Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements

Long-Read-Based de novo Genome Assembly and Comparative Genomics of the Wheat Leaf Rust Pathogen Puccinia triticina Identifies Candidates for Three Avirulence Genes

Leaf rust, caused by Puccinia triticina (Pt), is one of the most devastating diseases of wheat, affecting production in nearly all wheat-growing regions worldwide. Despite its economic importance, genomic resources for Pt are very limited. In the present study, we have used long-read sequencing (LRS) and the pipeline of FALCON and FALCON-Unzip (v4.1.0) to carry out the first LRS-based de novo genome assembly for Pt. Using 22.4-Gb data with an average read length of 11.6 kb and average coverage of 150-fold, we generated a genome assembly for Pt104 [strain 104-2,3,(6),(7),11; isolate S423], considered to be the founding isolate of a clonal lineage of Pt in Australia. The Pt104 genome contains 162 contigs with a total length of 140.5 Mb and N50 of 2 Mb, with the associated haplotigs providing haplotype information for 91% of the genome. This represents the best quality of Pt genome assembly to date, which reduces the contig number by 91-fold and improves the N50 by 4-fold as compared to the previous Pt race1 assembly. An annotation pipeline that combined multiple lines of evidence including the transcriptome assemblies derived from RNA-Seq, previously identified expressed sequence tags and Pt race 1 protein sequences predicted 29,043 genes for Pt104 genome. Based on the presence of a signal peptide, no transmembrane segment, and no target location to mitochondria, 2,178 genes were identified as secreted proteins (SPs). Whole-genome sequencing (Illumina paired-end) was performed for Pt104 and six additional strains with differential virulence profile on the wheat leaf rust resistance genes Lr26, Lr2a, and Lr3ka. To identify candidates for the corresponding avirulence genes AvrLr26, AvrLr2a, and AvrLr3ka, genetic variation within each strain was first identified by mapping to the Pt104 genome. Variants within predicted SP genes between the strains were then correlated to the virulence profiles, identifying 38, 31, and 37 candidates for AvrLr26, AvrLr2a, and AvrLr3ka, respectively. The identification of these candidate genes lays a good foundation for future studies on isolating these avirulence genes, investigating the molecular mechanisms underlying host-pathogen interactions, and the development of new diagnostic tools for pathogen monitoring.

Puccinia triticina pathotypes THTT and THTS display complex transcript profiles on wheat cultivar Thatcher

BACKGROUND

Wheat leaf rust is an important disease worldwide. Understanding the pathogenic molecular mechanism of Puccinia triticina Eriks. (Pt) and the inconstant toxic region is critical for managing the disease. The present study aimed to analyze the pathogenic divergence between Pt isolates.

RESULTS

Total RNA was extracted from the wheat cultivar Thatcher infected by two Pt isolates, Tc361_1 (THTT) and Tc284_2 (THTS), at 144 h post inoculation (hpi). The mRNA was then sequenced, and a total of 2784 differentially expressed genes (DEGs) were detected. Forty-five genes were specifically expressed in THTT; these genes included transcription initiation factors and genes with transmembrane transporter activity and other genes. Twenty-six genes were specifically expressed in THTS, including genes with GTPase activity, ABC transporters and other genes. Fifty-four differentially expressed candidate effectors were screened from the two isolates. Two candidate effectors were chosen and validated on tobacco, and the results showed that they could inhibit necrosis induced by BAX. qRT-PCR of 12 significant DEGs was carried out to validate that the results are similar to those of RNA-seq at 144 hpi, to show the expression levels of these DEGs in the early stage and to elucidate the differences in expression between the two Pt pathotypes.

CONCLUSION

The results obtained in this study showed that although the two pathotypes of THTT and THTS contribute similar virulence to wheat, there are a large number of genes participate in the interaction with the susceptible wheat cultivar Thatcher, and revealed the pathogenicity of rust is very complicated.

Progress on Molecular Genetics and Manipulation of Rust Fungi

Among the thousands of rust species described, many are known for their devastating effects on their hosts, which include major agriculture crops and trees. Hence, for over a century, these basidiomycete pathogenic fungi have been researched and experimented with. However, due to their biotrophic nature, they are challenging organisms to work with and, needing their hosts for propagation, represent pathosystems that are not easily experimentally accessible. Indeed, efforts to perform genetics have been few and far apart for the rust fungi, though one study performed in the 1940s was famously instrumental in formulating the gene-for-gene hypothesis describing pathogen-host interactions. By taking full advantage of the molecular genetic tools developed in the 1980s, research on many plant pathogenic microbes thrived, yet similar work on the rusts remained very challenging though not without some successes. However, the genomics era brought real breakthrough research for the biotrophic fungi and with innovative experimentation and the use of heterologous systems, molecular genetic analyses over the last 2 decades have significantly advanced our insight into the function of many rust fungus genes and their role in the interaction with their hosts. This has allowed optimizing efforts for resistance breeding and the design and testing of various novel strategies to reduce the devastating diseases they cause.

