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Whole-genome characterization and comparative genomics of a novel freshwater cyanobacteria species: Pseudanabaena punensis. Mol Phylogenet Evol 2021; 164:107272. [PMID: 34332035 DOI: 10.1016/j.ympev.2021.107272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/23/2022]
Abstract
Cyanobacteria are emerging as a potential source of novel, beneficial bioactive compounds. However, some cyanobacteria species can harm water quality and public health through the production of toxins. Therefore, surveying the occurrence and generating genomic resources of cyanobacteria producing harmful compounds could help develop the control methods necessary to manage their growth and limit the release contaminants into the water bodies. Here, we describe a novel strain, Pseudanabaena punensis isolated from the open ends of pipelines supplying freshwater. This isolate was characterized morphologically, biochemically and by whole-genome sequence analysis. We also provide genomic information for P. punensis to help understand and highlight the features unique to this isolate. Morphological and genetic (analysis using 16S rRNA and rbcL genes) data were used to assign this novel strain to phylogenetic and taxonomic groups. The isolate was identified as a filamentous and non-heterocystous cyanobacteria. Based on morphological and 16S rRNA phylogeny, this isolate shares characteristics with the Pseudanabaenaceae family, but remains distinct from well-characterized species suggesting its polyphyletic assemblage. The whole-genome sequence analysis suggests greater genomic and phenotypic plasticity. Genome-wide sequence and comparative genomic analyses, comparing against several closely related species, revealed diverse and important genes associated with synthesizing bioactive compounds, multi-drug resistance pathway, heavy metal resistance, and virulence factors. This isolate also produces several important fatty acids with potential industrial applications. The observations described in this study emphasize both industrial applications and risks associated with the freshwater contamination, and therefore genomic resources provided in this study offer an opportunity for further investigations.
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Chowdhury S, Ghosh S. Next Generation Sequencing and Stem Cells. Stem Cells 2021. [DOI: 10.1007/978-981-16-1638-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Neeragunda Shivaraj Y, Barbara P, Gugi B, Vicré-Gibouin M, Driouich A, Ramasandra Govind S, Devaraja A, Kambalagere Y. Perspectives on Structural, Physiological, Cellular, and Molecular Responses to Desiccation in Resurrection Plants. SCIENTIFICA 2018; 2018:9464592. [PMID: 30046509 PMCID: PMC6036803 DOI: 10.1155/2018/9464592] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/07/2018] [Accepted: 04/26/2018] [Indexed: 05/21/2023]
Abstract
Resurrection plants possess a unique ability to counteract desiccation stress. Desiccation tolerance (DT) is a very complex multigenic and multifactorial process comprising a combination of physiological, morphological, cellular, genomic, transcriptomic, proteomic, and metabolic processes. Modification in the sugar composition of the hemicellulosic fraction of the cell wall is detected during dehydration. An important change is a decrease of glucose in the hemicellulosic fraction during dehydration that can reflect a modification of the xyloglucan structure. The expansins might also be involved in cell wall flexibility during drying and disrupt hydrogen bonds between polymers during rehydration of the cell wall. Cleavages by xyloglucan-modifying enzymes release the tightly bound xyloglucan-cellulose network, thus increasing cell wall flexibility required for cell wall folding upon desiccation. Changes in hydroxyproline-rich glycoproteins (HRGPs) such as arabinogalactan proteins (AGPs) are also observed during desiccation and rehydration processes. It has also been observed that significant alterations in the process of photosynthesis and photosystem (PS) II activity along with changes in the antioxidant enzyme system also increased the cell wall and membrane fluidity resulting in DT. Similarly, recent data show a major role of ABA, LEA proteins, and small regulatory RNA in regulating DT responses. Current progress in "-omic" technologies has enabled quantitative monitoring of the plethora of biological molecules in a high throughput routine, making it possible to compare their levels between desiccation-sensitive and DT species. In this review, we present a comprehensive overview of structural, physiological, cellular, molecular, and global responses involved in desiccation tolerance.
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Affiliation(s)
- Yathisha Neeragunda Shivaraj
- Centre for Bioinformation, Department of Studies and Research in Environmental Science, Tumkur University, Tumakuru 57210, India
| | - Plancot Barbara
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, Normandie Univ, UniRouen, 76000 Rouen, France
- Fédération de Recherche “Normandie-Végétal”-FED 4277, 76000 Rouen, France
| | - Bruno Gugi
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, Normandie Univ, UniRouen, 76000 Rouen, France
- Fédération de Recherche “Normandie-Végétal”-FED 4277, 76000 Rouen, France
| | - Maïté Vicré-Gibouin
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, Normandie Univ, UniRouen, 76000 Rouen, France
- Fédération de Recherche “Normandie-Végétal”-FED 4277, 76000 Rouen, France
| | - Azeddine Driouich
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, Normandie Univ, UniRouen, 76000 Rouen, France
- Fédération de Recherche “Normandie-Végétal”-FED 4277, 76000 Rouen, France
| | - Sharatchandra Ramasandra Govind
- Centre for Bioinformation, Department of Studies and Research in Environmental Science, Tumkur University, Tumakuru 57210, India
| | - Akash Devaraja
- Centre for Bioinformation, Department of Studies and Research in Environmental Science, Tumkur University, Tumakuru 57210, India
| | - Yogendra Kambalagere
- Department of Studies and Research in Environmental Science, Kuvempu University, Shankaraghatta, Shimoga 577451, India
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Abstract
The use of controlled, structured vocabularies (ontologies) has become a critical tool for scientists in the post-genomic era of massive datasets. Adoption and integration of common vocabularies and annotation practices enables cross-species comparative analyses and increases data sharing and reusability. The Plant Ontology (PO; http://www.plantontology.org/ ) describes plant anatomy, morphology, and the stages of plant development, and offers a database of plant genomics annotations associated to the PO terms. The scope of the PO has grown from its original design covering only rice, maize, and Arabidopsis, and now includes terms to describe all green plants from angiosperms to green algae.This chapter introduces how the PO and other related ontologies are constructed and organized, including languages and software used for ontology development, and provides an overview of the key features. Detailed instructions illustrate how to search and browse the PO database and access the associated annotation data. Users are encouraged to provide input on the ontology through the online term request form and contribute datasets for integration in the PO database.
