1
|
Dziuba MK, McIntire KM, Davenport ES, Baird E, Huerta C, Jaye R, Corcoran F, McCreadie P, Nelson T, Duffy MA. Microsporidian coinfection reduces fitness of a fungal pathogen due to rapid host mortality. mBio 2024:e0058324. [PMID: 39194186 DOI: 10.1128/mbio.00583-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
Infection outcomes can be strongly context dependent, shifting a host-symbiont relationship along a parasitism-mutualism continuum. Numerous studies show that under stressful conditions, symbionts that are typically mutualistic can become parasitic. The reverse possibility, a parasite becoming mutualistic, has received much less study. We investigated whether the parasitic microsporidium Ordospora pajunii can become beneficial for its host Daphnia dentifera in the presence of the more virulent fungal pathogen Metschnikowia bicuspidata. We found that, even though infection with O. pajunii reduces the frequency of penetration of M. bicuspidata spores into the host body cavity, it does not improve the survival or reproduction of the host; conversely, coinfection increased the mortality of Daphnia. This shorter lifespan of coinfected hosts disrupted the life cycle of M. bicuspidata, greatly reducing its fitness. Thus, coinfection with both pathogens was detrimental to the host at the individual level but might be beneficial for the host population as a result of greatly reduced production of M. bicuspidata spores. If so, this would mean that O. pajunii outbreaks should delay or prevent M. bicuspidata outbreaks. In support of this, in an analysis of dynamics of naturally occurring outbreaks in two lakes where these pathogens co-occur, we found a time lag in occurrence between O. pajunii and M. bicuspidata, with M. bicuspidata epidemics only occurring after the collapse of O. pajunii epidemics. Thus, these results suggest that the interaction between co-occurring symbionts, and the net impact of a symbiont on a host, might be qualitatively different at different scales.IMPORTANCEUnderstanding the factors that modify infection probability and virulence is crucial for identifying the drivers of infection outbreaks and modeling disease epidemic progression, and increases our ability to control diseases and reduce the harm they cause. One factor that can strongly influence infection probability and virulence is the presence of other pathogens. However, while coexposures and coinfections are incredibly common, we still have only a limited understanding of how pathogen interactions alter infection outcomes or whether their impacts are scale dependent. We used a system of one host and two pathogens to show that sequential coinfection can have a tremendous impact on the host and the infecting pathogens and that the outcome of (co-)infection can be negative or positive depending on the focal organization level.
Collapse
Affiliation(s)
- Marcin K Dziuba
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kristina M McIntire
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth S Davenport
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Emma Baird
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Cristian Huerta
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Riley Jaye
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Fiona Corcoran
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Paige McCreadie
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Taleah Nelson
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Meghan A Duffy
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
2
|
Peyretaillade E, Akossi RF, Tournayre J, Delbac F, Wawrzyniak I. How to overcome constraints imposed by microsporidian genome features to ensure gene prediction? J Eukaryot Microbiol 2024:e13038. [PMID: 38934348 DOI: 10.1111/jeu.13038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
Since the advent of sequencing techniques and due to their continuous evolution, it has become easier and less expensive to obtain the complete genome sequence of any organism. Nevertheless, to elucidate all biological processes governing organism development, quality annotation is essential. In genome annotation, predicting gene structure is one of the most important and captivating challenges for computational biology. This aspect of annotation requires continual optimization, particularly for genomes as unusual as those of microsporidia. Indeed, this group of fungal-related parasites exhibits specific features (highly reduced gene sizes, sequences with high rate of evolution) linked to their evolution as intracellular parasites, requiring the implementation of specific annotation approaches to consider all these features. This review aimed to outline these characteristics and to assess the increasingly efficient approaches and tools that have enhanced the accuracy of gene prediction for microsporidia, both in terms of sensitivity and specificity. Subsequently, a final part will be dedicated to postgenomic approaches aimed at reinforcing the annotation data generated by prediction software. These approaches include the characterization of other understudied genes, such as those encoding regulatory noncoding RNAs or very small proteins, which also play crucial roles in the life cycle of these microorganisms.
