| 1. |
- Bernal, Ximena E., et al.
(författare)
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Empowering Latina scientists
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 363:6429, s. 825-826
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
- Abarenkov, Kessy, et al.
(författare)
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The curse of the uncultured fungus
- 2022
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Ingår i: MycoKeys. - 1314-4057 .- 1314-4049. ; 86, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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| 3. |
- Abarenkov, Kessy, et al.
(författare)
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The curse of the uncultured fungus
- 2022
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :86, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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| 4. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 5. |
- Eshghi Sahraei, Shadi, et al.
(författare)
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Bringing uncultured arbuscular mycorrhizal fungi to the genomic era – a case study with field spores of Funneliformis geosporum
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Arbuscular mycorrhizal (AM) fungi are ubiquitous microorganisms, forming symbiosis with most terrestrial plants. The fungal partner improves host performance by providing nutrients like P and N and increase tolerance of host plants against biotic and abiotic stresses. Most studies on AM fungi have focused on species and strains maintained on a single plant host under controlled conditions for several years. There is some evidence suggesting this cultivation system can render phenotypic and genotypic variations in AM fungi. In this study, we isolated spores of AM fungi from a field, the spores were identified as Funneliformis geosporum based on morphology and phylogenetic analyses. We assembled the genomes of two spores using individually amplified and sequenced nuclei. The genomes were compared with other members of Glomeraceae including two strains of F. mosseae, which have been maintained in culture for more than 20 years. No significant differences were observed among them in terms of gene content, while the SNP density was higher in the strains of F. geosporum when compared to the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble the genomes from AM fungal spores sampled in the field, which opens up the possibility to study genomic variation in natural populations of this important plant symbionts.
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| 6. |
- Eshghi Sahraei, Shadi, et al.
(författare)
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Evolution and genomic signatures of arbuscular mycorrhizal fungi
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungi include at least two lineages of mutualistic plant symbionts, the arbuscular mycorrhizal fungi and the mycorrhizal fungi in Endogonales, as well as fungi with saprotrophic, pathogenic and endophytic life styles. Their evolutionary relationships remained enigmatic and the taxonomic rank is currently fluid. We recognize three phyla and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as the sister to Mucoromycota and Mortierellomycota. Analysis of gene family contractions and expansions indicate that arbuscular mycorrhizae (AM) fungi and Endogonales represent two independent transitions to mutualistic plant symbiosis and that these occurred early in the divergence of these lineages.
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| 7. |
- Eshghi Sahraei, Shadi, et al.
(författare)
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Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum
- 2022
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Ingår i: Mycorrhiza. - : Springer. - 0940-6360 .- 1432-1890. ; 32:5-6, s. 361-371
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Tidskriftsartikel (refereegranskat)abstract
- Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis of AM fungi has long been restricted to species and strains that can be maintained under controlled conditions that facilitate collection of biological samples. There is some evidence suggesting that AM fungi can adapt to culture resulting in phenotypic and possibly also genotypic changes in the fungi. In this study, we used field isolated spores of AM fungi and identified them as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two representative spores using DNA sequences of 19 and 22 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum than in the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic and comparative genomic analysis and to study genomic variation in natural populations of these important plant symbionts.
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| 8. |
- Kluting, Kerri L., et al.
(författare)
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Another dark taxon comes to light: Eludereomycetes, class nov. (Pucciniomycotina, Basidiomycota), and its first known living representative, Eluderea minerophilus, gen. et sp. nov.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Only a small fraction of the world’s fungi is described, and the large number of unnamed fungal sequences from environmental DNA serves as a significant complication for taxonomic identification in metabarcoding studies. There are several deeply diverged fungal lineages—some hypothesized to represent class and order ranks—currently known only by environmental DNA sequences that represent them. Here, we describe a previously unidentified fungal culture as the first living representative of one of these lineages (previously referred to as ‘clade GS25’, hypothesized as an early diverging lineage sister to the Pucciniomycotina, Basidiomycota) and present its sequenced genome. We used a phylogenomic approach to test the placement and taxonomic rank of this lineage. We formally describe the first known species in Eludereomycetes, class nov. (Pucciniomycotina, Basidiomycota): Eluderea minerophilus, gen. et sp. nov. This species was isolated from Pinus sylvestris roots collected from a Swedish pine forest, where previously published environmental sequencing data from the site indicate that it is almost exclusively found in the deeper mineral soil horizons. Our analysis shows that the most closely related described species to E. minerophilus likely belongs to the Classiculomycetes, a class within the Pucciniomycotina that is morphologically, molecularly, and ecologically distinct from the Eludereomycetes. Identification of a living representative for this lineage previously detected in environmental DNA, ‘clade GS25’, and describing it as a new species was a somewhat serendipitous discovery made possible in part due to characteristics of two previously published studies. We call attention to some of these aspects and propose a set of practices that could be adopted by the research community to help facilitate more connections between living fungus and environmental DNA sequence. The use of such practices would in turn help to alleviate some of the complications associated with unidentified fungal DNA sequences in reference databases and contribute towards a more complete understanding of fungal diversity.
