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To date, most reports of horizontal gene transfer (HGT) in fungi rely on genome sequence data and are therefore an indirect measure of HGT after the event has occurred. However, a novel group of class II‐like transposons known as Starships may soon alter this status quo. Starships are giant transposable elements that carry dozens of genes, some of which are host‐beneficial, and are linked to many recent HGT events in the fungal kingdom. These transposons remain active and mobile in many fungal genomes and their transposition has recently been shown to be driven by a conserved tyrosine‐recombinase called 'Captain'. This perspective explores some of the remaining unanswered questions about how these Starship transposons move, both within a genome and between different species. We seek to outline several experimental approaches that can be used to identify the genes essential for Starship‐mediated HGT and draw links to other recently discovered giant transposons outside of the fungal kingdom. [ABSTRACT FROM AUTHOR]

Convergent evolution leads to identical phenotypic traits in different species or populations. Convergence can be driven by standing variation allowing selection to favour identical alleles in parallel or the same mutations can arise independently. However, the molecular basis of such convergent adaptation remains often poorly resolved. Pesticide resistance in agricultural ecosystems is a hallmark of convergence in phenotypic traits. Here, we analyse the major fungal pathogen Zymoseptoria tritici causing serious losses on wheat and with fungicide resistance emergence across several continents. We sampled three population pairs each from a different continent spanning periods early and late in the application of fungicides. To identify causal loci for resistance, we combined knowledge from molecular genetics work and performed genome‐wide association studies (GWAS) on a global set of isolates. We discovered yet unknown factors in azole resistance including a gene encoding membrane associated functions. We found strong support for the "hotspot" model of resistance evolution with convergent changes in a small set of loci but additional loci showed more population‐specific allele frequency changes. Genome‐wide scans of selection showed that half of all known resistance loci were overlapping a selective sweep region. Hence, the application of fungicides was one of the major selective agents acting on the pathogen over the past decades. Furthermore, loci identified through GWAS showed the highest overlap with selective sweep regions underlining the importance to map phenotypic trait variation in evolving populations. Our population genomic analyses highlighted that both de novo mutations and gene flow contributed to convergent pesticide adaptation. [ABSTRACT FROM AUTHOR]

Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is one of the most economically important diseases of wheat. Recently, both factors of a gene‐for‐gene interaction between Z. tritici and wheat, the wheat receptor‐like kinase Stb6 and the Z. tritici secreted effector protein AvrStb6, have been identified. Previous analyses revealed a high diversity of AvrStb6 haplotypes present in earlier Z. tritici isolate collections, with up to c.18% of analysed isolates possessing the avirulence isoform of AvrStb6 identical to that originally identified in the reference isolate IPO323. With Stb6 present in many commercial wheat cultivars globally, we aimed to assess potential changes in AvrStb6 genetic diversity and the incidence of haplotypes allowing evasion of Stb6‐mediated resistance in more recent Z. tritici populations. Here we show, using targeted resequencing of AvrStb6, that this gene is universally present in field isolates sampled from major wheat‐growing regions of the world in 2013–2017. However, in contrast to the data from previous AvrStb6 population studies, we report a complete absence of the originally described avirulence isoform of AvrStb6 amongst modern Z. tritici isolates. Moreover, a remarkably small number of haplotypes, each encoding AvrStb6 protein isoforms conditioning virulence on Stb6‐containing wheat, were found to predominate among modern Z. tritici isolates. A single virulence isoform of AvrStb6 was found to be particularly abundant throughout the global population. These findings indicate that, despite the ability of Z. tritici to sexually reproduce on resistant hosts, AvrStb6 avirulence haplotypes tend to be eliminated in subsequent populations. [ABSTRACT FROM AUTHOR]

Zymoseptoria tritici, the causal agent of Septoria tritici blotch, is a fungal wheat pathogen that causes significant global yield losses. Within Z. tritici populations, quantitative differences in virulence among different isolates are commonly observed; however, the genetic components that underpin these differences remain elusive. In this study, intraspecific comparative transcriptomic analysis was used to identify candidate genes that contribute to differences in virulence on the wheat cultivar WW2449. This led to the identification of a multicopy gene that was not expressed in the high‐virulence isolate when compared to the medium‐ and low‐virulence isolates. Further investigation suggested this gene resides in a 7.9‐kb transposon. Subsequent long‐read sequencing of the isolates used in the transcriptomic analysis confirmed that this gene did reside in an active Class II transposon, which is composed of four genes named REP9‐1 to ‐4. Silencing and overexpression of REP9‐1 in two distinct genetic backgrounds demonstrated that its expression alone reduces the number of pycnidia produced by Z. tritici during infection. The REP9‐1 gene identified within a Class II transposon is the first discovery of a gene in a transposable element that influences the virulence of Z. tritici. This discovery adds further complexity to genetic loci that contribute to quantitative virulence in this important pathogen. [ABSTRACT FROM AUTHOR]

