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Webster VL, Hemmings S, Pérez M, Fisher MC, Brown MJF, Farrer RA. Revealing the genome of the microsporidian Vairimorpha bombi, a potential driver of bumble bee declines in North America. G3 (BETHESDA, MD.) 2024; 14:jkae029. [PMID: 38334143 PMCID: PMC10989860 DOI: 10.1093/g3journal/jkae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Pollinators are vital for food security and the maintenance of terrestrial ecosystems. Bumblebees are important pollinators across northern temperate, arctic, and alpine ecosystems, yet are in decline across the globe. Vairimorpha bombi is a parasite belonging to the fungal class Microsporidia that has been implicated in the rapid decline of bumblebees in North America, where it may be an emerging infectious disease. To investigate the evolutionary basis of pathogenicity of V. bombi, we sequenced and assembled its genome using Oxford Nanopore and Illumina technologies and performed phylogenetic and genomic evolutionary analyses. The genome assembly for V. bombi is 4.73 Mb, from which we predicted 1,870 protein-coding genes and 179 tRNA genes. The genome assembly has low repetitive content and low GC content. V. bombi's genome assembly is the smallest of the Vairimorpha and closely related Nosema genera, but larger than those found in the Encephalitozoon and Ordospora sister clades. Orthology and phylogenetic analysis revealed 18 core conserved single-copy microsporidian genes including the histone acetyltransferase (HAT) GCN5. Surprisingly, V. bombi was unique to the microsporidia in not encoding the second predicted HAT ESA1. The V. bombi genome assembly annotation included 265 unique genes (i.e. not predicted in other microsporidia genome assemblies), 20% of which encode a secretion signal, which is a significant enrichment. Intriguingly, of the 36 microsporidian genomes we analyzed, 26 also had a significant enrichment of secreted signals encoded by unique genes, ranging from 6 to 71% of those predicted genes. These results suggest that microsporidia are under selection to generate and purge diverse and unique genes encoding secreted proteins, potentially contributing to or facilitating infection of their diverse hosts. Furthermore, V. bombi has 5/7 conserved spore wall proteins (SWPs) with its closest relative V. ceranae (that primarily infects honeybees), while also uniquely encoding four additional SWPs. This gene class is thought to be essential for infection, providing both environmental protection and recognition and uptake into the host cell. Together, our results show that SWPs and unique genes encoding a secretion signal are rapidly evolving in the microsporidia, suggesting that they underpin key pathobiological traits including host specificity and pathogenicity.
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Affiliation(s)
- Victoria L Webster
- Department of Biological Sciences, Royal Holloway University of London, London TW20 0EX, UK
| | - Samuel Hemmings
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK
| | - Marta Pérez
- Department of Biological Sciences, Royal Holloway University of London, London TW20 0EX, UK
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK
| | - Mark J F Brown
- Department of Biological Sciences, Royal Holloway University of London, London TW20 0EX, UK
| | - Rhys A Farrer
- MRC Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, UK
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Tournayre J, Polonais V, Wawrzyniak I, Akossi RF, Parisot N, Lerat E, Delbac F, Souvignet P, Reichstadt M, Peyretaillade E. MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation. Int J Mol Sci 2024; 25:880. [PMID: 38255958 PMCID: PMC10815200 DOI: 10.3390/ijms25020880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
With nearly 1700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help understand the biological functions of these microorganisms, complete genome sequencing is routinely used. Nevertheless, the proper prediction of their gene catalogue is challenging due to their taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small gene (<300 bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot's accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides an accurate prediction of translation initiation sites, an efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes, including those under 300 bp.
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Affiliation(s)
- Jérémy Tournayre
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Valérie Polonais
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Ivan Wawrzyniak
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Reginald Florian Akossi
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Nicolas Parisot
- UMR 203, BF2I, INRAE, INSA Lyon, Université de Lyon, 69621 Villeurbanne, France
| | - Emmanuelle Lerat
- VAS, CNRS, UMR5558, LBBE, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France;
| | - Frédéric Delbac
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Pierre Souvignet
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Matthieu Reichstadt
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Eric Peyretaillade
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
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Wijayawardene NN, Boonyuen N, Ranaweera CB, de Zoysa HKS, Padmathilake RE, Nifla F, Dai DQ, Liu Y, Suwannarach N, Kumla J, Bamunuarachchige TC, Chen HH. OMICS and Other Advanced Technologies in Mycological Applications. J Fungi (Basel) 2023; 9:688. [PMID: 37367624 DOI: 10.3390/jof9060688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.
