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Yang S, Li G, Li H. Molecular characterizations of genes in chloroplast genomes of the genus Arachis L. (Fabaceae) based on the codon usage divergence. PLoS One 2023; 18:e0281843. [PMID: 36917565 PMCID: PMC10013919 DOI: 10.1371/journal.pone.0281843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Studies on the molecular characteristics of chloroplast genome are generally important for clarifying the evolutionary processes of plant species. The base composition, the effective number of codons, the relative synonymous codon usage, the codon bias index, and their correlation coefficients of a total of 41 genes in 21 chloroplast genomes of the genus Arachis were investigated to further perform the correspondence and clustering analyses, revealing significantly higher variations in genomes of wild species than those of the cultivated taxa. The codon usage patterns of all 41 genes in the genus Arachis were AT-rich, suggesting that the natural selection was the main factor affecting the evolutionary history of these genomes. Five genes (i.e., ndhC, petD, atpF, rpl14, and rps11) and five genes (i.e., atpE, psbD, psaB, ycf2, and rps12) showed higher and lower base usage divergences, respectively. This study provided novel insights into our understanding of the molecular evolution of chloroplast genomes in the genus Arachis.
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Affiliation(s)
- Shuwei Yang
- School of Intelligent Science and Information Engineering, Xi’an Peihua University, Xi’An, Shaanxi, China
| | - Gun Li
- Department of Biomedical Engineering, Laboratory for Biodiversity Science, School of Electronic Information Engineering, Xi’An Technological University, Xi’An, Shaanxi, China
- * E-mail: (GL); (HL)
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, Jilin, China
- * E-mail: (GL); (HL)
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Raza A, Sharif Y, Chen K, Wang L, Fu H, Zhuang Y, Chitikineni A, Chen H, Zhang C, Varshney RK, Zhuang W. Genome-Wide Characterization of Ascorbate Peroxidase Gene Family in Peanut ( Arachis hypogea L.) Revealed Their Crucial Role in Growth and Multiple Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:962182. [PMID: 36186077 PMCID: PMC9524023 DOI: 10.3389/fpls.2022.962182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 06/16/2023]
Abstract
Ascorbate peroxidase (APX), an important antioxidant enzyme, plays a significant role in ROS scavenging by catalyzing the decrease of hydrogen peroxide under various environmental stresses. Nevertheless, information about the APX gene family and their evolutionary and functional attributes in peanut (Arachis hypogea L.) was not reported. Therefore, a comprehensive genome-wide study was performed to discover the APX genes in cultivated peanut genome. This study identified 166 AhAPX genes in the peanut genome, classified into 11 main groups. The gene duplication analysis showed that AhAPX genes had experienced segmental duplications and purifying selection pressure. Gene structure and motif investigation indicated that most of the AhAPX genes exhibited a comparatively well-preserved exon-intron pattern and motif configuration contained by the identical group. We discovered five phytohormones-, six abiotic stress-, and five growth and development-related cis-elements in the promoter regions of AhAPX. Fourteen putative ah-miRNAs from 12 families were identified, targeting 33 AhAPX genes. Furthermore, we identified 3,257 transcription factors from 38 families (including AP2, ARF, B3, bHLH, bZIP, ERF, MYB, NAC, WRKY, etc.) in 162 AhAPX genes. Gene ontology and KEGG enrichment analysis confirm the role of AhAPX genes in oxidoreductase activity, catalytic activity, cell junction, cellular response to stimulus and detoxification, biosynthesis of metabolites, and phenylpropanoid metabolism. Based on transcriptome datasets, some genes such as AhAPX4/7/17/77/82/86/130/133 and AhAPX160 showed significantly higher expression in diverse tissues/organs, i.e., flower, leaf, stem, roots, peg, testa, and cotyledon. Likewise, only a few genes, including AhAPX4/17/19/55/59/82/101/102/137 and AhAPX140, were significantly upregulated under abiotic (drought and cold), and phytohormones (ethylene, abscisic acid, paclobutrazol, brassinolide, and salicylic acid) treatments. qRT-PCR-based expression profiling presented the parallel expression trends as generated from transcriptome datasets. Our discoveries gave new visions into the evolution of APX genes and provided a base for further functional examinations of the AhAPX genes in peanut breeding programs.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Kun Chen
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Lihui Wang
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Huiwen Fu
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Annapurna Chitikineni
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
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Dang T, Lavagi-Craddock I, Bodaghi S, Vidalakis G. Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings. Front Microbiol 2021; 12:646273. [PMID: 33995303 PMCID: PMC8121382 DOI: 10.3389/fmicb.2021.646273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