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| 9. |
- Looney, Brian P., et al.
(författare)
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Into and out of the tropics : global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:2, s. 630-647
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Tidskriftsartikel (refereegranskat)abstract
- Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.
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| 10. |
- Manyara, David, et al.
(författare)
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Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198
- 2024
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Ingår i: G3. - London : Oxford University Press. - 2160-1836. ; 14:6
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Tidskriftsartikel (refereegranskat)abstract
- Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.
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| 11. |
- Manyara, David, et al.
(författare)
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Nuclei size variation within strains of arbuscular mycorrhizal fungi in Diversisporales
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Arbuscular mycorrhizal (AM) fungi are obligate root symbionts that play a crucial role in terrestrial ecosystems by aiding land plants in nutrient and water absorption in exchange for photosynthetically fixed carbon. AM fungal nuclear genomes exhibit considerable variation in size across families, ranging from approximately 40 megabases in Paraglomeraceae species to several hundred megabases in Gigasporaceae species. Notable variations in nuclei size have also been observed within the Diversisporales family. In this study, we investigated the genomic organization of three AM fungal isolates within the Diversisporales family. The three isolates exhibited a distinct separation of forward-scattered light during nuclei sorting with Fluorescence-Activated Cell Sorting (FACS), indicating variations in their nuclear sizes. Despite the significant differences in nuclear sizes between the large and small nuclei in two isolates, our analyses revealed that all nuclei in the three isolates were haploid and homokaryotic. The isolates exhibited low intra-isolate genetic variation, and only one putative mating-type (mat) locus was recovered in most single nuclei across the three isolates, further supporting their homokaryotic genome organization. Interestingly, we observed substantial structural divergence of the putative mat locus, corroborating a previous report where the HD-1-like and HD-2 mat genes were found on different genomic contigs in Gigasporaceae strains. Our findings suggest that the different nuclear sizes are likely due to asynchronous nuclear division within spores and provide insights into the genomic organization of the understudied Diversisporales lineage.
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| 12. |
- Manyara, David, et al.
(författare)
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Optimal practices: From Arbuscular Mycorrhizal Fungal spore to genome assembly
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Arbuscular mycorrhizal (AM) fungi are essential to terrestrial ecosystems, yet their genomic study is fraught with challenges. Traditional sequencing methods are often limited by difficulties in obtaining pure, high-quality DNA and the complexity of AM fungal genomes. This paper describes a refined protocol for single nuclei sequencing of AM fungi, addressing key obstacles and providing practical solutions to enhance genomic research in this ecologically important group. The protocol involves outsourcing certain steps, such as sequencing library preparation and Illumina sequencing, to other facilities, while other steps, like generating single nuclei and combined assemblies, follow a published method and are not described in detail here. This method allows for the direct acquisition of sequence data from single nuclei, circumventing the time-consuming and laborious process of cultivating axenic cultures.
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| 13. |
- Manyara, David, et al.
(författare)
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Purifying Selection and Persistent Polymorphism among Nuclei in the Multinucleate Arbuscular Mycorrhizal Fungi
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Arbuscular mycorrhizal (AM) fungi form an obligate symbiosis with the roots of the majority of land plants and are found in all terrestrial ecosystems. The source and structure of genetic variation in AM fungi has remained an enigma due to difficulties in the axenic cultivation and generation of high-quality genome assemblies from most species. Furthermore, how AM fungi survive long-term without a known single nucleus per cell stage in their life cycle is puzzling. Purifying selection acting at the nuclear level has been hypothesized as a mechanism to purge deleterious mutations. In this study, we aimed to characterize both intra- and inter-organismal genetic variation in AM fungi by analyzing genomic information from individual nuclei of three strains of two species in the genus Claroideoglomus. We observed overall low levels of genetic variation within the strains, most of which represent rare variants and with average dN/dS ratios within nuclei indicating that these are kept at low frequency by purifying selection. We also observed sites that are maintained as polymorphic across both strains and species, and discuss different models to explain this pattern. The results in this study affirm our conceptual understanding that nuclei in AM fungal strains function as populations of asexually reproducing units with strong signals of purifying selection on nuclei within the strains.
