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Wei X, Cao J, Lan H. Genome-Wide Characterization and Analysis of the bHLH Transcription Factor Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cell C4 Anatomy. Front Genet 2022; 13:927830. [PMID: 35873472 PMCID: PMC9301494 DOI: 10.3389/fgene.2022.927830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Basic helix-loop-helix (bHLH) transcription factors play important roles in plant growth, development, metabolism, hormone signaling pathways, and responses to abiotic stresses. However, comprehensive genomic and functional analyses of bHLH genes have not yet been reported in desert euhalophytes. Suaeda aralocaspica, an annual C4 halophyte without Kranz anatomy, presents high photosynthetic efficiency in harsh natural habitats and is an ideal plant for identifying transcription factors involved in stress resistance. In this study, 83 bHLH genes in S. aralocaspica were identified and categorized into 21 subfamilies based on conserved motifs, gene structures, and phylogenetic analysis. Functional annotation enrichment revealed that the majority of SabHLHs were enriched in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways involved in the response to stress conditions, as transcription factors. A number of cis-acting elements related to plant hormones and stress responses were also predicted in the promoter regions of SabHLHs, which were confirmed by expression analysis under various abiotic stress conditions (NaCl, mannitol, low temperature, ABA, GA3, MeJA, and SA); most were involved in tolerance to drought and salinity. SabHLH169 (076) protein localized in the nucleus was involved in transcriptional activity, and gene expression could be affected by different light qualities. This study is the first comprehensive analysis of the bHLH gene family in S. aralocaspica. These data will facilitate further characterization of their molecular functions in the adaptation of desert plants to abiotic stress.
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Optimum Sterilization Method for In Vitro Cultivation of Dimorphic Seeds of the Succulent Halophyte Suaeda aralocaspica. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Suaeda aralocaspica is an annual halophyte in the Amaranthaceae in the saline deserts of central Asia. This plant has succulent leaves and grape-like fruits and is a potential horticultural plant. To obtain the efficient sterilization method and optimal culture conditions, two types of seeds produced from a single plant of S. aralocaspica were treated with 75% ethanol for different time durations first, and then sodium hypochlorite (NaClO) or mercury chloride (HgCl2), with five different timing treatments were used for second seed surface sterilization. Sterilized seeds were germinated on a Murashige and Skoog (MS) medium at different potential hydrogenation (pH) levels, to examine germination and seedling performance. The results showed that the highest germination percentage of brown seeds was 100% and that of black seeds was 17%. Thus, brown seeds were more suitable for further culture experiments than black seeds. For brown seeds, the sterilization effect of NaClO was better than that of HgCl2, based on the results of seed germination, contamination, and seedling survival. Rinsing with 75% ethanol for 60 s, sterilizing with NaClO for 8 min, and cultivating at pH 8.0 MS for 7 days was the best of all sterilization procedures and cultivation methods tested, which has been successfully applied to S. aralocaspica in vitro culture. The optimized protocol described here can be used as the reference for the Suaeda genus.
