Reliable transformation system for Microbotryum lychnidis-dioicae informed by genome and transcriptome project

Toh, Su San; Treves, David S.; Barati, Michelle T.; Perlin, Michael H.

doi:10.1007/s00203-016-1244-2

Cited by 8 publications

(2 citation statements)

References 49 publications

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“…2017 ), and the genes displaying presence–absence polymorphism within MvSl and MvSd populations and corresponding to secreted proteins and/or located within selective sweeps represent potentially interesting candidates for future exploration. Functional validation assays using gene transformation tools recently established for anther-smut fungi ( Toh et al. 2016 ) should be performed in future studies to validate an adaptive role of the gene presence–absence events with relevant functions of genomic regions.…”

Section: Discussionmentioning

confidence: 99%

Gene Presence–Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure

Hartmann

Vega

Brandenburg

et al. 2018

Genome Biology and Evolution

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Gene presence–absence polymorphisms segregating within species are a significant source of genetic variation but have been little investigated to date in natural populations. In plant pathogens, the gain or loss of genes encoding proteins interacting directly with the host, such as secreted proteins, probably plays an important role in coevolution and local adaptation. We investigated gene presence–absence polymorphism in populations of two closely related species of castrating anther-smut fungi, Microbotryum lychnidis-dioicae (MvSl) and M. silenes-dioicae (MvSd), from across Europe, on the basis of Illumina genome sequencing data and high-quality genome references. We observed presence–absence polymorphism for 186 autosomal genes (2% of all genes) in MvSl, and only 51 autosomal genes in MvSd. Distinct genes displayed presence–absence polymorphism in the two species. Genes displaying presence–absence polymorphism were frequently located in subtelomeric and centromeric regions and close to repetitive elements, and comparison with outgroups indicated that most were present in a single species, being recently acquired through duplications in multiple-gene families. Gene presence–absence polymorphism in MvSl showed a phylogeographic structure corresponding to clusters detected based on SNPs. In addition, gene absence alleles were rare within species and skewed toward low-frequency variants. These findings are consistent with a deleterious or neutral effect for most gene presence–absence polymorphism. Some of the observed gene loss and gain events may however be adaptive, as suggested by the putative functions of the corresponding encoded proteins (e.g., secreted proteins) or their localization within previously identified selective sweeps. The adaptive roles in plant and anther-smut fungi interactions of candidate genes however need to be experimentally tested in future studies.

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Section: Discussionmentioning

confidence: 99%

Gene Presence–Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure

Hartmann

Vega

Brandenburg

et al. 2018

Genome Biology and Evolution

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“…By exploiting the newly acquired genomic and transcriptomic data for M. lychnidis - dioicae , a robust transformation system based on At MT has recently been developed [ 181 ]. The selection markers delivered through At MT consist of endogenous promoters of the most highly expressed genes under different phases of the fungal lifecycle, as assessed by previous transcriptomic data [ 182 ], fused with the HYG2 gene alone or in combination with eGFP.…”

Section: Fungal Species and Biological Questions In Which Amentioning

confidence: 99%

A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi

Idnurm

Bailey

Cairns

et al. 2017

Fungal Biol Biotechnol

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The implementation of Agrobacterium tumefaciens as a transformation tool revolutionized approaches to discover and understand gene functions in a large number of fungal species. A. tumefaciens mediated transformation (AtMT) is one of the most transformative technologies for research on fungi developed in the last 20 years, a development arguably only surpassed by the impact of genomics. AtMT has been widely applied in forward genetics, whereby generation of strain libraries using random T-DNA insertional mutagenesis, combined with phenotypic screening, has enabled the genetic basis of many processes to be elucidated. Alternatively, AtMT has been fundamental for reverse genetics, where mutant isolates are generated with targeted gene deletions or disruptions, enabling gene functional roles to be determined. When combined with concomitant advances in genomics, both forward and reverse approaches using AtMT have enabled complex fungal phenotypes to be dissected at the molecular and genetic level. Additionally, in several cases AtMT has paved the way for the development of new species to act as models for specific areas of fungal biology, particularly in plant pathogenic ascomycetes and in a number of basidiomycete species. Despite its impact, the implementation of AtMT has been uneven in the fungi. This review provides insight into the dynamics of expansion of new research tools into a large research community and across multiple organisms. As such, AtMT in the fungi, beyond the demonstrated and continuing power for gene discovery and as a facile transformation tool, provides a model to understand how other technologies that are just being pioneered, e.g. CRISPR/Cas, may play roles in fungi and other eukaryotic species.

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Parasitism in Yeasts

Begerow

Kemler

Feige

et al. 2017

Yeasts in Natural Ecosystems: Ecology

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Reliable transformation system for Microbotryum lychnidis-dioicae informed by genome and transcriptome project

Cited by 8 publications

References 49 publications

Gene Presence–Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure

Gene Presence–Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure

A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi

Parasitism in Yeasts

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