Venous thromboembolisms (VTEs) have been a leading secondary cause of death among ovarian cancer patients, prompting multiple studies of risk factors. The objective of this meta-analysis is to quantify the associations between VTE and the most commonly reported risk factors among ovarian cancer patients. PubMed, Embase, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) were used to identify observational studies. Two reviewers independently abstracted data and assessed quality via the Newcastle–Ottawa tool. A random effects model was used to calculate the pooled odds ratios for VTE with each of the following exposures: advanced cancer stage, clear cell histology, serous histology, ascites at diagnosis, and complete cytoreduction. The I2 and Q tests were used to evaluate heterogeneity. Twenty cohort studies with 6,324 total ovarian cancer patients, 769 of whom experienced a VTE, were included. The odds of VTE in ovarian cancer patients were higher among patients with cancer stage III/IV (versus cancer stage I/II, pooled odds ratio (OR) 2.73; 95% CI 1.84–4.06; I2= 64%), clear cell (versus nonclear cell) histology (OR 2.11; 95% CI 1.55–2.89; I2 = 6%), and ascites (versus no ascites) at diagnosis (OR 2.12; 95% CI 1.51–2.96; I2 = 32%). Serous (versus nonserous) histology (OR 1.26; 95% CI 0.91–1.75; I2 = 42%) and complete (versus incomplete) cytoreduction (OR 1.05; 95% CI 0.27–4.11; I2 = 88%) were not associated with VTE. This meta-analysis quantifies the significantly elevated odds of VTE in ovarian cancer patients with advanced stage at diagnosis, clear cell histology, and ascites at diagnosis. Further studies are needed to account for confounders and inform clinical decision-making tools. [ABSTRACT FROM AUTHOR]

Purpose: We aim to understand if rurality impacts patients' odds of presenting with stage IV ovarian cancer at diagnosis independent of distance to primary care provider and the socioeconomic status of a patient's residential census tract. Methods: A cohort of 1,000 women with ovarian cancer in Iowa, Kansas, and Missouri were sampled and analyzed from the cancer registries' statewide population data. The sample contained those with a histologically confirmed primary ovarian cancer diagnosis in 2011‐2012. All variables were captured through an extension of standard registry protocol using standardized definitions and abstraction manuals. Chi‐square tests and a multivariable logistic regression model were used. Findings: At diagnosis, 111 women in our sample had stage IV cancer and 889 had stage I‐III. Compared to patients with stage I‐III cancer, patients with stage IV disease had a higher average age, more comorbidities, and were more often living in rural areas. Multivariate analysis showed that rural women (vs metropolitan) had a greater odds of having stage IV ovarian cancer at diagnosis (odds ratio = 2.41 and 95% confidence interval = 1.33‐4.39). Conclusion: Rural ovarian cancer patients have greater odds of having stage IV cancer at diagnosis in Midwestern states independent of the distance they lived from their primary care physician and the socioeconomic status of their residential census tract. Rural women's greater odds of stage IV cancer at diagnosis could affect treatment options and mortality. Further investigation is needed into reasons for these findings. [ABSTRACT FROM AUTHOR]

Summary: The rice XA21‐mediated immune response is activated on recognition of the RaxX peptide produced by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The 60‐residue RaxX precursor is post‐translationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The 5‐kb raxX‐raxSTAB gene cluster of Xoo encodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type I secretion system. To assess raxX‐raxSTAB gene cluster evolution and to determine its phylogenetic distribution, we first identified rax gene homologues in other genomes. We detected the complete raxX‐raxSTAB gene cluster only in Xanthomonas spp., in five distinct lineages in addition to X. oryzae. The phylogenetic distribution of the raxX‐raxSTAB gene cluster is consistent with the occurrence of multiple lateral (horizontal) gene transfer events during Xanthomonas speciation. RaxX natural variants contain a restricted set of missense substitutions, as expected if selection acts to maintain peptide hormone‐like function. Indeed, eight RaxX variants tested all failed to activate the XA21‐mediated immune response, yet retained peptide hormone activity. Together, these observations support the hypothesis that the XA21 receptor evolved specifically to recognize Xoo RaxX. [ABSTRACT FROM AUTHOR]

