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Khalaf A, Lawniczak MKN, Blaxter ML, Jaron KS. Polyploidy is widespread in Microsporidia. Microbiol Spectr 2024; 12:e0366923. [PMID: 38214524 PMCID: PMC10845963 DOI: 10.1128/spectrum.03669-23] [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: 10/13/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024] Open
Abstract
Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in microsporidia is variable, with a few species formally identified as diploid and one as polyploid. Given the increase in the number of studies sequencing microsporidian genomes, it is now possible to assess ploidy levels across all currently explored microsporidian diversity. We estimate ploidy for all microsporidian data sets available on the Sequence Read Archive using k-mer-based analyses, indicating that polyploidy is widespread in Microsporidia and that ploidy change is dynamic in the group. Using genome-wide heterozygosity estimates, we also show that polyploid microsporidian genomes are relatively homozygous, and we discuss the implications of these findings on the timing of polyploidization events and their origin.IMPORTANCEMicrosporidia are single-celled intracellular parasites, distantly related to fungi, that can infect a broad range of hosts, from humans all the way to protozoans. Exploiting the wealth of microsporidian genomic data available, we use k-mer-based analyses to assess ploidy status across the group. Understanding a genome's ploidy is crucial in order to assemble it effectively and may also be relevant for better understanding a parasite's behavior and life cycle. We show that tetraploidy is present in at least six species in Microsporidia and that these polyploidization events are likely to have occurred independently. We discuss why these findings may be paradoxical, given that Microsporidia, like other intracellular parasites, have extremely small, reduced genomes.
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Affiliation(s)
- Amjad Khalaf
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Mark L. Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Kamil S. Jaron
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
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Svedberg D, Winiger RR, Berg A, Sharma H, Tellgren-Roth C, Debrunner-Vossbrinck BA, Vossbrinck CR, Barandun J. Functional annotation of a divergent genome using sequence and structure-based similarity. BMC Genomics 2024; 25:6. [PMID: 38166563 PMCID: PMC10759460 DOI: 10.1186/s12864-023-09924-y] [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: 08/27/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes. RESULTS In this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes. CONCLUSION We provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.
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Affiliation(s)
- Dennis Svedberg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Rahel R Winiger
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Himanshu Sharma
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Charles R Vossbrinck
- Department of Environmental Science, Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden.
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Milner DS, Galindo LJ, Irwin NAT, Richards TA. Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes. Annu Rev Microbiol 2023; 77:45-66. [PMID: 36944262 DOI: 10.1146/annurev-micro-032421-115538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.
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Affiliation(s)
- David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom;
| | | | - Nicholas A T Irwin
- Department of Biology, University of Oxford, Oxford, United Kingdom;
- Merton College, University of Oxford, Oxford, United Kingdom
| | - Thomas A Richards
- Department of Biology, University of Oxford, Oxford, United Kingdom;
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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.
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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
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Microsporidia: a new taxonomic, evolutionary, and ecological synthesis. Trends Parasitol 2022; 38:642-659. [PMID: 35667993 DOI: 10.1016/j.pt.2022.05.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 02/08/2023]
Abstract
Microsporidian diversity is vast. There is a renewed drive to understand how microsporidian pathological, genomic, and ecological traits relate to their phylogeny. We comprehensively sample and phylogenetically analyse 125 microsporidian genera for which sequence data are available. Comparing these results with existing phylogenomic analyses, we suggest an updated taxonomic framework to replace the inconsistent clade numbering system, using informal taxonomic names: Glugeida (previously clades 5/3), Nosematida (4a), Enterocytozoonida (4b), Amblyosporida (3/5), Neopereziida (1), and Ovavesiculida (2). Cellular, parasitological, and ecological traits for 281 well-defined species are compared with identify clade-specific patterns across long-branch Microsporidia. We suggest that future taxonomic circumscriptions of Microsporidia should involve additional markers (SSU/ITS/LSU), and that a comprehensive suite of phenotypic and ecological traits help to predict broad microsporidian functional and lineage diversity.