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Affiliation(s)
- Nalin N Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chathuranga B Ranaweera
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, General Sir John Kotelawala Defence University Sri Lanka, Kandawala Road, Rathmalana 10390, Sri Lanka
| | - Heethaka K S de Zoysa
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Rasanie E Padmathilake
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Pulliyankulama, Anuradhapura 50000, Sri Lanka
| | - Faarah Nifla
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Dong-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Yanxia Liu
- Guizhou Academy of Tobacco Science, No.29, Longtanba Road, Guanshanhu District, Guiyang 550000, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thushara C Bamunuarachchige
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Huan-Huan Chen
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Agricultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Xiong X, Geden CJ, Bergstralh DT, White RL, Werren JH, Wang X. New insights into the genome and transmission of the microsporidian pathogen Nosema muscidifuracis. Front Microbiol 2023; 14:1152586. [PMID: 37125197 PMCID: PMC10133504 DOI: 10.3389/fmicb.2023.1152586] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Nosema is a diverse genus of unicellular microsporidian parasites of insects and other arthropods. Nosema muscidifuracis infects parasitoid wasp species of Muscidifurax zaraptor and M. raptor (Hymenoptera: Pteromalidae), causing ~50% reduction in longevity and ~90% reduction in fecundity. Methods and Results Here, we report the first assembly of the N. muscidifuracis genome (14,397,169 bp in 28 contigs) of high continuity (contig N50 544.3 Kb) and completeness (BUSCO score 97.0%). A total of 2,782 protein-coding genes were annotated, with 66.2% of the genes having two copies and 24.0% of genes having three copies. These duplicated genes are highly similar, with a sequence identity of 99.3%. The complex pattern suggests extensive gene duplications and rearrangements across the genome. We annotated 57 rDNA loci, which are highly GC-rich (37%) in a GC-poor genome (25% genome average). Nosema-specific qPCR primer sets were designed based on 18S rDNA annotation as a diagnostic tool to determine its titer in host samples. We discovered high Nosema titers in Nosema-cured M. raptor and M. zaraptor using heat treatment in 2017 and 2019, suggesting that the remedy did not completely eliminate the Nosema infection. Cytogenetic analyses revealed heavy infections of N. muscidifuracis within the ovaries of M. raptor and M. zaraptor, consistent with the titer determined by qPCR and suggesting a heritable component of infection and per ovum vertical transmission. Discussion The parasitoids-Nosema system is laboratory tractable and, therefore, can serve as a model to inform future genome manipulations of Nosema-host system for investigations of Nosemosis.
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Affiliation(s)
- Xiao Xiong
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital, Shanghai Sunshine Rehabilitation Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Christopher J. Geden
- Center for Medical, Agricultural and Veterinary Entomology, USDA Agricultural Research Service, Gainesville, FL, United States
| | - Dan T. Bergstralh
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Roxie L. White
- Center for Medical, Agricultural and Veterinary Entomology, USDA Agricultural Research Service, Gainesville, FL, United States
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Department of Entomology and Plant Pathology, College of Agriculture, Auburn University, AL, United States
- Alabama Agricultural Experiment Station, Center for Advanced Science, Innovation and Commerce, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
- *Correspondence: Xu Wang,
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Wei X, Zheng J, Evans JD, Huang Q. Transgenerational genomic analyses reveal allelic oscillation and purifying selection in a gut parasite Nosema ceranae. Front Microbiol 2022; 13:927892. [PMID: 36386715 PMCID: PMC9664190 DOI: 10.3389/fmicb.2022.927892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Standing genetic variation is the predominant source acted on by selection. Organisms with high genetic diversity generally show faster responses toward environmental change. Nosema ceranae is a microsporidian parasite of honey bees, infecting midgut epithelial cells. High genetic diversity has been found in this parasite, but the mechanism for the parasite to maintain this diversity remains unclear. This study involved continuous inoculation of N. ceranae to honey bees. We found that the parasites slowly increased genetic diversity over three continuous inoculations. The number of lost single nucleotide variants (SNVs) was balanced with novel SNVs, which were mainly embedded in coding regions. Classic allele frequency oscillation was found at the regional level along the genome, and the associated genes were enriched in apoptosis regulation and ATP binding. The ratio of synonymous and non-synonymous substitution suggests a purifying selection, and our results provide novel insights into the evolutionary dynamics in microsporidian parasites.