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| 14. |
- Montoliu-Nerin, Merce, et al.
(författare)
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Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.
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| 15. |
- Montoliu-Nerin, Merce, et al.
(författare)
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In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
- 2021
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Ingår i: Frontiers in Fungal Biology. - : Frontiers Media S.A.. - 2673-6128. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.
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| 16. |
- Montoliu-Nerin, Merce, 1991-, et al.
(författare)
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In-depth phylogenomic analysis of Glomeromycota based on a comprehensive set of de novogenome assemblies
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have been the bases of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the AM fungi phylogeny will depend upon a more extensive ortholog sampling, resulting from a wider range of available whole genome sequences from a large set of taxa. To circumvent the need for axenic culturing of AM fungi we use single nuclei sequencing to generate de novogenome assemblies of AM fungi covering seven families of Glomeromycota. The predicted genes of these assemblies, together with the available protein sequences of AM fungi and sister clades, were used for phylogenomic analysis. We confirm that our novel workflow generates high quality genome assemblies suitable for phylogenomic analysis of AM fungi. Within the monophyletic phylum Glomeromycota, we identify three candidate topologies, in which the family Glomerales is recovered as polyphyletic in two of them. Our results support family level classification from previous phylogenetic studies using sequences of the rDNA operon. Our multi-locus analyses identify alternative evolutionary histories within this diverse phylum.
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| 17. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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How, not if, is the question mycologists should be asking about DNA-based typification
- 2023
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :96, s. 143-157
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Tidskriftsartikel (refereegranskat)abstract
- Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
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| 18. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Tidskriftsartikel (refereegranskat)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 19. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory
- 2017
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 26, s. 13-24
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Tidskriftsartikel (refereegranskat)abstract
- DNA sequences are increasingly used for taxonomic and functional assessment of environmental communities. In mycology, the nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen marker for such pursuits. Molecular identification is associated with many challenges, one of which is low read quality of the reference sequences used for inference of taxonomic and functional properties of the newly sequenced community (or single taxon). This study investigates whether public fungal ITS sequences are subjected to sufficient trimming in their distal (5’ and 3’) ends prior to deposition in the public repositories. We examined 86 species (and 10,584 sequences) across the fungal tree of life, and we found that on average 13.1% of the sequences were poorly trimmed in one or both of their 5’ and 3’ ends. Deposition of poorly trimmed entries was found to continue through 2016. Poorly trimmed reference sequences add noise and mask biological signal in sequence similarity searches and phylogenetic analyses, and we provide a set of recommendations on how to manage the sequence trimming problem.
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| 20. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Top 50 most wanted fungi
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
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Tidskriftsartikel (refereegranskat)abstract
- Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.
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| 21. |
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| 22. |
- Poorter, Lourens, et al.
(författare)
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Functional recovery of secondary tropical forests
- 2021
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 118:49, s. e2003405118-e2003405118
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Tidskriftsartikel (refereegranskat)abstract
- One-third of all Neotropical forests are secondary forests that regrow naturally after agricultural use through secondary succession. We need to understand better how and why succession varies across environmental gradients and broad geographic scales. Here, we analyze functional recovery using community data on seven plant characteristics (traits) of 1,016 forest plots from 30 chronosequence sites across the Neotropics. By analyzing communities in terms of their traits, we enhance understanding of the mechanisms of succession, assess ecosystem recovery, and use these insights to propose successful forest restoration strategies. Wet and dry forests diverged markedly for several traits that increase growth rate in wet forests but come at the expense of reduced drought tolerance, delay, or avoidance, which is important in seasonally dry forests. Dry and wet forests showed different successional pathways for several traits. In dry forests, species turnover is driven by drought tolerance traits that are important early in succession and in wet forests by shade tolerance traits that are important later in succession. In both forests, deciduous and compound-leaved trees decreased with forest age, probably because microclimatic conditions became less hot and dry. Our results suggest that climatic water availability drives functional recovery by influencing the start and trajectory of succession, resulting in a convergence of community trait values with forest age when vegetation cover builds up. Within plots, the range in functional trait values increased with age. Based on the observed successional trait changes, we indicate the consequences for carbon and nutrient cycling and propose an ecologically sound strategy to improve forest restoration success.