Citrus dwarfing viroid (CDVd) induces stunting on sweet orange trees [Citrus sinensis (L.) Osbeck], propagated on trifoliate orange rootstock [Citrus trifoliata (L.), syn. Poncirus trifoliata (L.) Raf.]. MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play important roles in the regulation of tree gene expression. To identify miRNAs in dwarfed citrus trees, grown in high-density plantings, and their response to CDVd infection, sRNA next-generation sequencing was performed on CDVd-infected and non-infected controls. A total of 1,290 and 628 miRNAs were identified in stem and root tissues, respectively, and among those, 60 were conserved in each of these two tissue types. Three conserved miRNAs (csi-miR479, csi-miR171b, and csi-miR156) were significantly downregulated (adjusted p-value < 0.05) in the stems of CDVd-infected trees compared to the non-infected controls. The three stem downregulated miRNAs are known to be involved in various physiological and developmental processes some of which may be related to the characteristic dwarfed phenotype displayed by CDVd-infected C. sinensis on C. trifoliata rootstock field trees. Only one miRNA (csi-miR535) was significantly downregulated in CDVd-infected roots and it was predicted to target genes controlling a wide range of cellular functions. Reverse transcription quantitative polymerase chain reaction analysis performed on selected miRNA targets validated the negative correlation between the expression levels of these targets and their corresponding miRNAs in CDVd-infected trees. Our results indicate that CDVd-responsive plant miRNAs play a role in regulating important citrus growth and developmental processes that may participate in the cellular changes leading to the observed citrus dwarf phenotype.
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Affiliation(s)
- Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Irene Lavagi-Craddock
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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Chen H, Yang Q, Chen K, Zhao S, Zhang C, Pan R, Cai T, Deng Y, Wang X, Chen Y, Chu W, Xie W, Zhuang W. Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.). BMC Genomics 2019; 20:392. [PMID: 31113378 PMCID: PMC6528327 DOI: 10.1186/s12864-019-5770-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
Background Peanut embryo development is a complex process involving a series of gene regulatory pathways and is easily affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortion in peanut, which provides an opportunity to determine the mechanism underlying this important event. MicroRNA (miRNA)-guided target gene regulation is vital to a wide variety of biological processes. However, whether miRNAs participate in peanut embryo abortion under calcium deficiency has yet to be explored. Results In this study, with the assistance of a recently established platform for genome sequences of wild peanut species, we analyzed small RNAs (sRNAs) in early peanut embryos. A total of 29 known and 132 potential novel miRNAs were discovered in 12 peanut-specific miRNA families. Among the identified miRNAs, 87 were differentially expressed during early embryo development under calcium deficiency and sufficiency conditions, and 117 target genes of the differentially expressed miRNAs were identified. Integrated analysis of miRNAs and transcriptome expression revealed 52 differentially expressed target genes of 20 miRNAs. The expression profiles for some differentially expressed targets by gene chip analysis were consistent with the transcriptome sequencing results. Together, our results demonstrate that seed/embryo development-related genes such as TCP3, AP2, EMB2750, and GRFs; cell division and proliferation-related genes such as HsfB4 and DIVARICATA; plant hormone signaling pathway-related genes such as CYP707A1 and CYP707A3, with which abscisic acid (ABA) is involved; and BR1, with which brassinosteroids (BRs) are involved, were actively modulated by miRNAs during early embryo development. Conclusions Both a number of miRNAs and corresponding target genes likely playing key roles in the regulation of peanut embryo abortion under calcium deficiency were identified. These findings provide for the first time new insights into miRNA-mediated regulatory pathways involved in peanut embryo abortion under calcium deficiency. Electronic supplementary material The online version of this article (10.1186/s12864-019-5770-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hua Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Qiang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Kun Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Shanshan Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Chong Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Ronglong Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan
| | - Tiecheng Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Ye Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Yuting Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Wenting Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Wenping Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Weijian Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. .,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. .,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.
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