaviors of insects in the detection of their hosts on the molecular level. More importantly, it provides a valuable resource for D. longicaudata research and will benefit the IPM programs and other researchers in this filed.
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Zhang L, Wu M, Yu D, Teng Y, Wei T, Chen C, Song W. Identification of Glutathione Peroxidase (GPX) Gene Family in Rhodiola crenulata and Gene Expression Analysis under Stress Conditions. Int J Mol Sci 2018; 19:E3329. [PMID: 30366446 PMCID: PMC6274781 DOI: 10.3390/ijms19113329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 01/14/2023] Open
Abstract
Glutathione peroxidases (GPXs) are important enzymes in the glutathione-ascorbate cycle for catalyzing the reduction of H₂O₂ or organic hydroperoxides to water. GPXs play an essential role in plant growth and development by participating in photosynthesis, respiration, and stress tolerance. Rhodiola crenulata is a popular traditional Chinese medicinal plant which displays an extreme energy of tolerance to harsh alpine climate. The GPXs gene family might provide R. crenulata for extensively tolerance to environment stimulus. In this study, five GPX genes were isolated from R. crenulata. The protein amino acid sequences were analyzed by bioinformation softwares with the results that RcGPXs gene sequences contained three conserve cysteine residues, and the subcellular location predication were in the chloroplast, endoplasmic reticulum, or cytoplasm. Five RcGPXs members presented spatial and temporal specific expression with higher levels in young and green organs. And the expression patterns of RcGPXs in response to stresses or plant hormones were investigated by quantitative real-time PCR. In addition, the putative interaction proteins of RcGPXs were obtained by yeast two-hybrid with the results that RcGPXs could physically interact with specific proteins of multiple pathways like transcription factor, calmodulin, thioredoxin, and abscisic acid signal pathway. These results showed the regulation mechanism of RcGPXs were complicated and they were necessary for R. crenulata to adapt to the treacherous weather in highland.
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Affiliation(s)
- Lipeng Zhang
- College of Life Science, Nankai University, Tianjin, 300071 China.
| | - Mei Wu
- College of Life Science, Nankai University, Tianjin, 300071 China.
| | - Deshui Yu
- College of Life Science, Nankai University, Tianjin, 300071 China.
| | - Yanjiao Teng
- College of Life Science, Nankai University, Tianjin, 300071 China.
| | - Tao Wei
- College of Life Science, Nankai University, Tianjin, 300071 China.
| | - Chengbin Chen
- College of Life Science, Nankai University, Tianjin, 300071 China.
| | - Wenqin Song
- College of Life Science, Nankai University, Tianjin, 300071 China.
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Liu X, Zhang R, Ou H, Gui Y, Wei J, Zhou H, Tan H, Li Y. Comprehensive transcriptome analysis reveals genes in response to water deficit in the leaves of Saccharum narenga (Nees ex Steud.) hack. BMC PLANT BIOLOGY 2018; 18:250. [PMID: 30342477 PMCID: PMC6195978 DOI: 10.1186/s12870-018-1428-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/16/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sugarcane is an important sugar and energy crop that is widely planted in the world. Among the environmental stresses, the water-deficit stress is the most limiting to plant productivity. Some groups have used PCR-based and microarray technologies to investigate the gene expression changes of multiple sugarcane cultivars under water stress. Our knowledge about sugarcane genes in response to water deficit is still poor. RESULTS A wild sugarcane type, Saccharum narenga, was selected and treated with drought stress for 22 days. Leaves from drought treated (DTS) and control (CK) plants were obtained for deep sequencing. Paired-end sequencing enabled us to assemble 104,644 genes (N50 = 1605 bp), of which 38,721 were aligned to other databases, such as UniProt, NR, GO, KEGG and Pfam. Single-end and paired-end sequencing identified 30,297 genes (> 5 TPM) in all samples. Compared to CK, 3389 differentially expressed genes (DEGs) were identified in DTS samples, comprising 1772 up-regulated and 1617 down-regulated genes. Functional analysis showed that the DEGs were involved in biological pathways like response to blue light, metabolic pathways and plant hormone signal transduction. We further observed the expression patterns of several important gene families, including aquaporins, late embryogenesis abundant proteins, auxin related proteins, transcription factors (TFs), heat shock proteins, light harvesting chlorophyll a-b binding proteins, disease resistance proteins, and ribosomal proteins. Interestingly, the regulation of genes varied among different subfamilies of aquaporin and ribosomal proteins. In addition, DIVARICATA and heat stress TFs were first reported in sugarcane leaves in response to water deficit. Further, we showed potential miRNAs that might be involved in the regulation of gene changes in sugarcane leaves under the water-deficit stress. CONCLUSIONS This is the first transcriptome study of Saccharum narenga and the assembled genes are a valuable resource for future research. Our findings will improve the understanding of the mechanism of gene regulation in sugarcane leaves under the water-deficit stress. The output of this study will also contribute to the sugarcane breeding program.