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| 23. |
- Poorter, Lourens, et al.
(författare)
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Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
- 2019
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Ingår i: Nature Ecology & Evolution. - : Nature Publishing Group. - 2397-334X. ; 3:6, s. 928-934
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Tidskriftsartikel (refereegranskat)abstract
- Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.
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| 24. |
- Rosling, Anna, 1974-, et al.
(författare)
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Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis
- 2024
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 25:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid.Results: In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89.Conclusion: Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.
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| 25. |
- Sanchez-Garcia, Marisol
(författare)
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A new order, Entrophosporales, and three new Entrophospora species in Glomeromycota
- 2022
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- As a result of phylogenomic, phylogenetic, and morphological analyses of members of the genus Claroideoglomus, four potential new glomoid spore-producing species and Entrophospora infrequens, a new order, Entrophosporales, with one family, Entrophosporaceae (=Claroideoglomeraceae), was erected in the phylum Glomeromycota. The phylogenomic analyses recovered the Entrophosporales as sister to a clade formed by Diversisporales and Glomeraceae. The strongly conserved entrophosporoid morph of E. infrequens, provided with a newly designated epitype, was shown to represent a group of cryptic species with the potential to produce different glomoid morphs. Of the four potential new species, three enriched the Entrophosporales as new Entrophospora species, E. argentinensis, E. glacialis, and E. furrazolae, which originated from Argentina, Sweden, Oman, and Poland. The fourth fungus appeared to be a glomoid morph of the E. infrequens epitype. The physical association of the E. infrequens entrophosporoid and glomoid morphs was reported and illustrated here for the first time. The phylogenetic analyses, using nuc rDNA and rpb1 concatenated sequences, confirmed the previous conclusion that the genus Albahypha in the family Entrophosporaceae sensu Oehl et al. is an unsupported taxon. Finally, the descriptions of the Glomerales, Entrophosporaceae, and Entrophospora were emended and new nomenclatural combinations were introduced.
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| 26. |
- Sanchez-Garcia, Marisol
(författare)
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Brazilian fungal diversity represented by DNA markers generated over 20 years
- 2020
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Ingår i: Brazilian Journal of Microbiology. - : Springer Science and Business Media LLC. - 1517-8382 .- 1678-4405. ; 51, s. 729-749
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Tidskriftsartikel (refereegranskat)abstract
- Molecular techniques using fungal DNA barcoding (ITS) and other markers have been key to identifying the biodiversity of different geographic areas, mainly in megadiverse countries. Here, we provide an overview of the fungal diversity in Brazil based on DNA markers of phylogenetic importance generated since 1996. We retrieved fungal sequences of ITS, LSU, SSU, tef1-alpha, beta-tubulin, rpb1, rpb2, actin, chitin synthase, and ATP6 from GenBank using different field keywords that indicated their origin in Brazil. A total of 19,440 sequences were recovered. ITS is the most representative marker (11,209 sequences), with 70.1% belonging to Ascomycota, 18.6% Basidiomycota, 10.2% unidentified, 1.1% Mucoromycota, two sequences of Olpidium bornovanus (Fungi incertae sedis), one sequence of Blastocladiomycota (Allomyces arbusculus), and one sequence of Chytridiomycota (Batrachochytrium dendrobatidis). Considering the sequences of all selected markers, only the phyla Cryptomycota and Entorrhizomycota were not represented. Based on ITS, using a cutoff of 98%, all sequences comprise 3047 OTUs, with the majority being Ascomycota (2088 OTUs) and Basidiomycota (681 OTUs). Previous numbers based mainly on morphological and bibliographical data revealed 5264 fungal species from Brazil, with a predominance of Basidiomycota (2741 spp.) and Ascomycota (1881 spp.). The unidentified ITS sequences not assigned to a higher taxonomic level represent 1.61% of all ITS sequences sampled and correspond to 38 unknown class-level lineages (75% cutoff). A maximum likelihood phylogeny based on LSU illustrates the fungal classes occurring in Brazil.
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| 27. |
- Sanchez-Garcia, Marisol, et al.