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Affiliation(s)
- Xiuxiu Wei
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang, China,Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Jialan Zheng
- College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Jay D. Evans
- USDA-ARS Bee Research Laboratory, Beltsville, MD, United States
| | - Qiang Huang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang, China,Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China,*Correspondence: Qiang Huang,
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Wei X, Evans JD, Chen Y, Huang Q. Spillover and genome selection of the gut parasite Nosema ceranae between honey bee species. Front Cell Infect Microbiol 2022; 12:1026154. [PMID: 36304932 PMCID: PMC9592821 DOI: 10.3389/fcimb.2022.1026154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
Nosema ceranae is a honey bee gut parasite that has recently spilled to another honey bee host through trading. The impact of infection on the native host is minor, which is substantial in the novel host. In this study, artificial inoculation simulated the parasite transmission from the native to the novel host. We found that the parasite initiated proliferation earlier in the novel host than in the native host. Additionally, parasite gene expression was significantly higher when infecting the novel host compared with the native host, leading to a significantly higher number of spores. Allele frequencies were similar for spores of parasites infecting both native and novel hosts. This suggests that the high number of spores found in the novel host was not caused by a subset of more fit spores from native hosts. Native hosts also showed a higher number of up-regulated genes in response to infection when compared with novel hosts. Our data further showed that native hosts suppressed parasite gene expression and arguably sacrificed cells to limit the parasite. The results provide novel insights into host defenses and gene selection during a parasite spillover event.
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Affiliation(s)
- Xiuxiu Wei
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Jay D. Evans
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, MD, United States
| | - Yanping Chen
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, MD, United States
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
- *Correspondence: Qiang Huang,
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Li YH, Chang ZT, Yen MR, Huang YF, Chen TH, Chang JC, Wu MC, Yang YL, Chen YW, Nai YS. Transcriptome of Nosema ceranae and Upregulated Microsporidia Genes during Its Infection of Western Honey Bee ( Apis mellifera). INSECTS 2022; 13:716. [PMID: 36005340 PMCID: PMC9409478 DOI: 10.3390/insects13080716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Nosema ceranae is one of the fungal parasites of Apis mellifera. It causes physical and behavioral effects in honey bees. However, only a few studies have reported on gene expression profiling during A. mellifera infection. In this study, the transcriptome profile of mature spores at each time point of infection (5, 10, and 20 days post-infection, d.p.i.) were investigated. Based on the transcriptome and expression profile analysis, a total of 878, 952, and 981 differentially expressed genes (DEGs) (fold change ≥ 2 or ≤ -2) were identified in N. ceranae spores (NcSp) at 5 d.p.i., 10 d.p.i., and 20 d.p.i., respectively. Moreover, 70 upregulated genes and 340 downregulated genes among common DEGs (so-called common DEGs) and 166 stage-specific genes at each stage of infection were identified. The Gene Ontology (GO) analysis indicated that the DEGs and corresponding common DEGs are involved in the functions of cytosol (GO:0005829), cytoplasm (GO:0005737), and ATP binding (GO:0005524). Furthermore, the pathway analysis found that the DEGs and common DEGs are involved in metabolism, environmental information processing, and organismal systems. Four upregulated common DEGs with higher fold-change values, highly associated with spore proteins and transcription factors, were selected for validation. In addition, the stage-specific genes are highly involved in the mechanism of pre-mRNA splicing according to GO enrichment analysis; thus, three of them showed high expression at each d.p.i. and were also subjected to validation. The relative gene expression levels showed a similar tendency as the transcriptome predictions at different d.p.i., revealing that the gene expression of N. ceranae during infection may be related to the mechanism of gene transcription, protein synthesis, and structural proteins. Our data suggest that the gene expression profiling of N. ceranae at the transcriptomic level could be a reference for the monitoring of nosemosis at the genetic level.