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Wang C, Tian M, Zhang Y. Characterization of microRNAs involved in asymbiotic germination of Bletilla striata (Orchidaceae) seeds. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:163-173. [PMID: 34358730 DOI: 10.1016/j.plaphy.2021.07.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Orchids are distributed worldwide, and some species have considerable economic value. Orchid seeds are minute in size, simple in structure, and deficient in nutrient reserves. Asymbiotic seed germination is an important propagation strategy for orchids. MicroRNAs (miRNAs) play an essential role in seed germination. However, few studies have examined miRNAs involved in seed germination in orchids. Here, we conducted comparative small RNA sequencing at five stages to characterize the miRNAs involved in asymbiotic seed germination in Bletilla striata. A total of 253 known and 125 novel miRNAs were identified. Of them, 71 known and 29 novel miRNAs showed distinct expression among the five stages. Quantitative PCR revealed negative correlations of expression between differentially expressed miRNAs (DE miRNAs) and their targets. Function annotation and enrichment analyses of the targets of DE miRNAs between adjacent stages indicate that miRNA-target regulations are involved in many important processes during germination, such as signaling, biosynthesis, and transport of plant hormones. Twenty-two miRNAs were inferred to participate in plant hormone-related processes. The contents of abscisic acid, gibberellin A3, indole-3-acetic acid, jasmonic acid, trans zeatin riboside, and N6-(Δ2-isopentenyl) adenine varied significantly among the five stages. Nine tested plant hormone-related miRNAs and their targets exhibited significant correlations with at least one plant hormone. 5'-RLM-RACE validated that a transcript encoding auxin response factor was cleaved by Bst-miR160e as predicted. For the first time, we characterized miRNAs associated with the asymbiotic seed germination of an orchid species, which will help understand the miRNA-mediated regulatory mechanism of seed germination in orchids.
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Affiliation(s)
- Caixia Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
| | - Min Tian
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Ying Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
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Cao J, Cheng G, Wang L, Maimaitijiang T, Lan H. Genome-Wide Identification and Analysis of the Phosphoenolpyruvate Carboxylase Gene Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cellular C 4 Anatomy. FRONTIERS IN PLANT SCIENCE 2021; 12:665279. [PMID: 34527003 PMCID: PMC8435749 DOI: 10.3389/fpls.2021.665279] [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: 03/04/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays pivotal roles in the carbon fixation of photosynthesis and a variety of metabolic and stress pathways. Suaeda aralocaspica belongs to a single-cellular C4 species and carries out a photosynthetic pathway in an unusually elongated chlorenchyma cell, which is expected to have PEPCs with different characteristics. To identify the different isoforms of PEPC genes in S. aralocaspica and comparatively analyze their expression and regulation patterns as well as the biochemical and enzymatic properties in this study, we characterized a bacterial-type PEPC (BTPC; SaPEPC-4) in addition to the two plant-type PEPCs (PTPCs; SaPEPC-1 and SaPEPC-2) using a genome-wide identification. SaPEPC-4 presented a lower expression level in all test combinations with an unknown function; two SaPTPCs showed distinct subcellular localizations and different spatiotemporal expression patterns but positively responded to abiotic stresses. Compared to SaPEPC-2, the expression of SaPEPC-1 specifically in chlorenchyma cell tissues was much more active with the progression of development and under various stresses, particularly sensitive to light, implying the involvement of SaPEPC-1 in a C4 photosynthetic pathway. In contrast, SaPEPC-2 was more like a non-photosynthetic PEPC. The expression trends of two SaPTPCs in response to light, development, and abiotic stresses were also matched with the changes in PEPC activity in vivo (native) or in vitro (recombinant), and the biochemical properties of the two recombinant SaPTPCs were similar in response to various effectors while the catalytic efficiency, substrate affinity, and enzyme activity of SaPEPC-2 were higher than that of SaPEPC-1 in vitro. All the different properties between these two SaPTPCs might be involved in transcriptional (e.g., specific cis-elements), posttranscriptional [e.g., 5'-untranslated region (5'-UTR) secondary structure], or translational (e.g., PEPC phosphorylation/dephosphorylation) regulatory events. The comparative studies on the different isoforms of the PEPC gene family in S. aralocaspica may help to decipher their exact role in C4 photosynthesis, plant growth/development, and stress resistance.
