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Shukla S, Singh P, Shukla S, Ali S, Didwania N. Scope of Onsite, Portable Prevention Diagnostic Strategies for Alternaria Infections in Medicinal Plants. BIOSENSORS 2023; 13:701. [PMID: 37504100 PMCID: PMC10377195 DOI: 10.3390/bios13070701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/18/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
Medicinal plants are constantly challenged by different biotic inconveniences, which not only cause yield and economic losses but also affect the quality of products derived from them. Among them, Alternaria pathogens are one of the harmful fungal pathogens in medicinal plants across the globe. Therefore, a fast and accurate detection method in the early stage is needed to avoid significant economic losses. Although traditional methods are available to detect Alternaria, they are more time-consuming and costly and need good expertise. Nevertheless, numerous biochemical- and molecular-based techniques are available for the detection of plant diseases, but their efficacy is constrained by differences in their accuracy, specificity, sensitivity, dependability, and speed in addition to being unsuitable for direct on-field studies. Considering the effect of Alternaria on medicinal plants, the development of novel and early detection measures is required to detect causal Alternaria species accurately, sensitively, and rapidly that can be further applied in fields to speed up the advancement process in detection strategies. In this regard, nanotechnology can be employed to develop portable biosensors suitable for early and correct pathogenic disease detection on the field. It also provides an efficient future scope to convert innovative nanoparticle-derived fabricated biomolecules and biosensor approaches in the diagnostics of disease-causing pathogens in important medicinal plants. In this review, we summarize the traditional methods, including immunological and molecular methods, utilized in plant-disease diagnostics. We also brief advanced automobile and efficient sensing technologies for diagnostics. Here we are proposing an idea with a focus on the development of electrochemical and/or colorimetric properties-based nano-biosensors that could be useful in the early detection of Alternaria and other plant pathogens in important medicinal plants. In addition, we discuss challenges faced during the fabrication of biosensors and new capabilities of the technology that provide information regarding disease management strategies.
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Affiliation(s)
- Sadhana Shukla
- Manav Rachna Centre for Medicinal Plant Pathology, Manav Rachna International Institute of Research and Studies, Faridabad 121004, India
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurgaon 122003, India
| | - Pushplata Singh
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurgaon 122003, India
| | - Shruti Shukla
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurgaon 122003, India
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Nidhi Didwania
- Manav Rachna Centre for Medicinal Plant Pathology, Manav Rachna International Institute of Research and Studies, Faridabad 121004, India
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Evaluation of the Characteristics and Infectivity of the Secondary Inoculum Produced by Plasmopara viticola on Grapevine Leaves by Means of Flow Cytometry and Fluorescence-Activated Cell Sorting. Appl Environ Microbiol 2022; 88:e0101022. [PMID: 36250698 PMCID: PMC9642012 DOI: 10.1128/aem.01010-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmopara viticola, the oomycete causing grapevine downy mildew, is one of the most important pathogens in viticulture. P. viticola is a polycyclic pathogen, able to carry out numerous secondary cycles of infection during a single vegetative grapevine season, by producing asexual spores (zoospores) within sporangia. The extent of these infections is strongly influenced by both the quantity (density) and quality (infectivity) of the inoculum produced by the pathogen. To date, the protocols for evaluating all these characteristics are quite limited and time-consuming and do not allow all the information to be obtained in a single run. In this study, a protocol combining flow cytometry (FCM) and fluorescence-activated cell sorting (FACS) was developed to investigate the composition, the infection efficiency and the dynamics of the inoculum produced by P. viticola for secondary infection cycles. In our analyses, we identified different structures within the inoculum, including degenerated and intact sporangia. The latter have been sorted, and single sporangia were directly inoculated on grapevine leaf discs, thus allowing a thorough investigation of the infection dynamics and efficiency. In detail, we determined that, in our conditions, 8% of sporangia were able to infect the leaves and that on a susceptible variety, the time required by the pathogen to reach 50% of total infection is about 10 days. The analytical approach developed in this study could open a new perspective to shed light on the biology and epidemiology of this important pathogen. IMPORTANCE P. viticola secondary infections contribute significantly to the epidemiology of this important plant pathogen. However, the infection dynamics of asexual spores produced by this organism are still poorly investigated. The main challenges in dissecting the grapevine-P. viticola interaction in vitro are attributable to the biotrophic adaptation of the pathogen. This work provides new insights into the infection efficiency and dynamics imputable to P. viticola sporangia, contributing useful information on grapevine downy mildew epidemiology. Moreover, future applications of the sorting protocol developed in this work could yield a significant and positive impact in the study of P. viticola, providing unmatched resolution, precision, and accuracy compared with the traditional techniques.
