Validation of standards suitable for genome size estimation of fungi

Talhinhas, Pedro; Tavares, Daniela; Ramos, Ana Paula; Gonçalves, Susana C.; Loureiro, João

doi:10.1016/j.mimet.2017.09.012

Cited by 15 publications

(14 citation statements)

References 14 publications

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“…The first sequenced genome of C. geophilum strain 1.58, isolated from Switzerland, was published in four years ago [27]. This genome is among the largest in the fungal kingdom, with a mapped size of 178 Mbp and a total estimated size of up to 203 Mbp [27,28]. Cenococcum geophilum has no documented means of sexual spore production [15,29,30], but is considered asexual species despite high levels of genetic and physiological diversity.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

et al. 2021

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The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C. geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C. geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C. geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C. geophilum, we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.

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Section: Introductionmentioning

confidence: 99%

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

et al. 2021

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“…Typical fungal nuclear genome sizes occupy an intermediate position between prokaryotes and other eukaryotes. On average, the size of the fungal genome is two orders of magnitude smaller than that of higher plants and varies from~2.19 to~3706 Mbp ( [35], see also DOE JGI Fungi Portal: https://mycocosm.jgi.doe.gov/mycocosm/home). The average genome size of Ascomycota and Basidiomycota divisions is~36.91 and~46.48 Mb, respectively [36].…”

Section: Discussionmentioning

confidence: 99%

De novo sequencing, assembly and functional annotation of Armillaria borealis genome

et al. 2020

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Background Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior. Results The de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity. Conclusions Pathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships.

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“…Veselská et al [9] selected S. cerevisiae strain BY4743aα (24.1 Mbp/1C) and Aspergillus fumigatus strain CEA10 (29.2 Mbp/1C) as DNA standards based on genome sequence information, considering the average genome size of the fungal kingdom to be 37 Mbp (and the median 28 Mbp). However, above‐average fungal genomes are not adequately covered by these standards, which led Talhinhas et al [16] to select and validate three fungal species as additional DNA standards: Inonotus hispidus isolate LPV629 (41 Mbp/1C); Colletotrichum acutatum isolate PT812 (68 Mbp/1C); Cenococcum geophilum isolate 844.1 (203 Mbp/1C). In most cases intra‐specific genome size variability is not characterized but cannot be disregarded, and therefore it is important to use specific fungal strains as DNA standards.…”

Section: Standards For Fungal Dna Amount Estimationmentioning

confidence: 99%

The use of flow cytometry for fungal nuclear DNA quantification

2021

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Genome size information is sparse across fungi, with information being available for less than 2000 species. So far, most records have been obtained using static, microscopebased cytometry methods or derived from genome sequencing projects. Flow cytometry is now considered the state-of-the-art method for obtaining genome size measurements, and appropriate methods and DNA standards are available, enabling the analysis of most genome size ranges in a rapid, robust and inexpensive way. The average fungal genome size is 60 Mbp, but sizes vary across phylogeny, ranging from 2.2 (Encephalitozoon romaleae) to 3706 Mbp (Jafnea semitosta). In several fungal clades, genome size expansion seems to accompany evolution either to plant mutualism or to plant parasitism (particularly biotrophy), and fungi that interact with plants seem to have larger genomes than saprobes and those that interact with animals. Whereas flow cytometry for nuclear DNA quantification is routinely employed in plant sciences for genome size and ploidy studies, its use in fungal biology is still infrequent. Appropriate standards, methods and best practices are described here, with the aim of stimulating a more generalized and widespread use of flow cytometry for fungal genome size measurement.

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Validation of standards suitable for genome size estimation of fungi

Cited by 15 publications

References 14 publications

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

De novo sequencing, assembly and functional annotation of Armillaria borealis genome

The use of flow cytometry for fungal nuclear DNA quantification

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