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Transcriptome response of Antarctic Phaeodactylum tricornutum ICE-H producing dimethylsulphoniopropionate to hypersaline stress. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Identification, Characteristics and Function of Phosphoglucomutase (PGM) in the Agar Biosynthesis and Carbon Flux in the Agarophyte Gracilariopsis lemaneiformis (Rhodophyta). Mar Drugs 2022; 20:md20070442. [PMID: 35877735 PMCID: PMC9319447 DOI: 10.3390/md20070442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
Agar is widely applied across the food, pharmaceutical and biotechnology industries, owing to its various bioactive functions. To better understand the agar biosynthesis in commercial seaweed Gracilariopsis lemaneiformis, the activities of four enzymes participating in the agar biosynthesis were detected, and phosphoglucomutase (PGM) was confirmed as highly correlated with agar accumulation. Three genes of PGM (GlPGM1, GlPGM2 and GlPGM3) were identified from the G. lemaneiformis genome. The subcellular localization analysis validated that GlPGM1 was located in the chloroplast and GlPGM3 was not significantly distributed in the organelles. Both the GlPGM1 and GlPGM3 protein levels showed a remarkable consistency with the agar variations, and GlPGM3 may participate in the carbon flux between (iso)floridoside, floridean starch and agar synthesis. After treatment with the PGM inhibitor, the agar and floridean starch contents and the activities of floridean starch synthase were significantly decreased; products identified in the Calvin cycle, the pentose phosphate pathway, the Embden-Meyerhof-Parnas pathway and the tricarboxylic acid cycle were depressed; however, lipids, phenolic acids and the intermediate metabolites, fructose-1,6-phosphate were upregulated. These findings reveal the essential role of PGM in regulating the carbon flux between agar and other carbohydrates in G. lemaneiformis, providing a guide for the artificial regulation of agar accumulation.
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Nakamura-Gouvea N, Alves-Lima C, Benites LF, Iha C, Maracaja-Coutinho V, Aliaga-Tobar V, Araujo Amaral Carneiro M, Yokoya NS, Marinho-Soriano E, Graminha MAS, Collén J, Oliveira MC, Setubal JC, Colepicolo P. Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales). JOURNAL OF PHYCOLOGY 2022; 58:406-423. [PMID: 35090189 DOI: 10.1111/jpy.13238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Gracilariales is a clade of florideophycean red macroalgae known for being the main source of agar. We present a de novo genome assembly and annotation of Gracilaria domingensis, an agarophyte alga with flattened thallus widely distributed along Central and South American Atlantic intertidal zones. In addition to structural analysis, an organizational comparison was done with other Rhodophyta genomes. The nuclear genome has 78 Mbp, with 11,437 predicted coding genes, 4,075 of which did not have hits in sequence databases. We also predicted 1,567 noncoding RNAs, distributed in 14 classes. The plastid and mitochondrion genome structures were also obtained. Genes related to agar synthesis were identified. Genes for type II galactose sulfurylases could not be found. Genes related to ascorbate synthesis were found. These results suggest an intricate connection of cell wall polysaccharide synthesis and the redox systems through the use of L-galactose in Rhodophyta. The genome of G. domingensis should be valuable to phycological and aquacultural research, as it is the first tropical and Western Atlantic red macroalgal genome to be sequenced.