(författare)
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Fruiting body form, not nutritional mode, is the major driver of diversification in mushroom-forming fungi
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 117:51, s. 32528-32534
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Tidskriftsartikel (refereegranskat)abstract
- With similar to 36,000 described species, Agaricomycetes are among the most successful groups of Fungi. Agaricomycetes display great diversity in fruiting body forms and nutritional modes. Most have pileate-stipitate fruiting bodies (with a cap and stalk), but the group also contains crust-like resupinate fungi, polypores, coral fungi, and gasteroid forms (e.g., puffballs and stinkhorns). Some Agaricomycetes enter into ectomycorrhizal symbioses with plants, while others are decayers (saprotrophs) or pathogens. We constructed a megaphylogeny of 8,400 species and used it to test the following five hypotheses regarding the evolution of morphological and ecological traits in Agaricomycetes and their impact on diversification: 1) resupinate forms are plesiomorphic, 2) pileate-stipitate forms promote diversification, 3) the evolution of gasteroid forms is irreversible, 4) the ectomycorrhizal (ECM) symbiosis promotes diversification, and 5) the evolution of ECM symbiosis is irreversible. The ancestor of Agaricomycetes was a saprotroph with a resupinate fruiting body. There have been 462 transitions in the examined morphologies, including 123 origins of gasteroid forms. Reversals of gasteroid forms are highly unlikely but cannot be rejected. Pileate-stipitate forms are correlated with elevated diversification rates, suggesting that this morphological trait is a key to the success of Agaricomycetes. ECM symbioses have evolved 36 times in Agaricomycetes, with several transformations to parasitism. Across the entire 8,400-species phylogeny, diversification rates of ectomycorrhizal lineages are no greater than those of saprotrophic lineages. However, some ECM lineages have elevated diversification rates compared to their non-ECMsister clades, suggesting that the evolution of symbioses may act as a key innovation at local phylogenetic scales.
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| 28. |
- Sanchez-Garcia, Marisol
(författare)
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Global phylogeny of the Shiitake mushroom and related Lentinula species uncovers novel diversity and suggests an origin in the Neotropics
- 2022
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 173
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Tidskriftsartikel (refereegranskat)abstract
- Lentinula (Basidiomycota, Agaricales) includes the most widely cultivated mushroom in the world, Lentinula edodes, also known as shiitake (Japanese) or xiang-gu (Chinese). At present, nine species are recognized in the genus, based on morphology, mating criteria, and geographic distribution. However, analyses of internal transcribed spacers (ITS) of ribosomal RNA genes have suggested that there are cryptic lineages. We analyzed a global-scale phylogenetic dataset from 325 Lentinula individuals from 24 countries in Asia-Australasia and the Americas plus Madagascar, with 325 sequences of ITS, 80 LSU sequences, and 111 sequences of translation elongation factor (tef1-alpha) genes. We recovered 15 independent lineages (Groups 1-15) that may correspond to species. Lineages in Asia-Australasia (Groups 1-5) and the Americas plus Madagascar (Groups 6-15) formed sister clades. Four lineages are represented only by sequences from single individuals and require further molecular sampling, including L. aff. raphanica (Group 7), L. ixodes (Group 8), L. boryana (Group 12), and L. aff. aciculospora (Group 14). Groups 1 and 5 are here referred to L. edodes and L. aff. edodes, respectively. However, these groups most likely represent the same species and are only recognized as (unsupported) monophyletic lineages by maximum likelihood analyses of ITS alone. Other putative species resolved here include L. lateritia (Group 2), L. novae-zelandieae (Group 3), L. aff. lateritia (Group 4), L. raphanica (Group 6), L. aff. detonsa (Group 9), L. detonsa (Group 10), L. guzmanii sp. nov. (Group 11), L. aciculospora (Group 13), andL. madagasikarensis (Group 15). Groups 9-12 represent the "L. boryana complex ". Molecular clock and historical biogeographic analyses suggest that the most recent common ancestor (MRCA) of Lentinula can be placed in the middle Oligocene, ca. 30 million years ago (Ma), and had a likely presence in neotropical America. The MRCA of Lentinula in the Americas and Madagascar lived ca. 22 Ma in the Neotropics and the MRCA of Lentinula in Asia-Australasia lived ca. 6 Ma in Oceania. Given the current knowledge about plate tectonics and paleoclimatic models of the last 30 Myr, our phylogenetic hypothesis suggests that the extant distribution of Lentinula is likely to have arisen, in large part, due to long-distance dispersal. Lentinula collections include at least four dubious taxa that need further taxonomic studies: L. reticeps from the USA (Ohio); L. guarapiensis from Paraguay; Lentinus puiggarii from Brazil (Sa & SIM;o Paulo); and "L. platinedodes " from Vietnam. Approximately ten of the fifteen Groups are reported on Fagaceae, which appears to be the ancestral substrate of Lentinula.