Collapse
Affiliation(s)
| | - Reginal F Akossi
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jérémy Tournayre
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Frédéric Delbac
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ivan Wawrzyniak
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| |
Collapse
|
3
|
Dziuba MK, McIntire KM, Seto K, Davenport ES, Rogalski MA, Gowler CD, Baird E, Vaandrager M, Huerta C, Jaye R, Corcoran FE, Withrow A, Ahrendt S, Salamov A, Nolan M, Tejomurthula S, Barry K, Grigoriev IV, James TY, Duffy MA. Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp. mBio 2024; 15:e0058224. [PMID: 38651867 PMCID: PMC11237803 DOI: 10.1128/mbio.00582-24] [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: 02/27/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
The impacts of microsporidia on host individuals are frequently subtle and can be context dependent. A key example of the latter comes from a recently discovered microsporidian symbiont of Daphnia, the net impact of which was found to shift from negative to positive based on environmental context. Given this, we hypothesized low baseline virulence of the microsporidian; here, we investigated the impact of infection on hosts in controlled conditions and the absence of other stressors. We also investigated its phylogenetic position, ecology, and host range. The genetic data indicate that the symbiont is Ordospora pajunii, a newly described microsporidian parasite of Daphnia. We show that O. pajunii infection damages the gut, causing infected epithelial cells to lose microvilli and then rupture. The prevalence of this microsporidian could be high (up to 100% in the lab and 77% of adults in the field). Its overall virulence was low in most cases, but some genotypes suffered reduced survival and/or reproduction. Susceptibility and virulence were strongly host-genotype dependent. We found that North American O. pajunii were able to infect multiple Daphnia species, including the European species Daphnia longispina, as well as Ceriodaphnia spp. Given the low, often undetectable virulence of this microsporidian and potentially far-reaching consequences of infections for the host when interacting with other pathogens or food, this Daphnia-O. pajunii symbiosis emerges as a valuable system for studying the mechanisms of context-dependent shifts between mutualism and parasitism, as well as for understanding how symbionts might alter host interactions with resources. IMPORTANCE The net outcome of symbiosis depends on the costs and benefits to each partner. Those can be context dependent, driving the potential for an interaction to change between parasitism and mutualism. Understanding the baseline fitness impact in an interaction can help us understand those shifts; for an organism that is generally parasitic, it should be easier for it to become a mutualist if its baseline virulence is relatively low. Recently, a microsporidian was found to become beneficial to its Daphnia hosts in certain ecological contexts, but little was known about the symbiont (including its species identity). Here, we identify it as the microsporidium Ordospora pajunii. Despite the parasitic nature of microsporidia, we found O. pajunii to be, at most, mildly virulent; this helps explain why it can shift toward mutualism in certain ecological contexts and helps establish O. pajunii is a valuable model for investigating shifts along the mutualism-parasitism continuum.
Collapse
Affiliation(s)
- Marcin K. Dziuba
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kristina M. McIntire
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kensuke Seto
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Elizabeth S. Davenport
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mary A. Rogalski
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Biology Department, Bowdoin College, Brunswick, Maine, USA
| | - Camden D. Gowler
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Emma Baird
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Megan Vaandrager
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Cristian Huerta
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Riley Jaye
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Fiona E. Corcoran
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alicia Withrow
- Center for Advanced Microscopy, Michigan State University, East Lansing, Michigan, USA
| | - Steven Ahrendt
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Asaf Salamov
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matt Nolan
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sravanthi Tejomurthula
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Igor V. Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Meghan A. Duffy
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
4
|
Julian AT, Pombert JF. SYNY: a pipeline to investigate and visualize collinearity between genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593317. [PMID: 38798446 PMCID: PMC11118330 DOI: 10.1101/2024.05.09.593317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Investigating collinearity between chromosomes is often used in comparative genomics to help identify gene orthologs, pinpoint genes that might have been overlooked as part of annotation processes and/or perform various evolutionary inferences. Collinear segments, also known as syntenic blocks, can be inferred from sequence alignments and/or from the identification of genes arrayed in the same order and relative orientations between investigated genomes. To help perform these analyses and assess their outcomes, we built a simple pipeline called SYNY (for synteny) that implements the two distinct approaches and produces different visualizations. The SYNY pipeline was built with ease of use in mind and runs on modest hardware. The pipeline is written in Perl and Python and is available on GitHub (https://github.com/PombertLab/SYNY) under the permissive MIT license.
