1
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Panahi B. Global transcriptome analysis identifies critical functional modules associated with multiple abiotic stress responses in microalgae Chromochloris zofingiensis. PLoS One 2024; 19:e0307248. [PMID: 39172989 PMCID: PMC11341014 DOI: 10.1371/journal.pone.0307248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/27/2024] [Indexed: 08/24/2024] Open
Abstract
In the current study, systems biology approach was applied to get a deep insight regarding the regulatory mechanisms of Chromochloris zofingiensis under overall stress conditions. Meta-analysis was performed using p-values combination of differentially expressed genes. To identify the informative models related to stress conditions, two distinct weighted gene co-expression networks were constructed and preservation analyses were performed using medianRankand Zsummary algorithms. Moreover, functional enrichment analysis of non-preserved modules was performed to shed light on the biological performance of underlying genes in the non-preserved modules. In the next step, the gene regulatory networks between top hub genes of non-preserved modules and transcription factors were inferred using ensemble of trees algorithm. Results showed that the power of beta = 7 was the best soft-thresholding value to ensure a scale-free network, leading to the determination of 12 co-expression modules with an average size of 128 genes. Preservation analysis showed that the connectivity pattern of the six modules including the blue, black, yellow, pink, greenyellow, and turquoise changed during stress condition which defined as non-preserved modules. Examples of enriched pathways in non-preserved modules were Oxidative phosphorylation", "Vitamin B6 metabolism", and "Arachidonic acid metabolism". Constructed regulatory network between identified TFs and top hub genes of non-preserved module such as Cz06g10250, Cz03g12130 showed that some specific TFs such as C3H and SQUAMOSA promoter binding protein (SBP) specifically regulates the specific hubs. The current findings add substantially to our understanding of the stress responsive underlying mechanism of C. zofingiensis for future studies and metabolite production programs.
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Affiliation(s)
- Bahman Panahi
- Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
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2
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Genot B, Grogan M, Yost M, Iacono G, Archer SD, Burns JA. Functional stress responses in Glaucophyta: Evidence of ethylene and abscisic acid functions in Cyanophora paradoxa. J Eukaryot Microbiol 2024:e13041. [PMID: 38952030 DOI: 10.1111/jeu.13041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]
Abstract
Glaucophytes, an enigmatic group of freshwater algae, occupy a pivotal position within the Archaeplastida, providing insights into the early evolutionary history of plastids and their host cells. These algae possess unique plastids, known as cyanelles that retain certain ancestral features, enabling a better understanding of the plastid transition from cyanobacteria. In this study, we investigated the role of ethylene, a potent hormone used by land plants to coordinate stress responses, in the glaucophyte alga Cyanophora paradoxa. We demonstrate that C. paradoxa produces gaseous ethylene when supplied with exogenous 1-aminocyclopropane-1-carboxylic acid (ACC), the ethylene precursor in land plants. In addition, we show that cells produce ethylene natively in response to abiotic stress, and that another plant hormone, abscisic acid (ABA), interferes with ethylene synthesis from exogenously supplied ACC, while positively regulating reactive oxygen species (ROS) accumulation. ROS synthesis also occurred following abiotic stress and ACC treatment, possibly acting as a second messenger in stress responses. A physiological response of C. paradoxa to ACC treatment is growth inhibition. Using transcriptomics, we reveal that ACC treatment induces the upregulation of senescence-associated proteases, consistent with the observation of growth inhibition. This is the first report of hormone usage in a glaucophyte alga, extending our understanding of hormone-mediated stress response coordination into the Glaucophyta, with implications for the evolution of signaling modalities across Archaeplastida.
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Affiliation(s)
- Baptiste Genot
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | | | | | - Gabriella Iacono
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Stephen D Archer
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - John A Burns
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
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3
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Bonthala VS, Stich B. StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes. PLANT CELL REPORTS 2024; 43:117. [PMID: 38622429 PMCID: PMC11018665 DOI: 10.1007/s00299-024-03201-2] [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: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.
