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Zhao X, Yang G, Liu X, Yu Z, Peng S. Integrated Analysis of Seed microRNA and mRNA Transcriptome Reveals Important Functional Genes and microRNA-Targets in the Process of Walnut ( Juglans regia) Seed Oil Accumulation. Int J Mol Sci 2020; 21:ijms21239093. [PMID: 33260456 PMCID: PMC7731449 DOI: 10.3390/ijms21239093] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/17/2020] [Accepted: 11/27/2020] [Indexed: 11/30/2022] Open
Abstract
Walnut (Juglans regia) is known as a promising woody oil crop with abundant polyunsaturated fatty acids in its kernel. However, the regulation mechanism of walnut oil accumulation and fatty acid metabolism is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. To reveal the molecular mechanism of walnut oil accumulation, considering the potential regulation of microRNA (miRNA) in seed development, in this study, the oil content of walnut kernel on the 80th, 100th and 120th day after flowering (DAF) was tested and the corresponding proportions are 11.51%, 40.40% and 53.20%. Between DAF of 80th~120th, the content of stearic acid and oleic acid tended to increase, but the proportion of other fatty acids tended to decrease. Meanwhile, comparative transcriptome and sRNA-seq analysis on three stages (80th, 100th and 120th DAF), found 204 conserved miRNAs and 554 novel miRNAs in walnut kernels, among which 104 key genes related to walnut oil accumulation were screened. The phospholipid:diacylglycerol acyltransferase metabolic pathway may contribute more to oil accumulation in walnut. 16 miRNA-mRNA regulatory modules related to walnut oil accumulation and fatty acid synthesis were constructed. 8 known miRNAs and 9 novel miRNAs regulate 28 genes involved in fatty acid (FA) metabolism and lipid synthesis. Among them, jre-miRn105, jre-miRn434, jre-miR477d and jre-miR156a.2 are key miRNAs that regulate walnut FA synthesis. Jre-miRn411 and jre-miR399a.1 are closely related to oil accumulation. These data provide new insights and lay the foundation for subsequent studies on walnut FA synthesis and oil accumulation.
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Affiliation(s)
- Xinchi Zhao
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China; (X.Z.); (G.Y.); (Z.Y.)
| | - Guiyan Yang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China; (X.Z.); (G.Y.); (Z.Y.)
| | - Xiaoqiang Liu
- Department of Foreign Languages, Northwest A & F University, Yangling 712100, Shaanxi, China;
| | - Zhongdong Yu
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China; (X.Z.); (G.Y.); (Z.Y.)
| | - Shaobing Peng
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China; (X.Z.); (G.Y.); (Z.Y.)
- Correspondence: ; Tel.: +86-135-7293-1369
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Yuan H, Chen J, Yang Y, Shen C, Xu D, Wang J, Yan D, He Y, Zheng B. Quantitative succinyl-proteome profiling of Chinese hickory (Carya cathayensis) during the grafting process. BMC PLANT BIOLOGY 2019; 19:467. [PMID: 31684873 PMCID: PMC6829946 DOI: 10.1186/s12870-019-2072-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/14/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Chinese hickory (Carya cathayensis) is a popular nut plant having high economic value. Grafting is applied to accelerate the transition from vegetative phase to reproductive phase. Lysine succinylation occurs frequently in the proteins associated with metabolic pathways, which may participate in the regulation of the grafting process. However, the exact regulatory mechanism underlying grafting process in Chinese hickory has not been studied at post-translational modification level. RESULTS A comprehensive proteome-wide lysine succinylation profiling of Chinese hickory was explored by a newly developed method combining affinity enrichment and high-resolution LC-MS/MS. In total, 259 succinylation sites in 202 proteins were identified, representing the first comprehensive lysine succinylome in Chinese hickory. The succinylation was biased to occur in the cytosolic proteins of Chinese hickory. Moreover, four conserved succinylation motifs were identified in the succinylated peptides. Comparison of two grafting stages of Chinese hickory revealed that the differential expressed succinylated proteins were mainly involved in sugar metabolism, carbon fixation, amino acid metabolism and plant-pathogen interaction. Besides, seven heat shock proteins (HSPs) with 11 succinylation sites were also identified, all of which were observed to be up-regulated during the grafting process. CONCLUSIONS Succinylation of the proteins involved in amino acid biosynthesis might be required for a successful grafting. Succinylated HSPs might play a role in stress tolerance of the grafted Chinese hickory plants. Our results can be a good resource for functional validation of the succinylated proteins and a starting point for the investigation of molecular mechanisms during lysine succinylation occurring at grafting site.