Collapse
|
5
|
Ide-Pérez MR, Sánchez-Reyes A, Folch-Mallol JL, Sánchez-Carbente MDR. Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family. PLoS One 2024; 19:e0297232. [PMID: 38354109 PMCID: PMC10866521 DOI: 10.1371/journal.pone.0297232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024] Open
Abstract
Exophiala is a black fungi of the family Herpotrichiellaceae that can be found in a wide range of environments like soil, water and the human body as potential opportunistic pathogen. Some species are known to be extremophiles, thriving in harsh conditions such as deserts, glaciers, and polluted habitats. The identification of novel Exophiala species across diverse environments underlines the remarkable biodiversity within the genus. However, its classification using traditional phenotypic and phylogenetic analyses has posed a challenges. Here we describe a novel taxon, Exophiala chapopotensis sp. nov., strain LBMH1013, isolated from oil-polluted soil in Mexico, delimited according to combined morphological, molecular, evolutionary and statistics criteria. This species possesses the characteristic dark mycelia growing on PDA and tends to be darker in the presence of hydrocarbons. Its growth is dual with both yeast-like and hyphal forms. LBMH1013 differs from closely related species such as E. nidicola due to its larger aseptate conidia and could be distinguished from E. dermatitidis and E. heteromorpha by its inability to thrive above 37°C or 10% of NaCl. A comprehensive genomic analyses using up-to-date overall genome relatedness indices, several multigene phylogenies and molecular evolutionary analyzes using Bayesian speciation models, further validate its species-specific transition from all current Exophiala/Capronia species. Additionally, we applied the phylophenetic conceptual framework to delineate the species-specific hypothesis in order to incorporate this proposal within an integrative taxonomic framework. We believe that this approach to delimit fungal species will also be useful to our peers.
Collapse
Affiliation(s)
- Martín R. Ide-Pérez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ayixon Sánchez-Reyes
- Investigador por México-Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | | |
Collapse
|
6
|
Davenport ES, Dziuba MK, Jacobson LE, Calhoun SK, Monell KJ, Duffy MA. How does parasite environmental transmission stage concentration change before, during, and after disease outbreaks? Ecology 2024; 105:e4235. [PMID: 38185479 DOI: 10.1002/ecy.4235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/09/2023] [Indexed: 01/09/2024]
Abstract
Outbreaks of environmentally transmitted parasites require that susceptible hosts encounter transmission stages in the environment and become infected, but we also know that transmission stages can be in the environment without triggering disease outbreaks. One challenge in understanding the relationship between environmental transmission stages and disease outbreaks is that the distribution and abundance of transmission stages outside of their hosts have been difficult to quantify. Thus, we have limited data about how changes in transmission stage abundance influence disease dynamics; moreover, we do not know whether the relationship between transmission stages and outbreaks differs among parasite species. We used digital PCR to quantify the environmental transmission stages of five parasites in six lakes in southeastern Michigan every 2 weeks from June to November 2021. At the same time, we quantified infection prevalence in hosts and host density. Our study focused on eight zooplankton host species (Daphnia spp. and Ceriodaphnia dubia) and five of their parasites from diverse taxonomic groups (bacteria, yeast, microsporidia, and oomycete) with different infection mechanisms. We found that parasite transmission stage concentration increased prior to disease outbreaks for all parasites. However, parasites differed significantly in the relative timing of peaks in transmission stage concentration and infection outbreaks. The "continuous shedder" parasites had transmission stage peaks at the same time as or slightly after the outbreak peaks. In contrast, parasites relying on host death for transmission ("obligate killers") had transmission stage peaks before outbreak peaks. For most parasites, lakes with outbreaks had higher spore concentrations than those without outbreaks, especially once an outbreak began; the exception was for a parasite, Pasteuria ramosa, with very strong genotypic specificity of infection. Overall, our results show that disease outbreaks are tightly linked to transmission stage concentration; outbreaks were preceded by increases in transmission stage concentration in the environment and then were fueled by the production of more transmission stages during the outbreak itself, with concentrations decreasing to pre-outbreak levels as outbreaks waned. Thus, tracking transmission stages in the environment improves our understanding of the drivers of disease outbreaks and reveals how parasite traits may affect these dynamics.
Collapse
Affiliation(s)
- Elizabeth S Davenport
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Marcin K Dziuba
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Logan E Jacobson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Siobhan K Calhoun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kira J Monell
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Meghan A Duffy
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
7
|
Wang Y, Chen J, Na Y, Li XC, Zhou JF, Fang WH, Tan HX. Ecytonucleospora hepatopenaei n. gen. et comb. (Microsporidia: Enterocytozoonidae): A redescription of the Enterocytozoon hepatopenaei (Tourtip et al., 2009), a microsporidian infecting the widely cultivated shrimp Penaeus vannamei. J Invertebr Pathol 2023; 201:107988. [PMID: 37657756 DOI: 10.1016/j.jip.2023.107988] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/16/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
The microsporidian Enterocytozoon hepatopenaei from Penaeus vannamei (EHPPv) was redescribed on the basis of spore morphology, life cycle, pathology, and molecular character. Compared with the Enterocytozoon hepatopenaei isolated from Penaeus monodon (EHPPm), described by Tourtip et al. in 2009, new features were found in EHPPv. Electron microscopy demonstrated that EHPPv was closely associated with the nucleus of host cell. The merogony and sporogony phages were in direct contact with the cytoplasm of host cells, whereas some of the sporoblasts and the spores were surrounded by the interfacial envelope. Mature spores of EHPPv were oval and monokaryotic, measuring 1.65 ± 0.15 μm × 0.92 ± 0.05 μm. Spores possessed many polyribosomes around a bipartite polaroplast and the polar filament with 4-5 coils in two rows. Phylogenetic analyses showed all Enterocytozoon hepatopenaei isolates shared a common ancestor. Based on the morphological and molecular analyses, we propose the establishment of a new genus Ecytonucleospora and transferring Enterocytozoon hepatopenaei to the genus Ecytonucleospora, retaining the specific epithet hepatopenaei that Tourtip et al. proposed in recognition of their first research, as the new combination Ecytonucleospora hepatopenaei n. comb. Furthermore, it was suggested Enterospora nucleophila, Enterocytozoon sp. isolate RA19015_21, and Enterocytozoon schreckii be assigned into this new genus.