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Angst P, Ebert D, Fields PD. Demographic history shapes genomic variation in an intracellular parasite with a wide geographic distribution. Mol Ecol 2022; 31:2528-2544. [DOI: 10.1111/mec.16419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Peter D. Fields
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
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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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Wadi L, Reinke AW. Evolution of microsporidia: An extremely successful group of eukaryotic intracellular parasites. PLoS Pathog 2020; 16:e1008276. [PMID: 32053705 PMCID: PMC7017984 DOI: 10.1371/journal.ppat.1008276] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Lina Wadi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aaron W. Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Li W, Xiao L. Multilocus Sequence Typing and Population Genetic Analysis of Enterocytozoon bieneusi: Host Specificity and Its Impacts on Public Health. Front Genet 2019; 10:307. [PMID: 31001333 PMCID: PMC6454070 DOI: 10.3389/fgene.2019.00307] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/20/2019] [Indexed: 01/13/2023] Open
Abstract
Microsporidia comprise a large class of unicellular eukaryotic pathogens that are medically and agriculturally important, but poorly understood. There have been nearly 1,500 microsporidian species described thus far, which are variable in biology, genetics, genomics, and host specificity. Among those, Enterocytozoon bieneusi is the well-known species responsible for the most recorded cases of human microsporidian affections. The pathogen can colonize a broad range of mammals and birds and most of the animals surveyed share some genotypes with humans, posing a threat to public health. Based on DNA sequence analysis of the ribosomal internal transcribed spacer (ITS) and phylogenetic analysis, several hundreds of E. bieneusi genotypes have been defined and clustered into different genetic groups with varied levels of host specificity. However, single locus-based typing using ITS might have insufficient resolution to discriminate among E. bieneusi isolates with complex genetic or hereditary characteristics and to assess the elusive reproduction or transmission modes of the organism, highlighting the need for exploration and application of multilocus sequence typing (MLST) and population genetic tools. The present review begins with a primer on microsporidia and major microsporidian species, briefly introduces the recent advances on E. bieneusi ITS genotyping and phylogeny, summarizes recent MLST and population genetic data, analyzes the inter- and intragroup host specificity at the MLST level, and interprets the public health implications of host specificity in zoonotic or cross-species transmission of this ubiquitous fungus.
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Affiliation(s)
- Wei Li
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Lihua Xiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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10
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Bass D, Czech L, Williams BAP, Berney C, Dunthorn M, Mahé F, Torruella G, Stentiford GD, Williams TA. Clarifying the Relationships between Microsporidia and Cryptomycota. J Eukaryot Microbiol 2018; 65:773-782. [PMID: 29603494 PMCID: PMC6282948 DOI: 10.1111/jeu.12519] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/02/2018] [Accepted: 03/20/2018] [Indexed: 01/27/2023]
Abstract
Some protists with microsporidian-like cell biological characters, including Mitosporidium, Paramicrosporidium, and Nucleophaga, have SSU rRNA gene sequences that are much less divergent than canonical Microsporidia. We analysed the phylogenetic placement and environmental diversity of microsporidian-like lineages that group near the base of the fungal radiation and show that they group in a clade with metchnikovellids and canonical microsporidians, to the exclusion of the clade including Rozella, in line with what is currently known of their morphology and cell biology. These results show that the phylogenetic scope of Microsporidia has been greatly underestimated. We propose that much of the lineage diversity previously thought to be cryptomycotan/rozellid is actually microsporidian, offering new insights into the evolution of the highly specialized parasitism of canonical Microsporidia. This insight has important implications for our understanding of opisthokont evolution and ecology, and is important for accurate interpretation of environmental diversity. Our analyses also demonstrate that many opisthosporidian (aphelid+rozellid+microsporidian) SSU V4 OTUs from Neotropical forest soils group with the short-branching Microsporidia, consistent with the abundance of their protist and arthropod hosts in soils. This novel diversity of Microsporidia provides a unique opportunity to investigate the evolutionary origins of a highly specialized clade of major animal parasites.
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Affiliation(s)
- David Bass
- Pathology and Microbial Systematics Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, DT4 8UB, UK.,Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Lucas Czech
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg, Heidelberg, 69118, Germany
| | - Bryony A P Williams
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Cédric Berney
- Sorbonne Université & CNRS, UMR 7144 (AD2M), Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Guifré Torruella
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Grant D Stentiford
- Pathology and Microbial Systematics Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, DT4 8UB, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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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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