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Affiliation(s)
- Huwei Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Juanjuan Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Ying Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Chenjia Shen
- College of Life and Environmental Sciences Hangzhou Normal University, Hangzhou, 310036 People’s Republic of China
| | - Dongbin Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Junfeng Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Daoliang Yan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Yi He
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
- Center for Cultivation of Subtropical Forest Resources (CCSFR, Zhejiang A&F University, Hangzhou, 311300 People’s Republic of China
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Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress. Int J Mol Sci 2019; 20:ijms20061474. [PMID: 30909604 PMCID: PMC6470939 DOI: 10.3390/ijms20061474] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 11/17/2022] Open
Abstract
Cadmium (Cd) has the potential to be chronically toxic to humans through contaminated crop products. MicroRNAs (miRNAs) can move systemically in plants. To investigate the roles of long-distance moving xylem miRNAs in regulating maize response to Cd stress, three xylem sap small RNA (sRNA) libraries were constructed for high-throughput sequencing to identify potential mobile miRNAs in Cd-stressed maize seedlings and their putative targets in maize transcriptomes. In total, about 199 miRNAs (20–22 nucleotides) were identified in xylem sap from maize seedlings, including 97 newly discovered miRNAs and 102 known miRNAs. Among them, 10 miRNAs showed differential expression in xylem sap after 1 h of Cd treatment. Two miRNAs target prediction tools, psRNAtarget (reporting the inhibition pattern of cleavage) and DPMIND (discovering Plant MiRNA-Target Interaction with degradome evidence), were used in combination to identify, via bioinformatics, the targets of 199 significantly expressed miRNAs in maize xylem sap. The integrative results of these two bioinformatic tools suggested that 27 xylem sap miRNAs inhibit 34 genes through cleavage with degradome evidence. Moreover, nearly 300 other genes were also the potential miRNAs cleavable targets without available degradome data support, and the majority of them were enriched in abiotic stress response, cell signaling, transcription regulation, as well as metal handling. These approaches and results not only enhanced our understanding of the Cd-responsive long-distance transported miRNAs from the view of xylem sap, but also provided novel insights for predicting the molecular genetic mechanisms mediated by miRNAs.
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Identification of miRNAs Associated with Graft Union Development in Pecan [Carya illinoinensis (Wangenh.) K. Koch]. FORESTS 2018. [DOI: 10.3390/f9080472] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pecan [Carya illinoinensis (Wangenh.) K. Koch] is a high-value fruit tree with a long juvenile period. The fruiting process of pecan seedlings can be largely accelerated through grafting. As non-coding small RNAs, plant miRNAs participate in various biological processes through negative regulation of gene expression. To reveal the roles of miRNAs in the graft union development of pecan, four small RNA libraries were constructed from the graft union at days 0, 8, 15, and 30 after grafting. A total of 47 conserved miRNAs belonging to 31 families and 39 novel miRNAs were identified. For identified miRNAs, 584 target genes were bioinformatically predicted, and 266 of them were annotated; 29 miRNAs (including 16 conserved and 13 novel miRNAs) were differentially expressed during the graft process. The expression profiles of 12 miRNA were further validated by quantitative reverse transcription PCR (qRT-PCR). In addition, qRT-PCR revealed that the expression levels of 3 target genes were negatively correlated with their corresponding miRNAs. We found that miRS26 might be involved in callus formation; miR156, miR160, miR164, miR166, and miRS10 might be associated with vascular bundle formation. These results indicate that the miRNA-mediated gene regulations play important roles in the graft union development of pecan.
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Sun ZC, Zhang LS, Wang ZJ. Genome-wide analysis of miRNAs in Carya cathayensis. BMC PLANT BIOLOGY 2017; 17:228. [PMID: 29187147 PMCID: PMC5708078 DOI: 10.1186/s12870-017-1180-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/20/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND MicroRNA (miRNA) plays an important role in plant development regulation. Hickory is an economically important plant in which the amount of flowering determines its production. RESULTS Here, 51 conserved miRNAs, which belong to 16 families and 195 novel miRNAs were identified in hickory genome. For each conserved miRNA family, we used sequences from hickory and other plants to construct a phylogenetic tree, which shows that each family has members in hickory. Some of the conserved miRNA families (i.e., miR167 and miR397) have more members in hickory than in other plants because of gene expansion. MiR166 exhibited tandem duplication with three copies being observed. Many members of these conserved miRNA families were detected in hickory flowers, and the expression patterns of target genes were opposite to those of the related miRNAs, indicating that miRNAs may have important functions in floral regulation of hickory. CONCLUSIONS Taken together, a comprehensive analysis was conducted to identify miRNAs produced in hickory flower organs, demonstrating functional conservation and diversity of miRNA families among hickory, Arabidopsis, grape, and poplar.