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Affiliation(s)
- Xihui Liu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning, 530005 China
| | - Ronghua Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Huiping Ou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Yiyun Gui
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Jinju Wei
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Hui Zhou
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Hongwei Tan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Yangrui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Guangxi Key Laboratory of Sugarcane Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning, 530005 China
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Lin W, Huang W, Ning S, Wang X, Ye Q, Wei D. De novo characterization of the Baphicacanthus cusia(Nees) Bremek transcriptome and analysis of candidate genes involved in indican biosynthesis and metabolism. PLoS One 2018; 13:e0199788. [PMID: 29975733 PMCID: PMC6033399 DOI: 10.1371/journal.pone.0199788] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/13/2018] [Indexed: 12/19/2022] Open
Abstract
Baphicacanthus cusia (Nees) Bremek is an herb widely used for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine. The roots, stems and leaves can be used as natural medicine, in which indigo and indirubin are two main active ingredients. In this study, quantification of indigo, indirubin, indican and adenosine among various tissues of B. cusia was conducted using HPLC-DAD. Leaves have significantly higher contents than stems and roots (380.66, 315.15, 20,978.26, 4323.15 μg/g in leaves, 306.36, 71.71, 3,056.78, 139.45 μg/g in stems, and 9.31, 7.82, 170.45, 197.48 μg/g in roots, respectively). De novo transcriptome sequencing of B. cusia was performed for the first time. The sequencing yielded 137,216,248, 122,837,394 and 140,240,688 clean reads from leaves, stems and roots respectively, which were assembled into 51,381 unique sequences. A total of 33,317 unigenes could be annotated using the databases of Nr, Swiss-Prot, KEGG and KOG. These analyses provided a detailed view of the enzymes involved in indican backbone biosynthesis, such as cytochrome P450, UDP-glycosyltransferase, glucosidase and tryptophan synthase. Analysis results showed that tryptophan synthase was the candidate gene involved in the tissue-specific biosynthesis of indican. We also detected sixteen types of simple sequence repeats in RNA-Seq data for use in future molecular mark assisted breeding studies. The results will be helpful in further analysis of B. cusia functional genomics, especially in increasing biosynthesis of indican through biotechnological approaches and metabolic regulation.
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Affiliation(s)
- Wenjin Lin
- School of Life science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Medical Measurement, Fujian Academy of Medical Sciences, Fuzhou, China
| | - Wei Huang
- School of Life science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuju Ning
- School of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohua Wang
- School of Life science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qi Ye
- School of Life science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Daozhi Wei
- School of Life science, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail:
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Gao H, Wang Y, Xu P, Zhang Z. Overexpression of a WRKY Transcription Factor TaWRKY2 Enhances Drought Stress Tolerance in Transgenic Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:997. [PMID: 30131813 PMCID: PMC6090177 DOI: 10.3389/fpls.2018.00997] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/19/2018] [Indexed: 05/18/2023]
Abstract
Drought is a major environmental stress that severely restricts plant growth and crop productivity. A previous study showed that TaWRKY2 from wheat (Triticum aestivum) plays an important role in drought stress tolerance. In the present study, we isolated the promoter of TaWRKY2 and identified multiple regulatory cis-elements in the promoter region. The activity of the TaWRKY2 promoter was induced by drought, salt, heat, and abscisic acid (ABA). We also generated TaWRKY2-overexpressing transgenic wheat, and found that the transgenic seedlings exhibited significantly enhanced tolerance to drought stress, as evidenced by a higher survival rate and lower water loss rate of detached leaves compared with wild type (WT) plants. In addition, the transgenic lines had higher contents of free proline, soluble sugar, and chlorophyll. During a prolonged period of drought stress before the heading stage, the growth of WT plants was inhibited, whereas the TaWRKY2-overexpressing lines progressed to the heading stage. The increased grain yield of the transgenic wheat lines reflected the cumulative effects of longer panicle length, more kernels per spike, and greater aboveground biomass. Our findings show that TaWRKY2 can enhance drought tolerance and increase grain yield in wheat, thus providing a promising candidate target for improving the drought tolerance of wheat cultivars through genetic engineering.
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Affiliation(s)
- Huiming Gao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yafei Wang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Xu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- *Correspondence: Zhengbin Zhang,
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Xin J, Zhang RC, Wang L, Zhang YQ. Researches on Transcriptome Sequencing in the Study of Traditional Chinese Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2017; 2017:7521363. [PMID: 28900463 PMCID: PMC5576426 DOI: 10.1155/2017/7521363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 04/21/2017] [Accepted: 05/16/2017] [Indexed: 12/12/2022]
Abstract
Due to its incomparable advantages, the application of transcriptome sequencing in the study of traditional Chinese medicine attracts more and more attention of researchers, which greatly promote the development of traditional Chinese medicine. In this paper, the applications of transcriptome sequencing in traditional Chinese medicine were summarized by reviewing recent related papers.