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

Three members of the Puccinia genus, Pucciniatriticina (Pt), Pstriiformis f.sp. tritici (Pst), and Pgraminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection.

Investigating Gene Function in Cereal Rust Fungi by Plant-Mediated Virus-Induced Gene Silencing

Cereal rust fungi are destructive pathogens, threatening grain production worldwide. Targeted breeding for resistance utilizing host resistance genes has been effective. However, breakdown of resistance occurs frequently and continued efforts are needed to understand how these fungi overcome resistance and to expand the range of available resistance genes. Whole genome sequencing, transcriptomic and proteomic studies followed by genome-wide computational and comparative analyses have identified large repertoire of genes in rust fungi among which are candidates predicted to code for pathogenicity and virulence factors. Some of these genes represent defence triggering avirulence effectors. However, functions of most genes still needs to be assessed to understand the biology of these obligate biotrophic pathogens. Since genetic manipulations such as gene deletion and genetic transformation are not yet feasible in rust fungi, performing functional gene studies is challenging. Recently, Host-induced gene silencing (HIGS) has emerged as a useful tool to characterize gene function in rust fungi while infecting and growing in host plants. We utilized Barley stripe mosaic virus-mediated virus induced gene silencing (BSMV-VIGS) to induce HIGS of candidate rust fungal genes in the wheat host to determine their role in plant-fungal interactions. Here, we describe the methods for using BSMV-VIGS in wheat for functional genomics study in cereal rust fungi.

Distinct cell cycle regulation during saprophytic and pathogenic growth in fungal pathogens

In a number of dimorphic and hemibiotrophic pathogens, cell cycle regulation has been shown to be important for morphological changes related to infectious growth or infection-related morphogenesis. However, the role of mitotic CDK kinase Cdc2, the key regulator of cell cycle, in pathogenic growth is not clear, because most fungal pathogens have a single CDC2 gene that is essential for cell cycle progression and viability. Interestingly, the wheat scab fungus Fusarium graminearum has two CDC2 genes. Although CDC2A and CDC2B have redundant functions in vegetative growth and asexual production, only CDC2A is required for invasive growth and plant infection. In this study, we showed that Cdc2A and Cdc2B interacted with each other and may form homo- and heterodimers in vegetative hyphae. We also identified sequence and structural differences between Cdc2A and Cdc2B that may be related to their functional divergence. These results, together with earlier studies with cyclins, important for differentiation and infection in Candida albicans and Ustilago maydis, indicated that dimorphic and hemibiotrophic fungal pathogens may have stage-specific cyclin-CDK combinations or CDK targets during saprophytic and pathogenic growth.

Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism

Research on obligate biotrophic plant parasites, which reproduce only on living hosts, has revealed a broad diversity of filamentous microbes that have independently acquired complex morphological structures, such as haustoria. Genome studies have also demonstrated a concerted loss of genes for metabolism and lytic enzymes, and gain of diversity of genes coding for effectors involved in host defense suppression. So far, these traits converge in all known obligate biotrophic parasites, but unexpected genome plasticity remains. This plasticity is manifested as transposable element (TE)-driven increases in genome size, observed to be associated with the diversification of virulence genes under selection pressure. Genome expansion could result from the governing of the pathogen response to ecological selection pressures, such as host or nutrient availability, or to microbial interactions, such as competition, hyperparasitism and beneficial cooperations. Expansion is balanced by alternating sexual and asexual cycles, as well as selfing and outcrossing, which operate to control transposon activity in populations. In turn, the prevalence of these balancing mechanisms seems to be correlated with external biotic factors, suggesting a complex, interconnected evolutionary network in host-pathogen-microbe interactions. Therefore, the next phase of obligate biotrophic pathogen research will need to uncover how this network, including multitrophic interactions, shapes the evolution and diversity of pathogens.

On the current status of Phakopsora pachyrhizi genome sequencing

Recent advances in the field of sequencing technologies and bioinformatics allow a more rapid access to genomes of non-model organisms at sinking costs. Accordingly, draft genomes of several economically important cereal rust fungi have been released in the last 3 years. Aside from the very recent flax rust and poplar rust draft assemblies there are no genomic data available for other dicot-infecting rust fungi. In this article we outline rust fungus sequencing efforts and comment on the current status of Phakopsora pachyrhizi (Asian soybean rust) genome sequencing.