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Affiliation(s)
- Zhi-Chao Sun
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Liang-Sheng Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China.
- Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zheng-Jia Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China.
- School of Forestry and Biotechnology, Zhejiang A and F University, Dong Hu Campus, 88 Northern Circle Road, Linan, 311300, China.
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Abstract
Non-coding RNAs such as microRNAs (miRNAs) are very tiny ribonucleotides having an essential role in gene regulation at both post-transcriptional and translational levels. They are very conserved and expressed in worms, flies, plants, and mammals in a sequence-specific manner. Furthermore, it is now possible to clone miRNAs using the new genome editing tool CRISPR/cas9, which shows benefit in control of untargeted effect. In this special issue, we tried to cover researches associated with functional roles of miRNAs accross model and complex organisms.
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Affiliation(s)
- Hikmet Budak
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
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Xu D, Yuan H, Tong Y, Zhao L, Qiu L, Guo W, Shen C, Liu H, Yan D, Zheng B. Comparative Proteomic Analysis of the Graft Unions in Hickory ( Carya cathayensis) Provides Insights into Response Mechanisms to Grafting Process. FRONTIERS IN PLANT SCIENCE 2017; 8:676. [PMID: 28496455 PMCID: PMC5406401 DOI: 10.3389/fpls.2017.00676] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 04/12/2017] [Indexed: 05/18/2023]
Abstract
Hickory (Carya cathayensis), a tree with high nutritional and economic value, is widely cultivated in China. Grafting greatly reduces the juvenile phase length and makes the large scale cultivation of hickory possible. To reveal the response mechanisms of this species to grafting, we employed a proteomics-based approach to identify differentially expressed proteins in the graft unions during the grafting process. Our study identified 3723 proteins, of which 2518 were quantified. A total of 710 differentially expressed proteins (DEPs) were quantified and these were involved in various molecular functional and biological processes. Among these DEPs, 341 were up-regulated and 369 were down-regulated at 7 days after grafting compared with the control. Four auxin-related proteins were down-regulated, which was in agreement with the transcription levels of their encoding genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the 'Flavonoid biosynthesis' pathway and 'starch and sucrose metabolism' were both significantly up-regulated. Interestingly, five flavonoid biosynthesis-related proteins, a flavanone 3-hyfroxylase, a cinnamate 4-hydroxylase, a dihydroflavonol-4-reductase, a chalcone synthase, and a chalcone isomerase, were significantly up-regulated. Further experiments verified a significant increase in the total flavonoid contents in scions, which suggests that graft union formation may activate flavonoid biosynthesis to increase the content of a series of downstream secondary metabolites. This comprehensive analysis provides fundamental information on the candidate proteins and secondary metabolism pathways involved in the grafting process for hickory.
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Affiliation(s)
- Dongbin Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityLinan, China
- Center for Cultivation of Subtropical Forest Resources, Zhejiang A&F UniversityLinan, China
| | - Huwei Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityLinan, China
- Center for Cultivation of Subtropical Forest Resources, Zhejiang A&F UniversityLinan, China
| | - Yafei Tong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityLinan, China
- Center for Cultivation of Subtropical Forest Resources, Zhejiang A&F UniversityLinan, China
| | - Liang Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityLinan, China
- Center for Cultivation of Subtropical Forest Resources, Zhejiang A&F UniversityLinan, China
| | - Lingling Qiu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityLinan, China
- Center for Cultivation of Subtropical Forest Resources, Zhejiang A&F UniversityLinan, China
| | - Wenbin Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityLinan, China
- Center for Cultivation of Subtropical Forest Resources, Zhejiang A&F UniversityLinan, China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Hongjia Liu
- Crop and Nuclear Technology Institute, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Daoliang Yan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityLinan, China
- Center for Cultivation of Subtropical Forest Resources, Zhejiang A&F UniversityLinan, China
- *Correspondence: Bingsong Zheng, Daoliang Yan,
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityLinan, China
- Center for Cultivation of Subtropical Forest Resources, Zhejiang A&F UniversityLinan, China
- *Correspondence: Bingsong Zheng, Daoliang Yan,
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