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Xiang R, Ahmad B, Liang C, Shi X, Yang L, Du G, Wang L. Systematic genome-wide and expression analysis of RNA-directed DNA methylation pathway genes in grapes predicts their involvement in multiple biological processes. FRONTIERS IN PLANT SCIENCE 2022; 13:1089392. [PMID: 36570893 PMCID: PMC9780290 DOI: 10.3389/fpls.2022.1089392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in plants and mediates transcriptional silencing by siRNAs. Different gene families have role in the regulation of the RdDM pathway and there is a lack of information about these gene families in the grapes (Vitis vinifera L.). Here, we mentioned the genome-wide identification, bioinformatics analysis, evolutionary history, and expression profiling of VvRdDM pathway genes against various stresses, hormonal treatments as well as in different organs. Sixty VvRdDM genes belonging to fourteen different families were identified. All the genes were unevenly distributed and chromosome 4 contained the highest number of genes (7). Most of the genes showed similar exon-intron and motif distribution patterns within the same subfamilies. Out of 14 families, only members of 4 families underwent duplication events during the evolutionary process and 50% of members of the AGO family are the result of duplication events. Based on Ka/Ks ratio all duplicated gene pairs have a negative mode of selection. VvRdDM pathway genes showed differential spatiotemporal expression patterns against different hormone and stress treatments. Further, with multiple transcriptome analysis, some VvRdDM genes showed a broad spectrum of high expression in different organs at various stages, and VvRdDM genes also displayed different expression in seeded and seedless cultivars during different phases of seed development. This proposed that VvRdDM genes may play multiple roles in grape growth and development, especially in seed development. qRT-PCR analysis of selected genes further verified the critical roles of RdDM genes in multiple biological processes, especially in seed development/ovule abortion i.e., VvIDN2a, VvDRD1a, VvRDR1a, and VvRDR6. Our study provides detailed information about VvRdDM genes in perspective of gene structure and evolution, as well as expression pattern against different stress, hormones and in different plants parts. It provides new candidate gene resources for further functional characterization and molecular breeding of grapes.
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Affiliation(s)
- Rui Xiang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Bilal Ahmad
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Department of Horticulture, Muhammad Nawaz Sharif (MNS)-University of Agriculture Multan, Multan, Pakistan
| | - Chen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaoxin Shi
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Lili Yang
- Shijiazhuang Fruit Research Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Guoqiang Du
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Li Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
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Epigenetic regulation of fetal brain development in pig. Gene 2022; 844:146823. [PMID: 35988784 DOI: 10.1016/j.gene.2022.146823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/27/2022] [Accepted: 08/15/2022] [Indexed: 02/01/2023]
Abstract
How fetal brain development is regulated at the molecular level is not well understood. Due to ethical challenges associated with research on the human fetus, large animals particularly pigs are increasingly used to study development and disorders of fetal brain. The pig fetal brain grows rapidly during the last ∼ 50 days before birth which is around day 60 (d60) of pig gestation. But what regulates the onset of accelerated growth of the brain is unknown. The current study tests the hypothesis that epigenetic alteration around d60 is involved in the onset of rapid growth of fetal brain of pig. To test this hypothesis, DNA methylation changes of fetal brain was assessed in a genome-wide manner by Enzymatic Methyl-seq (EM-seq) during two gestational periods (GP): d45 vs. d60 (GP1) and d60 vs. d90 (GP2). The cytosine-guanine (CpG) methylation data was analyzed in an integrative manner with the RNA-seq data generated from the same brain samples from our earlier study. A neural network based modeling approach was implemented to learn changes in methylation patterns of the differentially expressed genes, and then predict methylations of the brain in a genome-wide manner during rapid growth. This approach identified specific methylations that changed in a mutually informative manner during rapid growth of the fetal brain. These methylations were significantly overrepresented in specific genic as well as intergenic features including CpG islands, introns, and untranslated regions. In addition, sex-bias methylations of known single nucleotide polymorphic sites were also identified in the fetal brain ide during rapid growth.