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Plant Viral Disease Detection: From Molecular Diagnosis to Optical Sensing Technology—A Multidisciplinary Review. REMOTE SENSING 2022. [DOI: 10.3390/rs14071542] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Plant viral diseases result in productivity and economic losses to agriculture, necessitating accurate detection for effective control. Lab-based molecular testing is the gold standard for providing reliable and accurate diagnostics; however, these tests are expensive, time-consuming, and labour-intensive, especially at the field-scale with a large number of samples. Recent advances in optical remote sensing offer tremendous potential for non-destructive diagnostics of plant viral diseases at large spatial scales. This review provides an overview of traditional diagnostic methods followed by a comprehensive description of optical sensing technology, including camera systems, platforms, and spectral data analysis to detect plant viral diseases. The paper is organized along six multidisciplinary sections: (1) Impact of plant viral disease on plant physiology and consequent phenotypic changes, (2) direct diagnostic methods, (3) traditional indirect detection methods, (4) optical sensing technologies, (5) data processing techniques and modelling for disease detection, and (6) comparison of the costs. Finally, the current challenges and novel ideas of optical sensing for detecting plant viruses are discussed.
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Eng WH, Ho WS, Ling KH. In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment. PeerJ 2021; 9:e12399. [PMID: 34760387 PMCID: PMC8556713 DOI: 10.7717/peerj.12399] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Polyploidization has played a crucial role in plant breeding and crop improvement. However, studies on the polyploidization of tropical tree species are still very scarce in this region. This paper described the in vitro induction and identification of polyploid plants of Neolamarckia cadamba by colchicine treatment. N. cadamba belongs to the Rubiaceae family is a natural tetraploid plant with 44 chromosomes (2n = 4x = 44). Nodal segments were treated with colchicine (0.1%, 0.3% and 0.5%) for 24 h and 48 h before transferring to shoot regeneration medium. Flow cytometry (FCM) and chromosome count were employed to determine the ploidy level and chromosome number of the regenerants, respectively. Of 180 colchicine-treated nodal segments, 39, 14 and 22 were tetraploids, mixoploids and octoploids, respectively. The highest percentage of polyploidization (20% octoploids; 6.7% mixoploids) was observed after treated with 0.3% colchicine for 48 h. The DNA content of tetraploid (4C) and octoploid (8C) was 2.59 ± 0.09 pg and 5.35 ± 0.24 pg, respectively. Mixoploid plants are made up of mixed tetraploid and octoploid cells. Chromosome count confirmed that tetraploid cell has 44 chromosomes and colchicine-induced octoploid cell has 88 chromosomes. Both octoploids and mixoploids grew slower than tetraploids under in vitro conditions. Morphological characterizations showed that mixoploid and octoploid leaves had thicker leaf blades, thicker midrib, bigger stomata size, lower stomata density, higher SPAD value and smaller pith layer than tetraploids. This indicates that polyploidization has changed and resulted in traits that are predicted to increase photosynthetic capacity of N. cadamba. These novel polyploid plants could be valuable resources for advanced N. cadamba breeding programs to produce improved clones for planted forest development.