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Affiliation(s)
- Jie Xin
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Rong-chao Zhang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Lei Wang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yong-qing Zhang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
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Miao N, Zhang L, Li M, Fan L, Mao K. Development of EST-SSR markers for Taxillus nigrans (Loranthaceae) in southwestern China using next-generation sequencing. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1700010. [PMID: 28924510 PMCID: PMC5584814 DOI: 10.3732/apps.1700010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY We developed transcriptome microsatellite markers (simple sequence repeats) for Taxillus nigrans (Loranthaceae) to survey the genetic diversity and population structure of this species. METHODS AND RESULTS We used Illumina HiSeq data to reconstruct the transcriptome of T. nigrans by de novo assembly and used the transcriptome to develop a set of simple sequence repeat markers. Overall, 40 primer pairs were designed and tested; 19 of them amplified successfully and demonstrated polymorphisms. Two loci that detected null alleles were eliminated, and the remaining 17, which were subjected to further analyses, yielded two to 21 alleles per locus. CONCLUSIONS The markers will serve as a basis for studies to assess the extent and pattern of distribution of genetic variation in T. nigrans, and they may also be useful in conservation genetic, ecological, and evolutionary studies of the genus Taxillus, a group of plant species of importance in Chinese traditional medicine.
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Affiliation(s)
- Ning Miao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Lei Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Maoping Li
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Liqiang Fan
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Kangshan Mao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610064, People’s Republic of China
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Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development. Sci Rep 2017; 7:5401. [PMID: 28710486 PMCID: PMC5511223 DOI: 10.1038/s41598-017-05724-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/02/2017] [Indexed: 12/17/2022] Open
Abstract
Litchi (Litchi chinensis Sonn.) is an important fruit that is widely cultivated in tropical and subtropical areas. In this study, we used RNA-Seq and iTRAQ technologies to compare the transcriptomes and proteomes of pollinated (polLFs) and parthenocarpic (parLFs) litchi fruits during early development (1 day, 2 days, 4 days and 6 days). We identified 4,864 DEGs in polLFs and 3,672 in parLFs, of which 2,835 were shared and 1,051 were specifically identified in parLFs. Compared to po1LFs, 768 DEGs were identified in parLFs. iTRAQ analysis identified 551 DEPs in polLFs and 1,021 in parLFs, of which 305 were shared and 526 were exclusively identified in parLFs. We found 1,127 DEPs in parLFs compared to polLFs at different stages. Further analysis revealed some DEGs/DEPs associated with abscisic acid, auxin, ethylene, gibberellin, heat shock protein (HSP), histone, ribosomal protein, transcription factor and zinc finger protein (ZFP). WGCNA identified a large set of co-expressed genes/proteins in polLFs and parLFs. In addition, a cross-comparison of transcriptomic and proteomic data identified 357 consistent DEGs/DEPs in polLFs and parLFs. This is the first time that protein/gene changes have been studied in polLFs and parLFs, and the findings improve our understanding of litchi parthenocarpy.
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Jiang J, Ma S, Ye N, Jiang M, Cao J, Zhang J. WRKY transcription factors in plant responses to stresses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:86-101. [PMID: 27995748 DOI: 10.1111/jipb.12513] [Citation(s) in RCA: 487] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/16/2016] [Indexed: 05/20/2023]
Abstract
The WRKY gene family is among the largest families of transcription factors (TFs) in higher plants. By regulating the plant hormone signal transduction pathway, these TFs play critical roles in some plant processes in response to biotic and abiotic stress. Various bodies of research have demonstrated the important biological functions of WRKY TFs in plant response to different kinds of biotic and abiotic stresses and working mechanisms. However, very little summarization has been done to review their research progress. Not just important TFs function in plant response to biotic and abiotic stresses, WRKY also participates in carbohydrate synthesis, senescence, development, and secondary metabolites synthesis. WRKY proteins can bind to W-box (TGACC (A/T)) in the promoter of its target genes and activate or repress the expression of downstream genes to regulate their stress response. Moreover, WRKY proteins can interact with other TFs to regulate plant defensive responses. In the present review, we focus on the structural characteristics of WRKY TFs and the research progress on their functions in plant responses to a variety of stresses.
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Affiliation(s)
- Jingjing Jiang
- State Key Laboratory of Agrobiotechnology Shenzhen Base, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Shenghui Ma
- State Key Laboratory of Agrobiotechnology Shenzhen Base, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Nenghui Ye
- State Key Laboratory of Agrobiotechnology Shenzhen Base, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Ming Jiang
- Ecology Key Discipline of Zhejiang Province, College of Life Science, Taizhou University, Jiaojiang 318000, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology Shenzhen Base, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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