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Bayramova E, Petrova D, Marchenkov A, Morozov A, Galachyants Y, Zakharova Y, Bedoshvili Y, Likhoshway Y. Differential Expression of Stress Adaptation Genes in a Diatom Ulnaria acus under Different Culture Conditions. Int J Mol Sci 2024; 25:2314. [PMID: 38396992 PMCID: PMC10888605 DOI: 10.3390/ijms25042314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Diatoms are a group of unicellular eukaryotes that are essential primary producers in aquatic ecosystems. The dynamic nature of their habitat necessitates a quick and specific response to various stresses. However, the molecular mechanisms of their physiological adaptations are still underexplored. In this work, we study the response of the cosmopolitan freshwater diatom Ulnaria acus (Bacillariophyceae, Fragilariophycidae, Licmophorales, Ulnariaceae, Ulnaria) in relation to a range of stress factors, namely silica deficiency, prolonged cultivation, and interaction with an algicidal bacterium. Fluorescent staining and light microscopy were used to determine the physiological state of cells under these stresses. To explore molecular reactions, we studied the genes involved in the stress response-type III metacaspase (MC), metacaspase-like proteases (MCP), death-specific protein (DSP), delta-1-pyrroline-5-carboxylate dehydrogenase (ALDH12), and glutathione synthetase (GSHS). We have described the structure of these genes, analyzed the predicted amino acid sequences, and measured their expression dynamics in vitro using qRT-PCR. We demonstrated that the expression of UaMC1, UaMC3, and UaDSP increased during the first five days of silicon starvation. On the seventh day, it was replaced with the expression of UaMC2, UaGSHS, and UaALDH. After 45 days of culture, cells stopped growing, and the expression of UaMC1, UaMC2, UaGSHS, and UaDSP increased. Exposure to an algicidal bacterial filtrate induced a higher expression of UaMC1 and UaGSHS. Thus, we can conclude that these proteins are involved in diatoms' adaptions to environmental changes. Further, these data show that the molecular adaptation mechanisms in diatoms depend on the nature and exposure duration of a stress factor.
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Affiliation(s)
| | | | | | | | | | | | - Yekaterina Bedoshvili
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia; (E.B.); (D.P.); (A.M.); (A.M.); (Y.G.); (Y.Z.); (Y.L.)
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Machuca-Sepúlveda J, Miranda J, Lefin N, Pedroso A, Beltrán JF, Farias JG. Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring. BIOLOGY 2023; 12:923. [PMID: 37508354 PMCID: PMC10376755 DOI: 10.3390/biology12070923] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/30/2023]
Abstract
Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.
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Affiliation(s)
- Jorge Machuca-Sepúlveda
- Doctoral Program on Natural Resources Sciences, Universidad de La Frontera, Avenida Francisco Salazar, 01145, P.O. Box 54-D, Temuco 4780000, Chile
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Javiera Miranda
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Nicolás Lefin
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Alejandro Pedroso
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Jorge F Beltrán
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Jorge G Farias
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
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Acebal MC, Dalgaard LT, Jørgensen TS, Hansen BW. Embryogenesis of a calanoid copepod analyzed by transcriptomics. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101054. [PMID: 36565589 DOI: 10.1016/j.cbd.2022.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
The calanoid copepod Acartia tonsa (Dana) has attracted interest because of its use as a copepod model organism as well as its potential economic role as live fish larval feed. While the adult genome and transcriptome of A. tonsa has been investigated, no studies have been performed investigating the genome-wide transcriptional changes during the normal subitaneous embryogenesis. Thus, the aim of the current study was to investigate said transcriptional changes throughout A. tonsa embryonic development. RNA extraction and de novo transcriptome assembly for the subitaneous embryogenesis of the copepod was conducted. The assembly includes for the first-time samples describing quiescent development and overall helps establishing a framework for future studies on the molecular biology of our species of interest. Among the findings reported, sequences annotated to well-known developmental genes, were identified. At the same time are described the molecular changes and gene expression levels throughout the entire 42 h the embryonic development lasts. In conclusion, here we present the most complete genome-wide transcriptional map of early copepod embryonic development to date, enabling further use of A. tonsa as a model organism for crustacean development. Keywords: enrichment of pathways; subitaneous embryogenesis, comparative genomics; transcriptome assembly; invertebrate genomics.
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Affiliation(s)
- Miguel Cifuentes Acebal
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Louise Torp Dalgaard
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Tue Sparholt Jørgensen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark; Department of Environmental Science - Environmental Microbiology and Biotechnology, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark; The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at the Technical University of Denmark, Building 220, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark(1)
| | - Benni Winding Hansen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark.