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Affiliation(s)
- Wee Hiang Eng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Wei Seng Ho
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
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Talhinhas P, Carvalho R, Loureiro J. The use of flow cytometry for fungal nuclear DNA quantification. Cytometry A 2021; 99:343-347. [PMID: 33704904 DOI: 10.1002/cyto.a.24335] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 11/08/2022]
Abstract
Genome size information is sparse across fungi, with information being available for less than 2000 species. So far, most records have been obtained using static, microscope-based cytometry methods or derived from genome sequencing projects. Flow cytometry is now considered the state-of-the-art method for obtaining genome size measurements, and appropriate methods and DNA standards are available, enabling the analysis of most genome size ranges in a rapid, robust and inexpensive way. The average fungal genome size is 60 Mbp, but sizes vary across phylogeny, ranging from 2.2 (Encephalitozoon romaleae) to 3706 Mbp (Jafnea semitosta). In several fungal clades, genome size expansion seems to accompany evolution either to plant mutualism or to plant parasitism (particularly biotrophy), and fungi that interact with plants seem to have larger genomes than saprobes and those that interact with animals. Whereas flow cytometry for nuclear DNA quantification is routinely employed in plant sciences for genome size and ploidy studies, its use in fungal biology is still infrequent. Appropriate standards, methods and best practices are described here, with the aim of stimulating a more generalized and widespread use of flow cytometry for fungal genome size measurement.
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Affiliation(s)
- Pedro Talhinhas
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Rita Carvalho
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
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Hu Y, Wilson S, Schwessinger B, Rathjen JP. Blurred lines: integrating emerging technologies to advance plant biosecurity. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:127-134. [PMID: 32610220 DOI: 10.1016/j.pbi.2020.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/09/2020] [Accepted: 04/26/2020] [Indexed: 05/25/2023]
Abstract
Plant diseases threaten global food security and biodiversity. Rapid dispersal of pathogens particularly via human means has accelerated in recent years. Timely detection of plant pathogens is essential to limit their spread. At the same time, international regulations must keep abreast of advances in plant disease diagnostics. In this review we describe recent progress in developing modern plant disease diagnostics based on detection of pathogen components, high-throughput image analysis, remote sensing, and machine learning. We discuss how different diagnostic approaches can be integrated in detection frameworks that can work at different scales and account for sampling biases. Lastly, we briefly discuss the requirements to apply these advances under regulatory settings to improve biosecurity measures globally.
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Affiliation(s)
- Yiheng Hu
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Salome Wilson
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Benjamin Schwessinger
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - John P Rathjen
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.
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Evaluation of genome size and quantitative features of the dolipore septum as taxonomic predictors for the Serendipita 'williamsii' species complex. Fungal Biol 2020; 124:781-800. [PMID: 32883429 DOI: 10.1016/j.funbio.2020.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 05/23/2020] [Accepted: 06/10/2020] [Indexed: 11/21/2022]
Abstract
Despite multiple taxonomic revisions, several uncertainties at the genus and species level remain to be resolved within the Serendipitaceae family (Sebacinales). This volatile classification is attributed to the limited number of available axenic cultures and the scarcity of useful morphological traits. In the current study, we attempted to discover alternative taxonomic markers not relying on DNA sequences to differentiate among the closely related members of our Congolese Serendipita isolate collection and the reference strains S. indica (syn. Piriformospora indica) and S. williamsii (syn. P. williamsii). We demonstrated that nuclear distribution across hyphal cells and genome size (determined by flow cytometry) did not have enough resolving power, but quantitative and qualitative variations in the ultrastructure of the dolipore septa investigated by transmission electron microscopy did provide useful markers. Multivariate analysis revealed that subtle differences in ultrastructural characteristics of the parenthesome and the attached endoplasmic reticulum are most relevant when studying this fungal group. Moreover, the observed clustering pattern showed that there might be more diversity amongst the Congolese isolates within the S. 'williamsii' species complex than previously anticipated based on molecular data. Altogether, our results provide novel perspectives on the use of integrative approaches to support sebacinoid and Serendipitaceae taxonomy.