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Huang X, Tian T, Chen J, Wang D, Tong B, Liu J. Transcriptome analysis of Cinnamomum migao seed germination in medicinal plants of Southwest China. BMC PLANT BIOLOGY 2021; 21:270. [PMID: 34116632 PMCID: PMC8194011 DOI: 10.1186/s12870-021-03020-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cinnamomum migao is an endangered evergreen woody plant species endemic to China. Its fruit is used as a traditional medicine by the Miao nationality of China and has a high commercial value. However, its seed germination rate is extremely low under natural and artificial conditions. As the foundation of plant propagation, seed germination involves a series of physiological, cellular, and molecular changes; however, the molecular events and systematic changes occurring during C. migao seed germination remain unclear. RESULTS In this study, combined with the changes in physiological indexes and transcription levels, we revealed the regulation characteristics of cell structures, storage substances, and antioxidant capacity during seed germination. Electron microscopy analysis revealed that abundant smooth and full oil bodies were present in the cotyledons of the seeds. With seed germination, oil bodies and other substances gradually degraded to supply energy; this was consistent with the content of storage substances. In parallel to electron microscopy and physiological analyses, transcriptome analysis showed that 80-90 % of differentially expressed genes (DEGs) appeared after seed imbibition, reflecting important development and physiological changes. The unigenes involved in material metabolism (glycerolipid metabolism, fatty acid degradation, and starch and sucrose metabolism) and energy supply pathways (pentose phosphate pathway, glycolysis pathway, pyruvate metabolism, tricarboxylic acid cycle, and oxidative phosphorylation) were differentially expressed in the four germination stages. Among these DEGs, a small number of genes in the energy supply pathway at the initial stage of germination maintained high level of expression to maintain seed vigor and germination ability. Genes involved in lipid metabolism were firstly activated at a large scale in the LK (seed coat fissure) stage, and then genes involved in carbohydrates (CHO) metabolism were activated, which had their own species specificity. CONCLUSIONS Our study revealed the transcriptional levels of genes and the sequence of their corresponding metabolic pathways during seed germination. The changes in cell structure and physiological indexes also confirmed these events. Our findings provide a foundation for determining the molecular mechanisms underlying seed germination.
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Affiliation(s)
- Xiaolong Huang
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China
| | - Tian Tian
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, 550025, Guiyang, China
| | - Jingzhong Chen
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China
| | - Deng Wang
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China
| | - Bingli Tong
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China
| | - Jiming Liu
- Department of Ecology, College of Forestry, Guizhou University, 550025, Guiyang, China.
- Forest Ecology Research Center of Guizhou University, 550025, Guiyang, China.
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Wang H, Narsing Rao MP, Gao Y, Li X, Gao R, Xie Y, Li Q, Li W. Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca. BMC Microbiol 2021; 21:143. [PMID: 33980153 PMCID: PMC8114534 DOI: 10.1186/s12866-021-02206-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/19/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In this study, we used 16S rRNA high-throughput gene sequencing method to compare the community composition and bacterial diversity between brown and black seeds of Suaeda glauca. RESULTS A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e., pectinase, cellulolytic and xylanolytic activities). CONCLUSION The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different biological function roles. The endophytic bacterial communities of the dimorphic seeds may be influenced mainly by the seed coat structureand partly by the seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.
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Affiliation(s)
- Hongfei Wang
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanli Gao
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Xinyang Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Rui Gao
- Dandong Forestry and Grassland Development Service Center, Dandong, 118000, China
| | - Yuanguo Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiuli Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China.
