Biology subjects

Simpfendorfer, S.

Publications and source records attributed to Simpfendorfer, S..

4 recordsLinked to original sources

bioRxiv2024

Sanctuary: A Starship transposon facilitating the movement of the virulence factor ToxA in fungal wheat pathogens

There is increasing evidence that mobile genetic elements can drive the emergence of pathogenic fungal species by moving virulence genes horizontally. The 14 kbp ToxhAT transposon has been shown to be moving the necrotrophic effector, ToxA, horizontally between fungal species that infect Triticum aestivum (wheat), namely Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana. All three species utilise the ToxA protein to infect wheat. Previous genomic evidence found ToxhAT in distinct chromosomal positions in two isolates of B. sorokiniana, indicating that the transposon is still active in this species. Here we confirm the movement of ToxhAT using long-read Nanopore MinION sequencing of eight novel and one previously published B. sorokiniana isolates. One event of independent transposition of ToxhAT was observed, and target site duplications of "TA" were identified, confirming this was an autonomous movement facilitated by a yet unidentified transposase. Whole genome analysis revealed that ToxhAT is a passenger embedded in a much larger, conserved 170-196 kbp mobile genetic element. This element, termed Sanctuary, belongs to the newly described Starship transposon superfamily. This classification is based on the presence of short direct repeats, empty insertion sites, a putative tyrosine recombinase gene and other features of Starship transposons. We also show that ToxhAT has been independently captured by two different Starships, Sanctuary and Horizon which share little to no sequenced identity, outside of ToxhAT. This classification makes Horizon and Sanctuary part of a growing number of Starships involved in the horizontal gene transfer of adaptive genetic material between fungal species. ImportanceThe work presented here expands our understanding of a novel group of mobile genetic elements called Starships that facilitate the horizontal exchange of virulence genes in fungal pathogens. Our analysis shows that Sanctuary and ToxhAT are likely active and autonomous transposons in the B. sorokiniana genome. We also show that the smaller ToxhAT transposon has been independently captured by two different Starships, viz. Sanctuary in B. sorokiniana and Horizon in P. tritici-repentis and P. nodorum. Outside of ToxhAT these two Starships share no sequence identity. The capture of ToxhAT by two different mobile elements in three different fungal wheat pathogens demonstrates how horizontal transposon transfer is driving the evolution of virulence in these important wheat pathogens.

genomics↗

bioRxiv2022

Improved breeding for Fusarium pseudograminarium (Fusarium crown rot) using qPCR measurement of infection in multi-species winter cereal experiments

Fusarium crown rot (FCR) causes significant grain yield loss in winter cereals around the world. Breeding for resistance and/or tolerance to FCR has been slow with relatively limited success. In this study, multi-species experiments were used to demonstrate an improved method to quantify FCR infection levels at plant maturity using qPCR, as well as the genotype yield retention using residual regression deviation. Using qPCR to measure FCR infection allowed a higher degree of resolution between genotypes than traditional visual stem basal browning assessments. The results were consistent across three environments with different levels of disease expression. The improved measure of FCR infection along with genotype yield retention allows for partitioning of both tolerance and partial resistance. Together these methods offer new insights to FCR partial resistance and its relative importance to tolerance in bread wheat and barley. This new approach offers a more robust, cost-effective way to select for both FCR traits within breeding programs. Key messageGenetic gain for tolerance and partial resistance against Fusarium crown rot (FCR) in winter cereals has been impeded by laborious and variable visual measures of infection severity. This paper presents results of an improved method to quantify FCR infection that are strongly correlated to yield loss and reveal previously unrecognised partial resistance in barley and wheat varieties.