Collapse
Affiliation(s)
- Yuan Wang
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai 200090, China.
| | - Jie Chen
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Ying Na
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai 200090, China
| | - Xin-Cang Li
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai 200090, China
| | - Jun-Fang Zhou
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai 200090, China
| | - Wen-Hong Fang
- East China Sea Fisheries Research Institute, China Academy of Fishery Sciences, Shanghai 200090, China
| | - Hong-Xin Tan
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
| |
Collapse
|
8
|
Angst P, Ebert D, Fields PD. Population genetic analysis of the microsporidium Ordospora colligata reveals the role of natural selection and phylogeography on its extremely compact and reduced genome. G3 (BETHESDA, MD.) 2023; 13:jkad017. [PMID: 36655395 PMCID: PMC9997559 DOI: 10.1093/g3journal/jkad017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023]
Abstract
The determinants of variation in a species' genome-wide nucleotide diversity include historical, environmental, and stochastic aspects. This diversity can inform us about the species' past and present evolutionary dynamics. In parasites, the mode of transmission and the interactions with the host might supersede the effects of these aspects in shaping parasite genomic diversity. We used genomic samples from 10 populations of the microsporidian parasite Ordospora colligata to investigate present genomic diversity and how it was shaped by evolutionary processes, specifically, the role of phylogeography, co-phylogeography (with the host), natural selection, and transmission mode. Although very closely related microsporidia cause diseases in humans, O. colligata is specific to the freshwater crustacean Daphnia magna and has one of the smallest known eukaryotic genomes. We found an overlapping phylogeography between O. colligata and its host highlighting the long-term, intimate relationship between them. The observed geographic distribution reflects previous findings that O. colligata exhibits adaptations to colder habitats, which differentiates it from other microsporidian gut parasites of D. magna predominantly found in warmer areas. The co-phylogeography allowed us to calibrate the O. colligata phylogeny and thus estimate its mutation rate. We identified several genetic regions under potential selection. Our whole-genome study provides insights into the evolution of one of the most reduced eukaryotic genomes and shows how different processes shape genomic diversity of an obligate parasite.
Collapse
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| |
Collapse
|
9
|
de Albuquerque NRM, Haag KL. Using average nucleotide identity (ANI) to evaluate microsporidia species boundaries based on their genetic relatedness. J Eukaryot Microbiol 2023; 70:e12944. [PMID: 36039868 DOI: 10.1111/jeu.12944] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022]
Abstract
Microsporidia are obligatory intracellular parasites related to fungi and since their discovery their classification and origin has been controversial due to their unique morphology. Early taxonomic studies of microsporidia were based on ultrastructural spore features, characteristics of their life cycle and transmission modes. However, taxonomy and phylogeny based solely on these characteristics can be misleading. SSU rRNA is a traditional marker used in taxonomical classifications, but the power of SSU rRNA to resolve phylogenetic relationships between microsporidia is considered weak at the species level, as it may not show enough variation to distinguish closely related species. Overall genome relatedness indices (OGRI), such as average nucleotide identity (ANI), allows fast and easy-to-implement comparative measurements between genomes to assess species boundaries in prokaryotes, with a 95% cutoff value for grouping genomes of the same species. Due to the increasing availability of complete genomes, metrics of genome relatedness have been applied for eukaryotic microbes taxonomy such as microsporidia. However, the distribution of ANI values and cutoff values for species delimitation have not yet been fully tested in microsporidia. In this study we examined the distribution of ANI values for 65 publicly available microsporidian genomes and tested whether the 95% cutoff value is a good estimation for circumscribing species based on their genetic relatedness.
Collapse
Affiliation(s)
- Nathalia R M de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Karen L Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|