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Sun Y, Cai B, Wei X, Wang Z, Rao L, Meng QF, Liao Q, Liu W, Guo S, Zhao X. A valve-based microfluidic device for on-chip single cell treatments. Electrophoresis 2018; 40:961-968. [PMID: 30155963 DOI: 10.1002/elps.201800213] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/19/2018] [Accepted: 08/22/2018] [Indexed: 11/08/2022]
Abstract
Assays toward single-cell analysis have attracted the attention in biological and biomedical researches to reveal cellular mechanisms as well as heterogeneity. Yet nowadays microfluidic devices for single-cell analysis have several drawbacks: some would cause cell damage due to the hydraulic forces directly acting on cells, while others could not implement biological assays since they could not immobilize cells while manipulating the reagents at the same time. In this work, we presented a two-layer pneumatic valve-based platform to implement cell immobilization and treatment on-chip simultaneously, and cells after treatment could be collected non-destructively for further analysis. Target cells could be encapsulated in sodium alginate droplets which solidified into hydrogel when reacted with Ca2+ . The size of hydrogel beads could be precisely controlled by modulating flow rates of continuous/disperse phases. While regulating fluid resistance between the main channel and passages by the integrated pneumatic valves, on-chip capture and release of hydrogel beads was implemented. As a proof of concept for on-chip single-cell treatments, we showed cellular live/dead staining based on our devices. This method would have potential in single cell manipulation for biochemical cellular assays.
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Affiliation(s)
- Yue Sun
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
| | - Bo Cai
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiaoyun Wei
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
| | - Zixiang Wang
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
| | - Lang Rao
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
| | - Qian-Fang Meng
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
| | - Qingquan Liao
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
| | - Wei Liu
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
| | - Shishang Guo
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
| | - Xingzhong Zhao
- School of Physics and Technology, Wuhan University, Wuhan, P. R. China
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Xu C, Zhang R, Sun G, Gleason ML. Comparative Genome Analysis Reveals Adaptation to the Ectophytic Lifestyle of Sooty Blotch and Flyspeck Fungi. Genome Biol Evol 2017; 9:3137-3151. [PMID: 29126189 PMCID: PMC5737583 DOI: 10.1093/gbe/evx229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2017] [Indexed: 01/04/2023] Open
Abstract
Sooty blotch and flyspeck (SBFS) fungi are a distinctive group of plant pathogens which, although phylogenetically diverse, occupy an exclusively surface-dwelling niche. They cause economic losses by superficially blemishing the fruit of several tree crops, principally apple, in moist temperate regions worldwide. In this study, we performed genome-wide comparative analyses separately within three pairs of species of ascomycete pathogens; each pair contained an SBFS species as well as a closely related but plant-penetrating parasite (PPP) species. Our results showed that all three of the SBFS pathogens had significantly smaller genome sizes, gene numbers and repeat ratios than their counterpart PPPs. The pathogenicity-related genes encoding MFS transporters, secreted proteins (mainly effectors and peptidases), plant cell wall degrading enzymes, and secondary metabolism enzymes were also drastically reduced in the SBFS fungi compared with their PPP relatives. We hypothesize that the above differences in genome composition are due largely to different levels of acquisition, loss, expansion, and contraction of gene families and emergence of orphan genes. Furthermore, results suggested that horizontal gene transfer may have played a role, although limited, in the divergent evolutionary paths of SBFS pathogens and PPPs; repeat-induced point mutation could have inhibited the propagation of transposable elements and expansion of gene families in the SBFS group, given that this mechanism is stronger in the SBFS fungi than in their PPP relatives. These results substantially broaden understanding of evolutionary mechanisms of adaptation of fungi to the epicuticular niche of plants.