pathology↗

bioRxiv2020

Genetic Variance for Fusarium Crown Rot Tolerance in Durum Wheat

Tolerance to the cereal disease Fusarium crown rot (FCR) was investigated in a set of 34 durum wheat genotypes, with Suntop, (bread wheat) and EGA Bellaroi (durum) as tolerant and intolerant checks, in a series of replicated field trials over four years with inoculated (FCR-i) and non-inoculated (FCR-n) plots of the genotypes. The genotypes included conventional durum lines and lines derived from crossing durum with 2-49, a bread wheat line with the highest level of partial resistance to FCR. A split plot trial design was chosen to optimize the efficiency for the prediction of FCR tolerance for each genotype. A multi-environment trial (MET) analysis was undertaken which indicated that there was good repeatability of FCR tolerance across years. Based on an FCR tolerance index, Suntop was the most tolerant genotype and EGA Bellaroi was very intolerant, but many durum wheats had FCR tolerance indices which were comparable to Suntop. These included some conventional durum lines, V101030, TD1702, V11TD013*3X-63 and DBA Bindaroi, as well as genotypes from crosses with 2-49 (V114916 and V114942). The correlation between FCR tolerance and FCR-n yield predictions was moderately negative indicating it could be somewhat difficult to develop high yielding FCR-tolerant genotypes. However, FCR tolerance showed a positive correlation with FCR-i yield predictions in seasons of high disease expression indicating it could be possible to screen for FCR tolerance using only FCR-i treatments. These results are the first demonstration of genetic diversity in durum germplasm for FCR tolerance and they provide a basis for breeding for this trait.

plant biology↗

bioRxiv2019

Transposon mediated horizontal transfer of the host-specific virulence protein ToxA between three fungal wheat pathogens

Most known examples of horizontal gene transfer (HGT) between eukaryotes are ancient. These events are identified primarily using phylogenetic methods on coding regions alone. Only rarely are there examples of HGT where non-coding DNA is also reported. The gene encoding the wheat virulence protein ToxA and surrounding 14 kb is one of these rare examples. ToxA has been horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis and Bipolaris sorokiniana) as part of a conserved [~]14kb element, which contains coding and non-coding regions. Here we use long-read sequencing to define the extent of HGT between these three fungal species. Construction of near-chromosomal level assemblies enabled identification of terminal inverted repeats on either end of the 14kb region, typical of a Type II DNA transposon. This is the first description of ToxA with complete transposon features, which we call ToxhAT. In all three species, ToxhAT resides in a large (140-250 kb) transposon-rich genomic island which is absent in toxA- isolates. We demonstrate that the horizontal transfer of ToxhAT between Pyrenophora tritici-repentis and P. nodorum occurred as part of a large [~]80kb HGT which is now undergoing extensive decay. In contrast, in B. sorokiniana ToxhAT and its resident genomic island are mobile within the genome. Together these data provide insight into the non-coding regions that facilitate HGT between eukaryotes and the genomic processes which mask the extent of HGT between these species.\n\nIMPORTANCEThis work dissects the tripartite horizontal transfer of ToxA; a gene that has a direct negative impact on global wheat yields. Defining the extent of horizontally transferred DNA is important because it can provide clues as to the mechanisms that facilitate HGT. Our analysis of ToxA and its surrounding 14kb suggests that this gene was horizontally transferred in two independent events, with one event likely facilitated by a Type II DNA transposon. These horizontal transfer events are now in various processes of decay in each species due to the repeated insertion of new transposons and subsequent rounds of targeted mutation by a fungal genome defense mechanism known as repeat induced point-mutation. This work highlights the role that HGT plays in the evolution of host adaptation in eukaryotic pathogens. It also increases the growing body of evidence that transposons facilitate adaptive HGT events between fungi present in similar environments and hosts.\n\nDATA AVAILABILITYAll raw sequencing data is available under NCBI BioProject PRJNA505097.\n\nThe P. nodorum SN15 Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession SSHU00000000. The version SSHU01000000 is described in this paper. The P. nodorum SN79-1087 Whole Genome Shotgun project has been deposited under the accessions CP039668-CP039689. The Whole Genome shotgun project and accession numbers for B. sorokiniana isolates are as follows: CS10; SRZH00000000, CS27; SRZG00000000, WAI2406; SRZF00000000, WAI2411; SRZE00000000. Transposon annotations, CS10 and CS27 gene annotations are available at https://github.com/megancamilla/Transposon-Mediated-transfer-of-ToxA

genomics↗