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| 29. |
- Sanchez-Garcia, Marisol
(författare)
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Outline of Fungi and fungus-like taxa-2021
- 2022
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Ingår i: Mycosphere. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 13, s. 53-453
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Tidskriftsartikel (refereegranskat)abstract
- This paper provides an updated classification of the Kingdom Fungi (including fossil fungi) and fungus-like taxa. Five-hundred and twenty-three (535) notes are provided for newly introduced taxa and for changes that have been made since the previous outline. In the discussion, the latest taxonomic changes in Basidiomycota are provided and the classification of Mycosphaerellales are broadly discussed. Genera listed in Mycosphaerellaceae have been confirmed by DNA sequence analyses, while doubtful genera (DNA sequences being unavailable but traditionally accommodated in Mycosphaerellaceae) are listed in the discussion. Problematic genera in Glomeromycota are also discussed based on phylogenetic results.
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| 30. |
- Sánchez-García, Marisol, et al.
(författare)
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Single nuclei sequencing reveals low levels of intra-organismal genomic variation across strains in the genus Claroideoglomus
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Arbuscular mycorrhizal (AM) fungi are important plant symbionts that propagate predominantly with multinucleate asexual spores formed below ground. The degree of intra-organismal genetic variation in AM fungi has been a long-standing topic of debate due to difficulties in generating high quality genome assemblies from most species in this phylum in combination with exceptionally high levels of rDNA polymorphism compared to other eukaryotes.In the AM fungi Claroideoglomus etunicatum, visualization of nuclei migration during spore formation has demonstrated that sporogenesis is random or sectorial, firmly rejecting false sporogenesis with one or two founding nuclei (Jany and Pawlowska, 2010). We thus expect the composition of nuclei in a single Claroideoglomusspore to reflect that of the entire organism when we study intra-organismal genetic variation of individual spores from three strains in the genus Claroideoglomus. The three strains are all within the luteum/claroideumspecies complex that cannot be phylogenetically resolved based on rRNA large subunit genes (Vankuren et al., 2013). From each strain we generated 24 single nuclei genome assemblies to identify rRNA gene variants and MAT locus in each nucleus. Then, we map the reads of each individual nucleus to two different reference assemblies and identify SNPs within and between nuclei from single spores using two different softwares for variant calling. We identify the mating type locus and characterized intra-organismal genetic diversity in each strain and explore patterns of recombination and shared variants across strains. Based on earlier studies in the genus Rhizophagus, we expect nuclei to be haploid and within spore allele frequency patterns to be explained by the number of MAT type alleles.
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| 31. |
- Sanchez-Garcia, Marisol
(författare)
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The genus Dermoloma is more diverse than expected and forms a monophyletic lineage in the Tricholomataceae
- 2021
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Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 20, s. 11-25
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Tidskriftsartikel (refereegranskat)abstract
- We present the first phylogenetic evaluation of the genus Dermoloma, which is resolved as monophyletic and closely related to Pseudotricholoma, a poorly known Dermoloma-like lineage within the family Tricholomataceae. The position of Dermoloma is confirmed by the placement of the type species, Dermoloma cuneifolium, represented by multiple samples including the neotype. Based on our phylogenetic analyses, we recognised 25 European operational taxonomic units (OTUs) but could only assign species names to ten of them based on ex-type sequences. Furthermore, only five additional published Dermoloma names of uncertain status are available for the remaining 16 potential European species, thus demonstrating an unexpected amount of taxonomic diversity. Samples from Europe and North America seem to be endemic on a continental scale. North American samples formed six unique OTUs, but only one could be reliably named, Dermoloma hymenocephalum. Dermoloma is morphologically defined by basidiomata with brown, grey and white colours with a farinaceous odour and a pluristratous hymeniderm type of pileipellis. Our phylogenetic analyses support the subdivision of the genus into two subgenera and four sections, and species with inamyloid basidiospores are placed in subg. Dermoloma and those with amyloid basidiospores in subg. Amylospora. Both subgenera are further divided into two sections. The analysis of spore morphology shows that sect. Conica of subg. Dermoloma and sect. Nigrescentia of subg. Amylospora have a very distinctive spore shape. Sect. Atrobrunnea of subg. Amylospora showed relatively high variability of spores among species, but spores of sect. Dermoloma were similar and not useful for species discrimination.
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