Summary: Bipolaris sorokiniana is the causal agent of multiple diseases on wheat and barley and is the primary constraint to cereal production throughout South Asia. Despite its significance, the molecular basis of disease is poorly understood. To address this, the genomes of three Australian isolates of B. sorokiniana were sequenced and screened for known pathogenicity genes. Sequence analysis revealed that the isolate BRIP10943 harboured the ToxA gene, which has been associated previously with disease in the wheat pathogens Parastagonospora nodorum and Pyrenophora tritici‐repentis. Analysis of the regions flanking ToxA within B. sorokiniana revealed that it was embedded within a 12‐kb genomic element nearly identical to the corresponding regions in P. nodorum and P. tritici‐repentis. A screen of 35 Australian B. sorokiniana isolates confirmed that ToxA was present in 12 isolates. Sequencing of the ToxA genes within these isolates revealed two haplotypes, which differed by a single non‐synonymous nucleotide substitution. Pathogenicity assays showed that a B. sorokiniana isolate harbouring ToxA was more virulent on wheat lines that contained the sensitivity gene when compared with a non‐ToxA isolate. This work demonstrates that proteins that confer host‐specific virulence can be horizontally acquired across multiple species. This acquisition can dramatically increase the virulence of pathogenic strains on susceptible cultivars, which, in an agricultural setting, can have devastating economic and social impacts. [ABSTRACT FROM AUTHOR]

In this article, we describe the presence of genes encoding close homologues of an endogenous plant peptide, rapid alkalinization factor (RALF), within the genomes of 26 species of phytopathogenic fungi. Members of the RALF family are key growth factors in plants, and the sequence of the RALF active region is well conserved between plant and fungal proteins. RALF1-like sequences were observed in most cases; however, RALF27-like sequences were present in the Sphaerulina musiva and Septoria populicola genomes. These two species are pathogens of poplar and, interestingly, the closest relative to their respective RALF genes is a poplar RALF27-like sequence. RALF peptides control cellular expansion during plant development, but were originally defined on the basis of their ability to induce rapid alkalinization in tobacco cell cultures. To test whether the fungal RALF peptides were biologically active in plants, we synthesized RALF peptides corresponding to those encoded by two sequenced genomes of the tomato pathogen Fusarium oxysporum f. sp. lycopersici. One of these peptides inhibited the growth of tomato seedlings and elicited responses in tomato and Nicotiana benthamiana typical of endogenous plant RALF peptides (reactive oxygen species burst, induced alkalinization and mitogen-activated protein kinase activation). Gene expression analysis confirmed that a RALF-encoding gene in F. oxysporum f. sp. lycopersici was expressed during infection on tomato. However, a subsequent reverse genetics approach revealed that the RALF peptide was not required by F. oxysporum f. sp. lycopersici for infection on tomato roots. This study has demonstrated the presence of functionally active RALF peptides encoded within phytopathogens that harbour an as yet undetermined role in plant-pathogen interactions. [ABSTRACT FROM AUTHOR]

Population genetic and phylogenetic studies have shown that Phaeosphaeria nodorum is a member of a species complex that probably shares its center of origin with wheat ( Triticum aestivum and Triticum durum). We examined the evolutionary histories of three known necrotrophic effectors ( NEs) produced by P. nodorum and compared them with neutral loci., We screened over 1000 individuals for the presence/absence of each effector and assigned each individual to a multi-effector genotype. Diversity at each NE locus was assessed by sequencing c. 200 individuals for each locus., We found significant differences in effector frequency among populations. We propose that these differences reflect the presence/absence of the corresponding susceptibility gene in wheat cultivars. The population harboring the highest sequence diversity was different for each effector locus and never coincided with populations harboring the highest diversity at neutral loci. Coalescent and phylogenetic analyses showed a discontinuous presence of all three NEs among nine closely related Phaeosphaeria species. Only two of the nine species were found to harbor NEs., We present evidence that the three described NEs of P. nodorum were transmitted to its sister species, Phaeosphaeria avenaria tritici 1, via interspecific hybridization. [ABSTRACT FROM AUTHOR]