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Affiliation(s)
- Chao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
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Neu E, Featherston J, Rees J, Debener T. A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication. PLoS One 2017; 12:e0185310. [PMID: 28981525 PMCID: PMC5628827 DOI: 10.1371/journal.pone.0185310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/11/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Black spot is one of the most severe and damaging diseases of garden roses. We present the draft genome sequence of its causative agent Diplocarpon rosae as a working tool to generate molecular markers and to analyze functional and structural characteristics of this fungus. RESULTS The isolate DortE4 was sequenced with 191x coverage of different read types which were assembled into 2457 scaffolds. By evidence supported genome annotation with the MAKER pipeline 14,004 gene models were predicted and transcriptomic data indicated that 88.5% of them are expressed during the early stages of infection. Analyses of k-mer distributions resulted in unexpectedly large genome size estimations between 72.5 and 91.4 Mb, which cannot be attributed to its repeat structure and content of transposable elements alone, factors explaining such differences in other fungal genomes. In contrast, different lines of evidences demonstrate that a huge proportion (approximately 80%) of genes are duplicated, which might indicate a whole genome duplication event. By PCR-RFLP analysis of six paralogous gene pairs of BUSCO orthologs, which are expected to be single copy genes, we could show experimentally that the duplication is not due to technical error and that not all isolates tested possess all of the paralogs. CONCLUSIONS The presented genome sequence is still a fragmented draft but contains almost the complete gene space. Therefore, it provides a useful working tool to study the interaction of D. rosae with the host and the influence of a genome duplication outside of the model yeast in the background of a phytopathogen.
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Affiliation(s)
- Enzo Neu
- Institute for Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Jonathan Featherston
- Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, South Africa
| | - Jasper Rees
- Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, South Africa
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz University Hannover, Hannover, Germany
- * E-mail:
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Talhinhas P, Tavares D, Ramos AP, Gonçalves S, Loureiro J. Validation of standards suitable for genome size estimation of fungi. J Microbiol Methods 2017; 142:76-78. [PMID: 28923689 DOI: 10.1016/j.mimet.2017.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 11/24/2022]
Abstract
Genome size information is fundamental to genome sequencing and may also uncover genomic aspects of evolution. Flow Cytometry, the preferred method for genome size estimation, requires suitable standards. Here we validate Inonotus hispidus, Colletotrichum acutatum and Cenococcum geophilum (41, 68 and 203Mbp), as standards for fungal genome size estimation.
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Affiliation(s)
- Pedro Talhinhas
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal.
| | - Daniela Tavares
- CFE-Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Ana Paula Ramos
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Susana Gonçalves
- CFE-Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - João Loureiro
- CFE-Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
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Ramos AP, Tavares S, Tavares D, Silva MDC, Loureiro J, Talhinhas P. Flow cytometry reveals that the rust fungus, Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported--2489 Mbp. MOLECULAR PLANT PATHOLOGY 2015; 16:1006-1010. [PMID: 25784533 PMCID: PMC6638392 DOI: 10.1111/mpp.12255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Among the Eukaryotes, Fungi have relatively small genomes (average of 44.2 Mbp across 1850 species). The order Pucciniales (Basidiomycota) has the largest average genome size among fungi (305 Mbp), and includes the two largest fungal genomes reported so far (Puccinia chrysanthemi and Gymnosporangium confusum, with 806.5 and 893.2 Mbp, respectively). In this work, flow cytometry was employed to determine the genome size of the Bidens pilosa rust pathogen, Uromyces bidentis. The results obtained revealed that U. bidentis presents a surprisingly large haploid genome size of 2489 Mbp. This value is almost three times larger than the previous largest fungal genome reported and over 50 times larger than the average fungal genome size. Microscopic examination of U. bidentis nuclei also showed that they are not as different in size from the B. pilosa nuclei when compared with the differences between other rusts and their host plants. This result further reinforces the position of the Pucciniales as the fungal group with the largest genomes, prompting studies addressing the role of repetitive elements and polyploidy in the evolution, pathological specialization and diversity of fungal species.