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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Cao J, Chen L, Wang J, Xing J, Lv X, Maimaitijiang T, Lan H. Effects of genetic and environmental factors on variations of seed heteromorphism in Suaeda aralocaspica. AOB PLANTS 2020; 12:plaa044. [PMID: 33072248 PMCID: PMC7546916 DOI: 10.1093/aobpla/plaa044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/21/2020] [Indexed: 05/12/2023]
Abstract
Seed heteromorphism is an adaptive strategy towards adversity in many halophytes. However, the underlying mechanisms and ecological significance of seed heteromorphism have not been deeply explored. Using Suaeda aralocaspica, a typical C4 annual halophyte without Kranz anatomy, we studied seed morphology, differentiation of morphs and fruit-setting patterns, and correlated these traits with germination responses, seed characteristics and heteromorphic seed ratio. To elucidate the genetic basis of seed heteromorphism, we analysed correlated patterns of gene expression for seed development-related genes as well. We observed that S. aralocaspica produced three types of seed morph: brown, large black and small black with differences in colour, size, mass and germination behaviour; the latter two were further distinguished by their origin in female or bisexual flowers, respectively. Further analysis revealed that seed heteromorphism was associated with genetic aspects including seed positioning, seed coat differentiation and seed developmental gene expression, while variations in seed heteromorphism may be associated with environmental conditions, e.g. annual precipitation, temperature, daylight and their monthly distribution in different calendar years. Seed heteromorphism and its variations in S. aralocaspica show multilevel regulation of the bet-hedging strategy that influences phenotypic plasticity, which is a consequence of internal genetic and external environmental factor interaction. Our findings contribute to the understanding of seed heteromorphism as a potential adaptive trait of desert plant species.
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Affiliation(s)
- Jing Cao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Ling Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Juan Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Jiajia Xing
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xiuyun Lv
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Tayier Maimaitijiang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Haiyan Lan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Corresponding author’s e-mail address:
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Zhou C, Ge N, Guo J, Zhu L, Ma Z, Cheng S, Wang J. Enterobacter asburiae Reduces Cadmium Toxicity in Maize Plants by Repressing Iron Uptake-Associated Pathways. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10126-10136. [PMID: 31433635 DOI: 10.1021/acs.jafc.9b03293] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Soil microbes have recently been utilized to improve cadmium (Cd) tolerance and lower its accumulation in plants. Nevertheless, whether rhizobacteria can prevent Cd uptake by graminaceous plants and the underlying mechanisms remain elusive. In this study, inoculation with Enterobacter asburiae NC16 reduced transpiration rates and the expression of some iron (Fe) uptake-related genes including ZmFer, ZmYS1, ZmZIP, and ZmNAS2 in maize (Zea mays) plants, which contributed to mitigation of Cd toxicity. However, the inoculation with NC16 failed to suppress the transpiration rates and transcription of these Fe uptake-related genes in plants treated with fluridone, an abscisic acid (ABA) biosynthetic inhibitor, indicating that the impacts of NC16-inoculation observed were dependent on the actions of ABA. We found that NC16 increased the host ABA levels by mediating the metabolism of ABA rather than its synthesis. Moreover, the capacity of NC16 to inhibit plant uptake of Cd was greatly weakened in plants overexpressing ZmZIP, encoding a zinc/iron transporter. Collectively, our findings indicated that E. asburiae NC16 reduced Cd toxicity in maize plants at least partially by hampering the Fe uptake-associated pathways.
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Affiliation(s)
- Cheng Zhou
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers , Nanjing Agricultural University , Nanjing 210095 , China
| | - Ninggao Ge
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
| | - Jiansheng Guo
- School of Medicine , Zhejiang University , Hangzhou 310058 , China
| | - Lin Zhu
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
| | - Zhongyou Ma
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
| | - Shiyong Cheng
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
| | - Jianfei Wang
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