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Affiliation(s)
- Yi-Hsuan Li
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Zih-Ting Chang
- Department of Biotechnology and Animal Science, National Ilan University, Yi-Lan City 26047, Taiwan
| | - Ming-Ren Yen
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Yu-Feng Huang
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
- Department of Computer Science and Engineering, Yuan-Ze University, Tao-Yuan City 32003, Taiwan
| | - Tzu-Han Chen
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Ju-Chun Chang
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Ming-Cheng Wu
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei City 11529, Taiwan
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan
| | - Yue-Wen Chen
- Department of Biotechnology and Animal Science, National Ilan University, Yi-Lan City 26047, Taiwan
| | - Yu-Shin Nai
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
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Molecular Detection and Differentiation of Arthropod, Fungal, Protozoan, Bacterial and Viral Pathogens of Honeybees. Vet Sci 2022; 9:vetsci9050221. [PMID: 35622749 PMCID: PMC9145064 DOI: 10.3390/vetsci9050221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023] Open
Abstract
The honeybee Apis mellifera is highly appreciated worldwide because of its products, but also as it is a pollinator of crops and wild plants. The beehive is vulnerable to infections due to arthropods, fungi, protozoa, bacteria and/or viruses that manage to by-pass the individual and social immune mechanisms of bees. Due to the close proximity of bees in the beehive and their foraging habits, infections easily spread within and between beehives. Moreover, international trade of bees has caused the global spread of infections, several of which result in significant losses for apiculture. Only in a few cases can infections be diagnosed with the naked eye, by direct observation of the pathogen in the case of some arthropods, or by pathogen-associated distinctive traits. Development of molecular methods based on the amplification and analysis of one or more genes or genomic segments has brought significant progress to the study of bee pathogens, allowing for: (i) the precise and sensitive identification of the infectious agent; (ii) the analysis of co-infections; (iii) the description of novel species; (iv) associations between geno- and pheno-types and (v) population structure studies. Sequencing of bee pathogen genomes has allowed for the identification of new molecular targets and the development of specific genotypification strategies.
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Ke L, Yan WY, Zhang LZ, Zeng ZJ, Evans JD, Huang Q. Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae. MICROBIAL ECOLOGY 2022; 83:1105-1111. [PMID: 34342699 DOI: 10.1007/s00248-021-01827-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.
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Affiliation(s)
- Li Ke
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Wei Yu Yan
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Li Zhen Zhang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Zhi Jiang Zeng
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Jay D Evans
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, MD, 20705, USA
| | - Qiang Huang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China.
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Williams BAP, Williams TA, Trew J. Comparative Genomics of Microsporidia. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 114:43-69. [PMID: 35543998 DOI: 10.1007/978-3-030-93306-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The microsporidia are a phylum of intracellular parasites that represent the eukaryotic cell in a state of extreme reduction, with genomes and metabolic capabilities embodying eukaryotic cells in arguably their most streamlined state. Over the past 20 years, microsporidian genomics has become a rapidly expanding field starting with sequencing of the genome of Encephalitozoon cuniculi, one of the first ever sequenced eukaryotes, to the current situation where we have access to the data from over 30 genomes across 20+ genera. Reaching back further in evolutionary history, to the point where microsporidia diverged from other eukaryotic lineages, we now also have genomic data for some of the closest known relatives of the microsporidia such as Rozella allomycis, Metchnikovella spp. and Amphiamblys sp. Data for these organisms allow us to better understand the genomic processes that shaped the emergence of the microsporidia as a group. These intensive genomic efforts have revealed some of the processes that have shaped microsporidian cells and genomes including patterns of genome expansions and contractions through gene gain and loss, whole genome duplication, differential patterns of invasion and purging of transposable elements. All these processes have been shown to occur across short and longer time scales to give rise to a phylum of parasites with dynamic genomes with a diversity of sizes and organisations.
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Affiliation(s)
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jahcub Trew
- School of Biosciences, University of Exeter, Exeter, UK
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