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Affiliation(s)
- Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Düsseldorf, Germany
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4
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Jiang W, He J, Babla M, Wu T, Tong T, Riaz A, Zeng F, Qin Y, Chen G, Deng F, Chen ZH. Molecular evolution and interaction of 14-3-3 proteins with H+-ATPases in plant abiotic stresses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:689-707. [PMID: 37864845 DOI: 10.1093/jxb/erad414] [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: 05/18/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
Environmental stresses severely affect plant growth and crop productivity. Regulated by 14-3-3 proteins (14-3-3s), H+-ATPases (AHAs) are important proton pumps that can induce diverse secondary transport via channels and co-transporters for the abiotic stress response of plants. Many studies demonstrated the roles of 14-3-3s and AHAs in coordinating the processes of plant growth, phytohormone signaling, and stress responses. However, the molecular evolution of 14-3-3s and AHAs has not been summarized in parallel with evolutionary insights across multiple plant species. Here, we comprehensively review the roles of 14-3-3s and AHAs in cell signaling to enhance plant responses to diverse environmental stresses. We analyzed the molecular evolution of key proteins and functional domains that are associated with 14-3-3s and AHAs in plant growth and hormone signaling. The results revealed evolution, duplication, contraction, and expansion of 14-3-3s and AHAs in green plants. We also discussed the stress-specific expression of those 14-3-3and AHA genes in a eudicotyledon (Arabidopsis thaliana), a monocotyledon (Hordeum vulgare), and a moss (Physcomitrium patens) under abiotic stresses. We propose that 14-3-3s and AHAs respond to abiotic stresses through many important targets and signaling components of phytohormones, which could be promising to improve plant tolerance to single or multiple environmental stresses.
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Affiliation(s)
- Wei Jiang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Jing He
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Mohammad Babla
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Ting Wu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Tao Tong
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Adeel Riaz
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Fanrong Zeng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yuan Qin
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Fenglin Deng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
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5
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Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat Commun 2023; 14:986. [PMID: 36813788 PMCID: PMC9946954 DOI: 10.1038/s41467-023-36517-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression between Arabidopsis and Marchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic multiplication to respond to multiple stresses. Lastly, two online resources ( https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi ) are provided to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.
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Affiliation(s)
- Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Zhong Chen
- Amoeba Education Hub, 1 West Coast Road, 128020, Singapore, Singapore
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Marius Arend
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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6
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Julca I, Tan QW, Mutwil M. Toward kingdom-wide analyses of gene expression. TRENDS IN PLANT SCIENCE 2023; 28:235-249. [PMID: 36344371 DOI: 10.1016/j.tplants.2022.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Gene expression data for Archaeplastida are accumulating exponentially, with more than 300 000 RNA-sequencing (RNA-seq) experiments available for hundreds of species. The gene expression data stem from thousands of experiments that capture gene expression in various organs, tissues, cell types, (a)biotic perturbations, and genotypes. Advances in software tools make it possible to process all these data in a matter of weeks on modern office computers, giving us the possibility to study gene expression in a kingdom-wide manner for the first time. We discuss how the expression data can be accessed and processed and outline analyses that take advantage of cross-species analyses, allowing us to generate powerful and robust hypotheses about gene function and evolution.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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7
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Lim PK, Zheng X, Goh JC, Mutwil M. Exploiting plant transcriptomic databases: Resources, tools, and approaches. PLANT COMMUNICATIONS 2022; 3:100323. [PMID: 35605200 PMCID: PMC9284291 DOI: 10.1016/j.xplc.2022.100323] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 05/11/2023]
Abstract
There are now more than 300 000 RNA sequencing samples available, stemming from thousands of experiments capturing gene expression in organs, tissues, developmental stages, and experimental treatments for hundreds of plant species. The expression data have great value, as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data. Because gene expression provides essential clues to where and when a gene is active, the data provide powerful tools for predicting gene function, and comparative analyses allow us to study plant evolution from a new perspective. This review describes how we can gain new knowledge from gene expression profiles, expression specificities, co-expression networks, differential gene expression, and experiment correlation. We also introduce and demonstrate databases that provide user-friendly access to these tools.
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Affiliation(s)
- Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xinghai Zheng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jong Ching Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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8
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Russell S, Jackson C, Reyes-Prieto A. High Sequence Divergence but Limited Architectural Rearrangements in Organelle Genomes of Cyanophora (Glaucophyta) Species. J Eukaryot Microbiol 2020; 68:e12831. [PMID: 33142007 DOI: 10.1111/jeu.12831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/16/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
Abstract
Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3-fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups.
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Affiliation(s)
- Sarah Russell
- Department of Biology, University of New Brunswick, 10 Bailey Drive, Fredericton, NB, E3B 5A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher Jackson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Royal Botanic Gardens Victoria, Melbourne, Vic., Australia
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, 10 Bailey Drive, Fredericton, NB, E3B 5A3, Canada
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