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Affiliation(s)
- Natalia Nakamura-Gouvea
- Laboratory of Algal Biochemistry and Molecular Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu, Prestes, 748, São Paulo, SP, 05508-000, Brazil
| | - Cicero Alves-Lima
- Laboratory of Algal Biochemistry and Molecular Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu, Prestes, 748, São Paulo, SP, 05508-000, Brazil
| | - Luiz Felipe Benites
- CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Sorbonne Université, Observatoire Océanologique - F-66650, Banyuls-sur-Mer, France
| | - Cintia Iha
- Department of Botany, Institute of Biosciences, University of São Paulo, R Matão 277, São Paulo, SP, 05508-090, Brazil
| | - Vinicius Maracaja-Coutinho
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Universidad de Chile - Independencia, Santiago, 8380492, Chile
| | - Victor Aliaga-Tobar
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Universidad de Chile - Independencia, Santiago, 8380492, Chile
| | - Marcella Araujo Amaral Carneiro
- Department of Oceanography and Limnology, Federal University of Rio Grande do Norte - Via Costeira, Praia de Mãe Luiza, s/n, Natal, RN, 59014-002, Brazil
| | - Nair S Yokoya
- Phycology Research Center, Institute of Botany, Secretary of Infrastructure and Environment of São Paulo State, Brazil - Av. Miguel Estefano, 3687, Água Funda, São Paulo, SP, 04301-012, Brazil
| | - Eliane Marinho-Soriano
- Department of Oceanography and Limnology, Federal University of Rio Grande do Norte - Via Costeira, Praia de Mãe Luiza, s/n, Natal, RN, 59014-002, Brazil
| | - Marcia A S Graminha
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rod. Araraquara-Jaú km 1, Campus Ville, Araraquara, SP, 14800-903, Brazil
| | - Jonas Collén
- Station Biologique de Roscoff, UMR 8227, Integrative Biology of Marine Models - CS 90074, Roscoff cedex, 29688, France
| | - Mariana C Oliveira
- Department of Botany, Institute of Biosciences, University of São Paulo, R Matão 277, São Paulo, SP, 05508-090, Brazil
| | - Joao C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP, 05508-000, Brazil
| | - Pio Colepicolo
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP, 05508-000, Brazil
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Sambhwani K, Kazi MA, Mishra A, Mantri VA. De novo transcriptome analysis of industrially important agarophyte Gracilaria dura (Rhodophyta: Gracilariacae) revealed differential expression of genes in gametophyte and sporophyte life-phases. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice. Int J Mol Sci 2022; 23:ijms23116203. [PMID: 35682882 PMCID: PMC9181796 DOI: 10.3390/ijms23116203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
Sulfur (S) is an essential mineral nutrient required for plant growth and development. Plants usually face temporal and spatial variation in sulfur availability, including the heterogeneous sulfate content in soils. As sessile organisms, plants have evolved sophisticated mechanisms to modify their gene expression and physiological processes in order to optimize S acquisition and usage. Such plasticity relies on a complicated network to locally sense S availability and systemically respond to S status, which remains poorly understood. Here, we took advantage of a split-root system and performed transcriptome-wide gene expression analysis on rice plants in S deficiency followed by sulfate resupply. S deficiency altered the expressions of 6749 and 1589 genes in roots and shoots, respectively, accounting for 18.07% and 4.28% of total transcripts detected. Homogeneous sulfate resupply in both split-root halves recovered the expression of 27.06% of S-deficiency-responsive genes in shoots, while 20.76% of S-deficiency-responsive genes were recovered by heterogeneous sulfate resupply with only one split-root half being resupplied with sulfate. The local sulfate resupply response genes with expressions only recovered in the split-root half resupplied with sulfate but not in the other half remained in S deficiency were identified in roots, which were mainly enriched in cellular amino acid metabolic process and root growth and development. Several systemic response genes were also identified in roots, whose expressions remained unchanged in the split-root half resupplied with sulfate but were recovered in the other split-root half without sulfate resupply. The systemic response genes were mainly related to calcium signaling and auxin and ABA signaling. In addition, a large number of S-deficiency-responsive genes exhibited simultaneous local and systemic responses to sulfate resupply, such as the sulfate transporter gene OsSULTR1;1 and the O-acetylserine (thiol) lyase gene, highlighting the existence of a systemic regulation of sulfate uptake and assimilation in S deficiency plants followed by sulfate resupply. Our studies provided a comprehensive transcriptome-wide picture of a local and systemic response to heterogeneous sulfate resupply, which will facilitate an understanding of the systemic regulation of S homeostasis in rice.