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Delimitation of Some Taxa of Ulnaria and Fragilaria (Bacillariophyceae) Based on Genetic, Morphological Data and Mating Compatibility. DIVERSITY 2023. [DOI: 10.3390/d15020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Fragilaria and Ulnaria are two closely related diatom genera for which the delimitation and circumscription of several species is unclear. We studied strains isolated from Lake Baikal and compared them with the species from freshwater reservoirs in Europe and Asia using phylogenetic and species delimitation methods, microscopy and interclonal crossing experiments. The results of the phylogenetic analyses of the fragments of rbcL and 18S rRNA genes revealed that baikalian F. radians clade was independent from the representatives of the genus from other localities. Among Ulnaria we found the following 18S rRNA phylogenetic tree groups at species level: U. acus, U. ulna and U. danica. Genetic distance between genera varied between 3.9–10.2% substitutions in rbcL gene and 3.2–11.5% in 18S rRNA. The boundary between intraspecies and interspecies polymorphism for studied species of Ulnaria and Fragilaria in these marker genes was around 0.8% substitutions. Morphometric characters of individual strains showed their variability and division into F. radians, U. acus and U. ulna together with U. danica. Strains of U. acus and U. danica from different localities of Europe and Asia were sexually compatible inside the species. Sexual reproduction has never been observed in monoclonal cultures, either between this species or with strains of the Fragilaria.
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Chen XH, Yang MK, Li YY, Xie ZX, Zhang SF, Töpel M, Amin SA, Lin L, Ge F, Wang DZ. Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:102-115. [PMID: 37073328 PMCID: PMC10077189 DOI: 10.1007/s42995-022-00161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 12/17/2022] [Indexed: 05/03/2023]
Abstract
Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic strategy. In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins, accounting for ~ 81% of the predicted protein-coding genes. Proteogenomic analysis identified 1235 novel genes, 975 revised genes, 104 splice variants and 234 single amino acid variants. Furthermore, our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions. These findings substantially improve the genome annotation of T. pseudonana and provide insights into new biological functions of diatoms. This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00161-y.
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Affiliation(s)
- Xiao-Huang Chen
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China
- College of Chemistry, Chemical Engineering and Environment, Minnan Normal University, Zhangzhou, 363000 China
| | - Ming-Kun Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China
| | - Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
- IVL-Swedish Environmental Research Institute, Box 53021, 40014 Gothenburg, Sweden
| | - Shady A. Amin
- New York University Abu Dhabi, Saadiyat Island, 129188 Abu Dhabi, United Arab Emirates
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China
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Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS. Using genome-wide expression compendia to study microorganisms. Comput Struct Biotechnol J 2022; 20:4315-4324. [PMID: 36016717 PMCID: PMC9396250 DOI: 10.1016/j.csbj.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/07/2022] [Accepted: 08/07/2022] [Indexed: 11/30/2022] Open
Abstract
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a tremendous opportunity for gaining a systems level understanding of the transcriptional responses that influence phenotypes. Variety in experimental design is particularly important for studying microbes, where the transcriptional responses integrate many signals and demonstrate plasticity across strains including response to what nutrients are available and what microbes are present. Advances in high-throughput measurement technology have made it feasible to construct compendia for many microbes. In this review we discuss how these compendia are constructed and analyzed to reveal transcriptional patterns.
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Affiliation(s)
- Alexandra J. Lee
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Taylor Reiter
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO, USA
| | - Georgia Doing
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth, Hanover, NH, USA
| | - Casey S. Greene
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO, USA
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Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey. BIOLOGY 2021; 10:biology10090826. [PMID: 34571703 PMCID: PMC8465370 DOI: 10.3390/biology10090826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Alexandrium minutum is one of the causing organisms for the occurrence of harmful algae bloom (HABs) in marine ecosystems. This species produces saxitoxin, one of the deadliest neurotoxins which can cause human mortality. However, molecular information such as genes and proteins catalog on this species is still lacking. Therefore, this study has successfully characterized several new molecular mechanisms regarding A. minutum environmental adaptation and saxitoxin biosynthesis. Ultimately, this study provides a valuable resource for facilitating future dinoflagellates’ molecular response to environmental changes. Abstract The toxin-producing dinoflagellate Alexandrium minutum is responsible for the outbreaks of harmful algae bloom (HABs). It is a widely distributed species and is responsible for producing paralytic shellfish poisoning toxins. However, the information associated with the environmental adaptation pathway and toxin biosynthesis in this species is still lacking. Therefore, this study focuses on the functional characterization of A. minutum unigenes obtained from transcriptome sequencing using the Illumina Hiseq 4000 sequencing platform. A total of 58,802 (47.05%) unigenes were successfully annotated using public databases such as NCBI-Nr, UniprotKB, EggNOG, KEGG, InterPRO and Gene Ontology (GO). This study has successfully identified key features that enable A. minutum to adapt to the marine environment, including several carbon metabolic pathways, assimilation of various sources of nitrogen and phosphorus. A. minutum was found to encode homologues for several proteins involved in saxitoxin biosynthesis, including the first three proteins in the pathway of saxitoxin biosynthesis, namely sxtA, sxtG and sxtB. The comprehensive transcriptome analysis presented in this study represents a valuable resource for understanding the dinoflagellates molecular metabolic model regarding nutrient acquisition and biosynthesis of saxitoxin.