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Liu R, Vasupalli N, Hou D, Stalin A, Wei H, Zhang H, Lin X. Genome-wide identification and evolution of WNK kinases in Bambusoideae and transcriptional profiling during abiotic stress in Phyllostachys edulis. PeerJ 2022; 10:e12718. [PMID: 35070502 PMCID: PMC8761366 DOI: 10.7717/peerj.12718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 01/11/2023] Open
Abstract
With-no-lysine (WNK) kinases play vital roles in abiotic stress response, circadian rhythms, and regulation of flowering time in rice, Arabidopsis, and Glycine max. However, there are no previous reports of WNKs in the Bambusoideae, although genome sequences are available for diploid, tetraploid, and hexaploid bamboo species. In the present study, we identified 41 WNK genes in five bamboo species and analysed gene evolution, phylogenetic relationship, physical and chemical properties, cis-elements, and conserved motifs. We predicted the structure of PeWNK proteins of moso bamboo and determined the exposed, buried, structural and functional amino acids. Real-time qPCR analysis revealed that PeWNK5, PeWNK7, PeWNK8, and PeWNK11 genes are involved in circadian rhythms. Analysis of gene expression of different organs at different developmental stages revealed that PeWNK genes are tissue-specific. Analysis of various abiotic stress transcriptome data (drought, salt, SA, and ABA) revealed significant gene expression levels in all PeWNKs except PeWNK11. In particular, PeWNK8 and PeWNK9 were significantly down- and up-regulated, respectively, after abiotic stress treatment. A co-expression network of PeWNK genes also showed that PeWNK2, PeWNK4, PeWNK7, and PeWNK8 were co-expressed with transcriptional regulators related to abiotic stress. In conclusion, our study identified the PeWNKs of moso bamboo involved in circadian rhythms and abiotic stress response. In addition, this study serves as a guide for future functional genomic studies of the WNK genes of the Bambusoideae.
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Affiliation(s)
- RongXiu Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang, China
| | - Naresh Vasupalli
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang, China
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang, China
| | - Antony Stalin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang, China,State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A & F University, Lin’an, Zhejiang, China
| | - Hantian Wei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang, China
| | - Huicong Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang, China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang, China
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Fu L, Su W, Chen F, Zhao S, Zhang H, Karimi-Maleh H, Yu A, Yu J, Lin CT. Early sex determination of Ginkgo biloba based on the differences in the electrocatalytic performance of extracted peroxidase. Bioelectrochemistry 2021; 140:107829. [PMID: 33964612 DOI: 10.1016/j.bioelechem.2021.107829] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022]
Abstract
Ginkgo biloba is a dioecious plant. Male ginkgoes are mainly used in landscaping, while females are mainly used for fruit production. However, sex identification of ginkgo is a difficult task, especially at the seedling stage. In this work, we present for the first time the use of electrochemical techniques for the identification of ginkgo sex based on the differences in peroxides within male and female ginkgos. Graphene was used to concentrate peroxides in ginkgo extract, thereby improving electrochemical signal sensitivity. The electrochemical reduction of hydrogen peroxide catalyzed by peroxidase was used as a prob for sex determination in ginkgo. This electrochemical identification technique can be used not only for the analysis of adult ginkgo, but also successfully for the analysis of tissue culture seedlings and live seedlings. This electrochemical sensor has excellent discrimination ability due to the difference in peroxidase content in the leaves and petiole of ginkgo of different sexes. This electrochemical sensor allows for a rapid identification of the sex of ginkgo and has a very strong potential for field analysis.
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Affiliation(s)
- Li Fu
- Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, PR China.
| | - Weitao Su
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, PR China
| | - Fei Chen
- Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, PR China
| | - Shichao Zhao
- Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, PR China
| | - Huaiwei Zhang
- Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, PR China
| | - Hassan Karimi-Maleh
- School of Resources and Environment, University of Electronic Science and Technology of China, Xiyuan Ave, P. O. Box 611731, Chengdu, PR China
| | - Aimin Yu
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Jinhong Yu
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, PR China
| | - Cheng-Te Lin
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, PR China
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