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Wang L, Mo Z, Yu X, Mao Y. Characterization of the basic leucine zipper transcription factor family of Neoporphyra haitanensis and its role in acclimation to dehydration stress. BMC PLANT BIOLOGY 2023; 23:617. [PMID: 38049766 PMCID: PMC10696790 DOI: 10.1186/s12870-023-04636-7] [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: 05/29/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Neoporphyra haitanensis, a major marine crop native to southern China, grows in the harsh intertidal habitats of rocky coasts. The thallus can tolerate fluctuating and extreme environmental stresses, for example, repeated desiccation/rehydration due to the turning tides. It is also a typical model system for investigating stress tolerance mechanisms in intertidal seaweed. The basic leucine zipper (bZIP) transcription factors play important roles in the regulation of plants' responses to environmental stress stimuli. However, little information is available regarding the bZIP family in the marine crop Nh. haitanensis. RESULTS We identified 19 bZIP genes in the Nh. haitanensis genome and described their conserved domains. Based on phylogenetic analysis, these 19 NhhbZIP genes, distributed unevenly on the 11 superscaffolds, were divided into four groups. In each group, there were analogous exon/intron numbers and motif compositions, along with diverse exon lengths. Cross-species collinearity analysis indicated that 17 and 9 NhhbZIP genes were orthologous to bZIP genes in Neopyropia yezoensis and Porphyra umbilicalis, respectively. Evidence from RNA sequencing (RNA-seq) data showed that the majority of NhhbZIP genes (73.68%) exhibited transcript abundance in all treatments. Furthermore, genes NN 2, 4 and 5 showed significantly altered expression in response to moderate dehydration, severe dehydration, and rehydration, respectively. Gene co-expression network analysis of the representative genes was carried out, followed by gene set enrichment analysis. Two NhhbZIP genes collectively responding to dehydration and rehydration and their co-expressing genes mainly participated in DNA repair, DNA metabolic process, and regulation of helicase activity. Two specific NhhbZIP genes responding to severe dehydration and their corresponding network genes were mainly involved in macromolecule modification, cellular catabolic process, and transmembrane transport. Three specific NhhbZIP genes responding to rehydration and their co-expression gene networks were mainly involved in the regulation of the cell cycle process and defense response. CONCLUSIONS This study provides new insights into the structural composition, evolution, and function of the NhhbZIP gene family. Our results will help us to further study the functions of bZIP genes in response to dehydration and rehydration in Nh. haitanensis and improve Nh. haitanensis in southern China.
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Affiliation(s)
- Li Wang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Biotechnology and Bioresources Utilization (Ministry of Education), Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
| | - Zhaolan Mo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Xinzi Yu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Yazhou Bay Innovation Institute & Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Ministry of Education), College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, China.
- Laboratory of Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266700, China.
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Wu Y, Chaumier T, Manirakiza E, Veluchamy A, Tirichine L. PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum. Sci Rep 2023; 13:8320. [PMID: 37221245 DOI: 10.1038/s41598-023-35403-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/17/2023] [Indexed: 05/25/2023] Open
Abstract
Recent advances in DNA sequencing technologies particularly long-read sequencing, greatly improved genomes assembly. However, this has created discrepancies between published annotations and epigenome tracks, which have not been updated to keep pace with the new assemblies. Here, we used the latest improved telomere-to-telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genes annotation and newly published transposable elements to map the epigenome landscape, namely DNA methylation and post-translational modifications of histones. This provides the community with PhaeoEpiView, a browser that allows the visualization of epigenome data and transcripts on an updated and contiguous reference genome, to better understand the biological significance of the mapped data. We updated previously published histone marks with a more accurate peak calling using mono instead of poly(clonal) antibodies and deeper sequencing. PhaeoEpiView ( https://PhaeoEpiView.univ-nantes.fr ) will be continuously updated with the newly published epigenomic data, making it the largest and richest epigenome browser of any stramenopile. In the upcoming era of molecular environmental studies, where epigenetics plays a significant role, we anticipate that PhaeoEpiView will become a widely used tool.
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Affiliation(s)
- Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, 44000, Nantes, France
| | | | - Eric Manirakiza
- Nantes Université, CNRS, US2B, UMR 6286, 44000, Nantes, France
| | | | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, 44000, Nantes, France.
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An B, Cai H, Li B, Zhang S, He Y, Wang R, Jiao C, Guo Y, Xu L, Xu Y. Molecular Evolution of Histone Methylation Modification Families in the Plant Kingdom and Their Genome-Wide Analysis in Barley. Int J Mol Sci 2023; 24:ijms24098043. [PMID: 37175750 PMCID: PMC10178440 DOI: 10.3390/ijms24098043] [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: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
In this study, based on the OneKP database and through comparative genetic analysis, we found that HMT and HDM may originate from Chromista and are highly conserved in green plants, and that during the evolution from algae to land plants, histone methylation modifications gradually became complex and diverse, which is more conducive to the adaptation of plants to complex and variable environments. We also characterized the number of members, genetic similarity, and phylogeny of HMT and HDM families in barley using the barley pangenome and the Tibetan Lasa Goumang genome. The results showed that HMT and HDM were highly conserved in the domestication of barley, but there were some differences in the Lasa Goumang SDG subfamily. Expression analysis showed that HvHMTs and HvHDMs were highly expressed in specific tissues and had complex expression patterns under multiple stress treatments. In summary, the amplification and variation of HMT and HDM facilitate plant adaptation to complex terrestrial environments, while they are highly conserved in barley and play an important role in barley growth and development with abiotic stresses. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant HvHMTs and HvHDMs, and lay a foundation for further investigation of their functions in barley.