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Cheng HN, Klasson KT, Asakura T, Wu Q. Nanotechnology in Agriculture. ACS SYMPOSIUM SERIES 2016. [DOI: 10.1021/bk-2016-1224.ch012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- H. N. Cheng
- Southern Regional Research Center, USDA Agricultural Research Service, 1100 Robert E. Lee Blvd., New Orleans, Louisiana 70124, United States
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- School of Renewable Natural Resources, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - K. T. Klasson
- Southern Regional Research Center, USDA Agricultural Research Service, 1100 Robert E. Lee Blvd., New Orleans, Louisiana 70124, United States
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- School of Renewable Natural Resources, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Tetsuo Asakura
- Southern Regional Research Center, USDA Agricultural Research Service, 1100 Robert E. Lee Blvd., New Orleans, Louisiana 70124, United States
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- School of Renewable Natural Resources, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Qinglin Wu
- Southern Regional Research Center, USDA Agricultural Research Service, 1100 Robert E. Lee Blvd., New Orleans, Louisiana 70124, United States
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- School of Renewable Natural Resources, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Genome-wide identification and characterization of Fox genes in the silkworm, Bombyx mori. Funct Integr Genomics 2015; 15:511-22. [DOI: 10.1007/s10142-015-0440-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 03/25/2015] [Accepted: 04/06/2015] [Indexed: 12/28/2022]
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Appels R, Nystrom J, Webster H, Keeble-Gagnere G. Discoveries and advances in plant and animal genomics. Funct Integr Genomics 2015; 15:121-9. [PMID: 25763751 PMCID: PMC4361718 DOI: 10.1007/s10142-015-0434-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/04/2022]
Abstract
Plant and animal genomics is a broad area of research with respect to the biological issues covered because it continues to deal with the structure and function of genetic material underpinning all organisms. This mini-review utilizes the plenary lectures from the Plant and Animal Genome Conference as a basis for summarizing the trends in the genome-level studies of organisms.
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Affiliation(s)
- Rudi Appels
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Australia, 6150,
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Lingutla NT, Preece J, Todorovic S, Cooper L, Moore L, Jaiswal P. AISO: Annotation of Image Segments with Ontologies. J Biomed Semantics 2014; 5:50. [PMID: 25584184 PMCID: PMC4290088 DOI: 10.1186/2041-1480-5-50] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/26/2014] [Indexed: 01/24/2023] Open
Abstract
Background Large quantities of digital images are now generated for biological collections, including those developed in projects premised on the high-throughput screening of genome-phenome experiments. These images often carry annotations on taxonomy and observable features, such as anatomical structures and phenotype variations often recorded in response to the environmental factors under which the organisms were sampled. At present, most of these annotations are described in free text, may involve limited use of non-standard vocabularies, and rarely specify precise coordinates of features on the image plane such that a computer vision algorithm could identify, extract and annotate them. Therefore, researchers and curators need a tool that can identify and demarcate features in an image plane and allow their annotation with semantically contextual ontology terms. Such a tool would generate data useful for inter and intra-specific comparison and encourage the integration of curation standards. In the future, quality annotated image segments may provide training data sets for developing machine learning applications for automated image annotation. Results We developed a novel image segmentation and annotation software application, “Annotation of Image Segments with Ontologies” (AISO). The tool enables researchers and curators to delineate portions of an image into multiple highlighted segments and annotate them with an ontology-based controlled vocabulary. AISO is a freely available Java-based desktop application and runs on multiple platforms. It can be downloaded at http://www.plantontology.org/software/AISO. Conclusions AISO enables curators and researchers to annotate digital images with ontology terms in a manner which ensures the future computational value of the annotated images. We foresee uses for such data-encoded image annotations in biological data mining, machine learning, predictive annotation, semantic inference, and comparative analyses.
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Affiliation(s)
- Nikhil Tej Lingutla
- School of Electrical Engineering and Computer Science, Kelley Engineering Center, Oregon State University, Corvallis, OR 97331-2902 USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Sinisa Todorovic
- School of Electrical Engineering and Computer Science, Kelley Engineering Center, Oregon State University, Corvallis, OR 97331-2902 USA
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Laura Moore
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
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