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Paul S, Reyes-Pérez P, Angulo-Bejarano PI, Srivastava A, Ramalingam S, Sharma A. Characterization of microRNAs from neem ( Azadirachta indica) and their tissue-specific expression study in leaves and stem. 3 Biotech 2021; 11:277. [PMID: 34040926 DOI: 10.1007/s13205-021-02839-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/08/2021] [Indexed: 01/29/2023] Open
Abstract
Neem (Azadirachta indica) is a very popular traditional medicinal plant used since ancient times to treat numerous ailments. MicroRNAs (miRNAs) are highly conserved, non-coding, short RNA molecules that play important regulatory roles in plant development and metabolism. In this study, deploying a high stringent genome-wide computational-based approach and following a set of strict filtering norms a total of 44 potential conserved neem miRNAs belonging to 21 families and their corresponding 48 potential target transcripts were identified. Important targets include Squamosa promoter binding protein-like proteins, NAC, Scarecrow proteins, Auxin response factor, and F-box proteins. A biological network has also been developed to understand the miRNA-mediated gene regulation using the minimum free energy (MFE) values of the miRNA-target interaction. Moreover, six selected miRNAs were reported to be involved in secondary metabolism in other plant species (miR156a, miR156l, miR160, miR164, miR171, miR395) were validated by qPCR and their tissue-specific differential expression pattern was observed in leaves and stem. Except for ain-miR395, all the other miRNAs were found overexpressed in the stem as compared to leaves. To the best of our knowledge, this is the first report of neem miRNAs and we believe the finding of the present study will be useful for the functional genomic study of medicinal plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02839-z.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Paula Reyes-Pérez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Paola Isabel Angulo-Bejarano
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
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Ye J, Zhang Y, Cui H, Liu J, Wu Y, Cheng Y, Xu H, Huang X, Li S, Zhou A, Zhang X, Bolund L, Chen Q, Wang J, Yang H, Fang L, Shi C. WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. Nucleic Acids Res 2019; 46:W71-W75. [PMID: 29788377 PMCID: PMC6030983 DOI: 10.1093/nar/gky400] [Citation(s) in RCA: 331] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/10/2018] [Indexed: 12/20/2022] Open
Abstract
WEGO (Web Gene Ontology Annotation Plot), created in 2006, is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. Owing largely to the rapid development of high-throughput sequencing and the increasing acceptance of GO, WEGO has benefitted from outstanding performance regarding the number of users and citations in recent years, which motivated us to update to version 2.0. WEGO uses the GO annotation results as input. Based on GO's standardized DAG (Directed Acyclic Graph) structured vocabulary system, the number of genes corresponding to each GO ID is calculated and shown in a graphical format. WEGO 2.0 updates have targeted four aspects, aiming to provide a more efficient and up-to-date approach for comparative genomic analyses. First, the number of input files, previously limited to three, is now unlimited, allowing WEGO to analyze multiple datasets. Also added in this version are the reference datasets of nine model species that can be adopted as baselines in genomic comparative analyses. Furthermore, in the analyzing processes each Chi-square test is carried out for multiple datasets instead of every two samples. At last, WEGO 2.0 provides an additional output graph along with the traditional WEGO histogram, displaying the sorted P-values of GO terms and indicating their significant differences. At the same time, WEGO 2.0 features an entirely new user interface. WEGO is available for free at http://wego.genomics.org.cn.
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Affiliation(s)
- Jia Ye
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Huihai Cui
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jiawei Liu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Yuqing Wu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,University of Auckland, Auckland, 1010, New Zealand
| | - Yun Cheng
- Zhejiang Hospital, Hangzhou, Zhejiang, 310013, China
| | - Huixing Xu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Shengting Li
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - An Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, Shandong, 266555, China.,Institute of Biomedicine, Aarhus University, Aarhus, DK-8000, Denmark
| | - Qiang Chen
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350014, China.,Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian, 350000, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | | | - Lin Fang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Chunmei Shi
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350014, China.,Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian, 350000, China
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Unraveling the nuclear and chloroplast genomes of an agar producing red macroalga, Gracilaria changii (Rhodophyta, Gracilariales). Genomics 2018; 110:124-133. [DOI: 10.1016/j.ygeno.2017.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/23/2022]
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9
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Reducing the number of artifactual repeats in de novo assembly of RNA-Seq data by optimizing the assembly pipeline. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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