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Affiliation(s)
- Bingzhuang An
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Haiya Cai
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Bo Li
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yonggang He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Rong Wang
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Le Xu
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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Li Y. Algal epigenetics: insights from DNA methylation in a symbiotic dinoflagellate. JOURNAL OF PHYCOLOGY 2023; 59:289-291. [PMID: 36468447 DOI: 10.1111/jpy.13090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science and University of Maryland, 701 E. Pratt St., Baltimore, Maryland, 21202, USA
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Ferrari M, Muto A, Bruno L, Cozza R. DNA Methylation in Algae and Its Impact on Abiotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:241. [PMID: 36678953 PMCID: PMC9861306 DOI: 10.3390/plants12020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.
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Takeue N, Kuroyama A, Hayashi Y, Tanaka K, Imamura S. Autofluorescence-based high-throughput isolation of nonbleaching Cyanidioschyzon merolae strains under nitrogen-depletion. FRONTIERS IN PLANT SCIENCE 2022; 13:1036839. [PMID: 36589047 PMCID: PMC9794624 DOI: 10.3389/fpls.2022.1036839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Photosynthetic organisms maintain optimum levels of photosynthetic pigments in response to environmental changes to adapt to the conditions. The identification of cyanobacteria strains that alleviate bleaching has revealed genes that regulate levels of phycobilisome, the main light-harvesting complex. In contrast, the mechanisms of pigment degradation in algae remain unclear, as no nonbleaching strains have previously been isolated. To address this issue, this study attempted to isolate nonbleaching strains of the unicellular red alga Cyanidioschyzon merolae after exposure to nitrogen (N)-depletion based on autofluorescence information. After four weeks under N-depletion, 13 cells from 500,000 cells with almost identical pre- and post-depletion chlorophyll a (Chl a) and/or phycocyanin autofluorescence intensities were identified. These nonbleaching candidate strains were sorted via a cell sorter, isolated on solid medium, and their post-N-depletion Chl a and phycocyanin levels were analyzed. Chl a levels of these nonbleaching candidate strains were lower at 1-4 weeks of N-depletion similar to the control strains, however, their phycocyanin levels were unchanged. Thus, we successfully isolated nonbleaching C. merolae strains in which phycocyanin was not degraded under N-depletion, via autofluorescence spectroscopy and cell sorting. This versatile method will help to elucidate the mechanisms regulating pigments in microalgae.
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Affiliation(s)
- Nozomi Takeue
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Ayaka Kuroyama
- Product and Business Planning Section, Planning and Marketing Department, Life Science Business Division, Medical Business Group, Sony Corporation, Nishi-ku, Yokohama, Japan
| | - Yoshiharu Hayashi
- Product and Business Planning Section, Planning and Marketing Department, Life Science Business Division, Medical Business Group, Sony Corporation, Nishi-ku, Yokohama, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi, Tokyo, Japan
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Reddy K, Renuka N, Kumari S, Bux F. Algae-mediated processes for the treatment of antiretroviral drugs in wastewater: Prospects and challenges. CHEMOSPHERE 2021; 280:130674. [PMID: 34162077 DOI: 10.1016/j.chemosphere.2021.130674] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 06/13/2023]
Abstract
The prevalence of pharmaceuticals (PCs), especially antiretroviral (ARV) drugs in various aquatic ecosystems has been expansively reported, wherein wastewater treatment plants (WWTPs) are identified as the primary point source. Consequently, the occurrence, ecotoxicity and treatment of ARV drugs in WWTPs have drawn much attention in recent years. Numerous studies have shown that the widely employed activated sludge-based WWTPs are incapable of removing ARV drugs efficiently from wastewater. Recently, algae-based wastewater treatment processes have shown promising results in PCs removal from wastewater, either completely or partially, through different processes such as biosorption, bioaccumulation, and intra-/inter-cellular degradation. Algal species have also shown to tolerate high concentrations of ARV drugs than the reported concentrations in the environmental matrices. In this review, emphasis has been given on discussing the current status of the occurrence of ARV drugs in the aquatic environment and WWTPs. Besides, the current trends and future perspectives of PCs removal by algae are critically reviewed and discussed. The potential pathways and mechanisms of ARV drugs removal by algae have also been discussed.
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Affiliation(s)
- Karen Reddy
- Institute for Water and Wastewater Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Nirmal Renuka
- Institute for Water and Wastewater Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa.
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