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Affiliation(s)
- Ana Paula Ramos
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, 1349-017, Lisbon, Portugal
| | - Sílvia Tavares
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical, 2780-505, Oeiras, Portugal
| | - Daniela Tavares
- CFE, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Maria Do Céu Silva
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, 1349-017, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical, 2780-505, Oeiras, Portugal
| | - João Loureiro
- CFE, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Pedro Talhinhas
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, 1349-017, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical, 2780-505, Oeiras, Portugal
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Husson C, Aguayo J, Revellin C, Frey P, Ioos R, Marçais B. Evidence for homoploid speciation in Phytophthora alni supports taxonomic reclassification in this species complex. Fungal Genet Biol 2015; 77:12-21. [DOI: 10.1016/j.fgb.2015.02.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/18/2015] [Accepted: 02/19/2015] [Indexed: 01/25/2023]
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Veselská T, Svoboda J, Růžičková Ž, Kolařík M. Application of flow cytometry for genome size determination inGeosmithiafungi: A comparison of methods. Cytometry A 2014; 85:854-61. [DOI: 10.1002/cyto.a.22500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 04/18/2014] [Accepted: 06/03/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Tereza Veselská
- Department of Botany; Faculty of Science; Charles University; Czech Republic
- Institute of Microbiology of the ASCR; 142 20 Praha 4 Czech Republic
| | - Jan Svoboda
- Institute of Microbiology of the ASCR; 142 20 Praha 4 Czech Republic
| | - Žaneta Růžičková
- Institute of Microbiology of the ASCR; 142 20 Praha 4 Czech Republic
| | - Miroslav Kolařík
- Department of Botany; Faculty of Science; Charles University; Czech Republic
- Institute of Microbiology of the ASCR; 142 20 Praha 4 Czech Republic
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Tavares S, Ramos AP, Pires AS, Azinheira HG, Caldeirinha P, Link T, Abranches R, Silva MDC, Voegele RT, Loureiro J, Talhinhas P. Genome size analyses of Pucciniales reveal the largest fungal genomes. FRONTIERS IN PLANT SCIENCE 2014; 5:422. [PMID: 25206357 PMCID: PMC4143883 DOI: 10.3389/fpls.2014.00422] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/07/2014] [Indexed: 05/09/2023]
Abstract
Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.
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Affiliation(s)
- Sílvia Tavares
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica TropicalOeiras, Portugal
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de LisboaOeiras, Portugal
| | - Ana Paula Ramos
- CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de LisboaLisbon, Portugal
| | - Ana Sofia Pires
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica TropicalOeiras, Portugal
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de LisboaOeiras, Portugal
| | - Helena G. Azinheira
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica TropicalOeiras, Portugal
- CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de LisboaLisbon, Portugal
| | - Patrícia Caldeirinha
- Department of Life Sciences, Centre for Functional Ecology, University of CoimbraCoimbra, Portugal
| | - Tobias Link
- Institut für Phytomedizin, Universität HohenheimStuttgart, Germany
| | - Rita Abranches
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de LisboaOeiras, Portugal
| | - Maria do Céu Silva
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica TropicalOeiras, Portugal
- CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de LisboaLisbon, Portugal
| | - Ralf T. Voegele
- Institut für Phytomedizin, Universität HohenheimStuttgart, Germany
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, University of CoimbraCoimbra, Portugal
| | - Pedro Talhinhas
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica TropicalOeiras, Portugal
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de LisboaOeiras, Portugal
- CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de LisboaLisbon, Portugal