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Wang L, Ma G, Wang H, Cheng C, Mu S, Quan W, Jiang L, Zhao Z, Zhang Y, Zhang K, Wang X, Tian C, Zhang Y. A draft genome assembly of halophyte Suaeda aralocaspica, a plant that performs C4 photosynthesis within individual cells. Gigascience 2019; 8:giz116. [PMID: 31513708 PMCID: PMC6741815 DOI: 10.1093/gigascience/giz116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/11/2019] [Accepted: 08/27/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The halophyte Suaeda aralocaspica performs complete C4 photosynthesis within individual cells (SCC4), which is distinct from typical C4 plants, which require the collaboration of 2 types of photosynthetic cells. However, despite SCC4 plants having features that are valuable in engineering higher photosynthetic efficiencies in agriculturally important C3 species such as rice, there are no reported sequenced SCC4 plant genomes, limiting our understanding of the mechanisms involved in, and evolution of, SCC4 photosynthesis. FINDINGS Using Illumina and Pacific Biosciences sequencing platforms, we generated ∼202 Gb of clean genomic DNA sequences having a 433-fold coverage based on the 467 Mb estimated genome size of S. aralocaspica. The final genome assembly was 452 Mb, consisting of 4,033 scaffolds, with a scaffold N50 length of 1.83 Mb. We annotated 29,604 protein-coding genes using Evidence Modeler based on the gene information from ab initio predictions, homology levels with known genes, and RNA sequencing-based transcriptome evidence. We also annotated noncoding genes, including 1,651 long noncoding RNAs, 21 microRNAs, 382 transfer RNAs, 88 small nuclear RNAs, and 325 ribosomal RNAs. A complete (circular with no gaps) chloroplast genome of S. aralocaspica 146,654 bp in length was also assembled. CONCLUSIONS We have presented the genome sequence of the SCC4 plant S. aralocaspica. Knowledge of the genome of S. aralocaspica should increase our understanding of the evolution of SCC4 photosynthesis and contribute to the engineering of C4 photosynthesis into economically important C3 crops.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi 830011, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Ganglong Ma
- Center for Genome Analysis, ABLife Inc., 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China
| | - Hongling Wang
- Central Lab, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi 830011, China
| | - Chao Cheng
- Center for Genome Analysis, ABLife Inc., 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China
| | - Shuyong Mu
- Central Lab, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi 830011, China
| | - Weili Quan
- Center for Genome Analysis, ABLife Inc., 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China
| | - Li Jiang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi 830011, China
| | - Zhenyong Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi 830011, China
| | - Yu Zhang
- Center for Genome Analysis, ABLife Inc., 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China
| | - Ke Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi 830011, China
| | - Xuelian Wang
- Center for Genome Analysis, ABLife Inc., 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi 830011, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China
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Zhou C, Zhu L, Guo J, Xiao X, Ma Z, Wang J. Bacillus subtilis STU6 Ameliorates Iron Deficiency in Tomato by Enhancement of Polyamine-Mediated Iron Remobilization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:320-330. [PMID: 30540908 DOI: 10.1021/acs.jafc.8b05851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Iron (Fe) deficiency often triggers arginine overproduction in plants. However, it remains elusive whether Fe deficiency-induced increases of arginine levels are involved in beneficial rhizobacteria recruitment and that the mechanism underlying rhizobacteria induced plant Fe deficiency tolerance. Here, Bacillus subtilis STU6 increased soluble Fe content in tomato, thereby alleviating Fe deficiency-induced chlorosis. In a split-root system, STU6 significantly induced arginine exudation by Fe-deficient roots, and increased arginine levels promoted spermidine (Spd) production by STU6 and bacterial colonization. Deletion of the STU6 speB gene inhibited Spd synthesis and abrogated STU6-induced increments of soluble Fe content in the Fe-deficient plants. Increased host Spd levels by STU6 greatly stimulated the NO accumulation in the Fe-deficient roots. Furthermore, disruption of NO signaling markedly repressed STU6-mediated cell wall Fe remobilization. Collectively, our data provide important evidence that chemical dialogues between tomato and STU6 contribute to enhancement of microbe-mediated plant adaptation to Fe deficiency.
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Affiliation(s)
- Cheng Zhou
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization , Nanjing Agricultural University , Nanjing 210095 , China
| | - Lin Zhu
- School of Life Science and Technology , Tongji University , Shanghai 200092 , China
| | - Jiansheng Guo
- School of Medicine , Zhejiang University , Hangzhou 310058 , China
| | - Xin Xiao
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
| | - Zhongyou Ma
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
| | - Jianfei Wang
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture , Anhui Science and Technology University , Bengbu 233100 , China
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