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Cheng H, Bowler C, Xing X, Bulone V, Shao Z, Duan D. Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes. Mar Drugs 2021; 19:392. [PMID: 34356817 PMCID: PMC8307304 DOI: 10.3390/md19070392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022] Open
Abstract
β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.
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Affiliation(s)
- Haomiao Cheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France;
| | - Xiaohui Xing
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691 Stockholm, Sweden; (X.X.); (V.B.)
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
- Adelaide Glycomics, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691 Stockholm, Sweden; (X.X.); (V.B.)
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
- Adelaide Glycomics, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
| | - Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co., Ltd., Qingdao 266400, China
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Bhattacharjya R, Tiwari A, Marella TK, Bansal H, Srivastava S. New paradigm in diatom omics and genetic manipulation. BIORESOURCE TECHNOLOGY 2021; 325:124708. [PMID: 33487514 DOI: 10.1016/j.biortech.2021.124708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are one of the most heterogeneous eukaryotic plankton known for regulating earth's biogeochemical cycles and maintaining the marine ecosystems ever since the late Eocene epoch. The advent of multidisciplinary omics approach has both epitomized and revolutionized the nature of their chimeric genetic toolkit, ecophysiology, and metabolic adaptability as well as their interaction with other communities. In addition, advanced functional annotation of transcriptomic and proteomic data using cutting edge bioinformatics tools together with high-resolution genome-scale mathematical modeling has effectively proven as the catapult in solving genetic bottlenecks in microbial as well as diatom exploration. In this review, a corroborative summation of the robust work done in manipulating, engineering, and sequencing of the diatom genomes besides underpinning the holistic application of omics in transcription and translation has been discussed in order to shrewd their multifarious novel potential in the field of biotechnology and provide an insight into their dynamic evolutionary relevance.
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Affiliation(s)
- Raya Bhattacharjya
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India.
| | - Thomas Kiran Marella
- Algae Biomass Energy System Development Research Center (ABES), Tennodai, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
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Petrova DP, Bedoshvili YD, Zakharova YR, Volokitina NA, Likhoshway YV, Grachev MA. Changes in valve morphology of two pennate diatom species during long-term culture. ACTA BIOLOGICA SIBIRICA 2020. [DOI: 10.3897/abs.6.e57888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The morphology of diatom siliceous is a primary basis for their species identification. This study aims to measure the range of morphological changes induced in the monoclonal cultures of Fragilaria radians strains 280 and A6 and Ulnaria danica strain BK17 by cultivation in the lab for a year or more. The scanning electron microscopy revealed that the number of abnormal valves increases during the first year of culture maintenance. Specific abnormalities observed include curved valves and apices, axial areas and rimoportulae shifted from their normal positions, disordered or otherwise abnormal striae, and various growths on the valves. Similar morphological abnormalities are known to occur in diatoms exposed to microtubule inhibitors. These results show the limits of morphological variance in studied species and could be used to estimate the effect of toxic agents in natural and experimental conditions.
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11
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Shah M, Alharby HF, Hakeem KR, Ali N, Rahman IU, Munawar M, Anwar Y. De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway. Sci Rep 2020; 10:13726. [PMID: 32792567 PMCID: PMC7426850 DOI: 10.1038/s41598-020-70635-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/28/2020] [Indexed: 11/25/2022] Open
Abstract
Lantana camara L. is an economically important essential oil producing plant belonging to family Verbenaceae. It is used in medication for treating various diseases like cancer, ulcers, tumor, asthma and fever. The plant is a useful source of essential bioactive compounds such as steroids, flavonoids and phenylpropanoid glycosides etc. Nonetheless, very little is known about the genomic or transcriptomic resources of L. camara, and this might be the reason of hindering molecular studies leading to identification of improved lines. Here we used Illumina sequencing platform and performed the L. camara leaf (LCL) and root (LCR) de novo transcriptome analyses. A total of 70,155,594 and 84,263,224 clean reads were obtained and de novo assembly generated 72,877 and 513,985 unigenes from leaf (LCL) and root (LCR) respectively. Furthermore, the pathway analysis revealed the presence of 229 and 943 genes involved in the phenylpropanoid biosynthesis in leaf and root tissues respectively. Similarity search was performed against publically available genome databases and best matches were found with Sesamum indicum (67.5%) that were much higher than that of Arabidopsis thaliana (3.9%). To the best of our knowledge, this is the first comprehensive transcriptomic analysis of leaf and root tissues of this non-model plant from family Verbenaceae and may serve as a baseline for further molecular studies.
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Affiliation(s)
- Muzammil Shah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Hesham F Alharby
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Niaz Ali
- Department of Botany, Hazara University, Mansehra, KP, 21300, Pakistan.
| | - Inayat Ur Rahman
- Department of Botany, Hazara University, Mansehra, KP, 21300, Pakistan.
- William L. Brown Center, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA.
| | - Mohd Munawar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Yasir Anwar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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