- *Correspondence: Pedro Talhinhas, Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical, Quinta do Marquês, 2784-505 Oeiras, Portugal e-mail:
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Salma M, Rousseaux S, Sequeira-Le Grand A, Alexandre H. Cytofluorometric detection of wine lactic acid bacteria: application of malolactic fermentation to the monitoring. ACTA ACUST UNITED AC 2013; 40:63-73. [DOI: 10.1007/s10295-012-1200-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/15/2012] [Indexed: 11/29/2022]
Abstract
Abstract
In this study we report for the first time a rapid, efficient and cost-effective method for the enumeration of lactic acid bacteria (LAB) in wine. Indeed, up to now, detection of LAB in wine, especially red wine, was not possible. Wines contain debris that cannot be separated from bacteria using flow cytometry (FCM). Furthermore, the dyes tested in previous reports did not allow an efficient staining of bacteria. Using FCM and a combination of BOX/PI dyes, we were able to count bacteria in wines. The study was performed in wine inoculated with Oenococcus oeni (106 CFU ml−1) stained with either FDA or BOX/PI and analyzed by FCM during the malolactic fermentation (MLF). The analysis show a strong correlation between the numbers of BOX/PI-stained cells determined by FCM and the cell numbers determined by plate counts (red wine: R2 ≥ 0.97, white wine R2 ≥ 0.965). On the other hand, we found that the enumeration of O. oeni labeled with FDA was only possible in white wine (R2 ≥ 0.97). Viable yeast and LAB populations can be rapidly discriminated and quantified in simultaneous malolactic-alcoholic wine fermentations using BOX/PI and scatter parameters in a one single measurement. This rapid procedure is therefore a suitable method for monitoring O. oeni populations during winemaking, offers a detection limit of <104 CFU ml−1 and can be considered a useful method for investigating the dynamics of microbial growth in wine and applied for microbiological quality control in wineries.
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Affiliation(s)
- Mohammad Salma
- grid.5613.1 0000000122989313 UMR 02102 PAM Université de Bourgogne-AgroSup Dijon Laboratoire VALMIS Institut Universitaire de la Vigne et du Vin Jules Guyot Université de Bourgogne 21078 Dijon Cedex France
| | - Sandrine Rousseaux
- grid.5613.1 0000000122989313 UMR 02102 PAM Université de Bourgogne-AgroSup Dijon Laboratoire VALMIS Institut Universitaire de la Vigne et du Vin Jules Guyot Université de Bourgogne 21078 Dijon Cedex France
| | - Anabelle Sequeira-Le Grand
- grid.5613.1 0000000122989313 Plateforme de Cytométrie, Structure Fédérative de Recherche Santé STIC, Fac. Médecine Université de Bourgogne 7, Bd Jeanne D’Arc 21000 Dijon France
| | - Hervé Alexandre
- grid.5613.1 0000000122989313 UMR 02102 PAM Université de Bourgogne-AgroSup Dijon Laboratoire VALMIS Institut Universitaire de la Vigne et du Vin Jules Guyot Université de Bourgogne 21078 Dijon Cedex France
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Fritzsch FS, Dusny C, Frick O, Schmid A. Single-Cell Analysis in Biotechnology, Systems Biology, and Biocatalysis. Annu Rev Chem Biomol Eng 2012; 3:129-55. [DOI: 10.1146/annurev-chembioeng-062011-081056] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Frederik S.O. Fritzsch
- Single Cell Laboratory, Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V., D-44227 Dortmund, Germany;
| | - Christian Dusny
- Single Cell Laboratory, Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V., D-44227 Dortmund, Germany;
| | - Oliver Frick
- Laboratory of Chemical Biotechnology, Technische Universität Dortmund, D-44227 Dortmund, Germany
| | - Andreas Schmid
- Single Cell Laboratory, Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V., D-44227 Dortmund, Germany;
- Laboratory of Chemical Biotechnology, Technische Universität Dortmund, D-44227 Dortmund, Germany
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Montañez-Izquierdo VY, Salas-Vázquez DI, Rodríguez-Jerez JJ. Use of epifluorescence microscopy to assess the effectiveness of phage P100 in controlling Listeria monocytogenes biofilms on stainless steel surfaces. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.08.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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