The largest fungal genome discovered in Jafnea semitosta

Egertová, Zuzana; Sochor, Michal

doi:10.1007/s00606-017-1424-9

Cited by 9 publications

(8 citation statements)

References 26 publications

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“…The A. psidii genome is particularly large compared with the average fungal genome, around 44.2 Mbp (Tavares et al 2014), and relative to its Myrtaceae hosts, around 300 - 650 Mbp (Thrimawithana et al 2019; Myburg et al 2014). Data based on flow cytometry determined the largest fungal genome at ∼3.6 Gbp (Egertová & Sochor 2017) and the largest known rust-type (Basidiomycota, Pucciniales) fungal genomes; Gymnosporangium confusum and Uromyces bidentis , at 893.2 Mbp and 2,489 Mbp, respectively (Ramos et al 2015). Rust genomes appear to be larger on average than other fungal genomes and rusts infecting Poaceae (monocotyledon) are significantly smaller than those infecting Fabaceae (eudicotyledon) hosts, with average sizes of 170.6 Mbp, and 556.6 Mbp respectively.…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, genome size does not appear to correlate with the perennial nature of host plants with the assembled genome of two important tree rust pathogens, Melampsora larici-populina (101 Mbp) (Duplessis et al 2011) and Cronartium quercuum (22 Mbp) having modest-sized genomes, though sharing orthologs with A. psidii (Figure 6 B, right) that are absent in the cereal-infecting rust. While ploidy has been postulated as a possible reason for large fungal genome sizes (Egertová & Sochor 2017), the evidence to date is that genome expansion in rust species is due to repetitive elements, notably a proliferation of transposable elements (TEs) (Duplessis et al 2011; Schwessinger et al 2018; Foulongne-Oriol et al 2013).…”

Section: Discussionmentioning

confidence: 99%

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Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Tobias

Schwessinger

Deng

et al. 2020

Preprint

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Austropuccinia psidii, originating in South America, is a globally invasive plant pathogen causing rust disease on Myrtaceae. Several biotypes are recognized with the most widely distributed pandemic strain spreading throughout the Asia-Pacific and Oceania regions within the last decade. Austropuccinia psidii has a broad host range (currently 480 myrtaceous species), making it a particularly dangerous plant pathogen. In the nine years since the pandemic biotype was first found in Australia in 2010, the pathogen has caused the near extinction of at least three species, the decline of at least one keystone species, and negatively affected commercial production of several Myrtaceae. To enable molecular and genomic studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype based on PacBio sequence data and scaffolding with Hi-C technology. With an estimated haploid genome size of just over 1 Gbp, it is the largest assembled fungal genome to date. We found the A. psidii genome to have a lower GC content (33.8 %), greatly expanded telomeric and intergenic regions and more repetitive regions (> 90 %) compared to other genomes of species in the Pucciniales, however numbers of predicted coding regions (18,875) are comparable. Most of the increase in genome size is caused by a recent expansion of transposable elements belonging to the Gypsy superfamily. Post-inoculation mRNA sequence capture from a susceptible host provides expression evidence for 10,613 predicted coding genes, including 210 of the 367 putative effectors. The completeness of the genome provides a greatly needed resource for strategic approaches to combat disease spread.3

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Tobias

Schwessinger

Deng

et al. 2020

Preprint

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“…Furthermore, the ribosomal cistron can be repeated anywhere up to 100–200 times in a fungal genome, and this figure is highly variable for different taxa ( Herrera et al, 2009 ; Lindahl et al, 2013 ; Tang et al, 2015 ; Diaz et al, 2017 ). Similarly, genome size can range anywhere from 2.2 to 3625 mb ( Gregory et al, 2007 ; Xu et al, 2007 ; Mohanta and Bae, 2015 ; Egertová and Sochor, 2017 ). As such, the estimated relative abundances of the mixed mock community taxa (based on equal proportions of template DNA) are limited to the extent that different taxa may have markedly different ribosomal cistron copy numbers despite equal DNA concentrations.…”

Section: Discussionmentioning

confidence: 99%

Characterizing the Human Mycobiota: A Comparison of Small Subunit rRNA, ITS1, ITS2, and Large Subunit rRNA Genomic Targets

et al. 2018

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Interest in the human microbiome has increased dramatically in the last decade. However, much of this research has focused on bacteria, while the composition and roles of their fungal counterparts remain less understood. Furthermore, a variety of methodological approaches have been applied, and the comparability between studies is unclear. This study compared four primer pairs targeting the small subunit (SSU) rRNA (18S), ITS1, ITS2, and large subunit (LSU) rRNA (26S) genomic regions for their ability to accurately characterize fungal communities typical of the human mycobiota. All four target regions of 21 individual fungal mock community taxa were capable of being amplified adequately and sequenced. Mixed mock community analyses revealed marked variability in the ability of each primer pair to accurately characterize a complex community. ITS target regions outperformed LSU and SSU. Of the ITS regions, ITS1 failed to generate sequences for Yarrowia lipolytica and all three Malassezia species when in a mixed community. These findings were further supported in studies of human sinonasal and mouse fecal samples. Based on these analyses, previous studies using ITS1, SSU, or LSU markers may omit key taxa that are identified by the ITS2 marker. Of methods commonly used in human mycobiota studies to date, we recommend selection of the ITS2 marker. Further investigation of more recently developed fungal primer options will be essential to ultimately determine the optimal methodological approach by which future human mycobiota studies ought to be standardized.

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“…Even then, fungal genomes have shown to be several times smaller than the standards used. While fungal species with large genomes can be compared with plant or animal nuclei, as in the case of the Pucciniales [8, 14] or of Jafnea semitosta [15], most fungal species are not reliably comparable to eukaryotes other than fungi. 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).…”

Section: Standards For Fungal Dna Amount Estimationmentioning

confidence: 99%

“…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. Considering that fungal genome sizes range between 2.19 (for Encephalitozoon romaleae ; Pombert et al [17]) and 3706 Mbp (for J. semitosta ; Egertová and Sochor [15]), with an overall average upgraded to 44.2 Mbp by Ramos et al [14], taken together these standards enable adequate analysis of the vast majority of fungal species (with the larger genomes being covered by plant or animal DNA standards). To this end, Carvalho et al [18] have validated the nuclei of the plant Rhamnus alaternus (664 Mbp/2C) as a standard, useful for the analysis of fungal species with high amounts of DNA.…”

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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The largest fungal genome discovered in Jafnea semitosta

Cited by 9 publications

References 26 publications

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Characterizing the Human Mycobiota: A Comparison of Small Subunit rRNA, ITS1, ITS2, and Large Subunit rRNA Genomic Targets

The use of flow cytometry for fungal nuclear DNA quantification

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