Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

Abstract

Pyrenophora teres, P. teres f. teres (PTT) and P. teres f. maculata (PTM) cause significant diseases in barley, but little is known about the large-scale genomic differences that may distinguish the two forms. Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. The genomes of the two forms are highly collinear, each composed of 12 chromosomes. Genome evolution in P. teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a process that isolates blocks of genic sequence. The phenomenon is particularly pronounced in PTT, which has a larger, more repetitive genome than PTM and more recent transposon activity measured by the frequency and size of genome fissures. PTT has a longer cultivated host association and, notably, a greater range of host–pathogen genetic interactions compared to other Pyrenophora spp., a property which associates better with genome size than pathogen lifestyle. The two forms possess similar complements of TE families with Tc1/Mariner and LINE-like Tad-1 elements more abundant in PTT. Tad-1 was only detectable as vestigial fragments in PTM and, within the forms, differences in genome sizes and the presence and absence of several TE families indicated recent lineage invasions. Gene differences between P. teres forms are mainly associated with gene-sparse regions near or within TE-rich regions, with many genes possessing characteristics of fungal effectors. Instances of gene interruption by transposons resulting in pseudogenization were detected in PTT. In addition, both forms have a large complement of secondary metabolite gene clusters indicating significant capacity to produce an array of different molecules. This study provides genomic resources for functional genetics to help dissect factors underlying the host–pathogen interactions.

Parallel evolution of multiple mechanisms for demethylase inhibitor fungicide resistance in the barley pathogenPyrenophora teresf. sp.maculata

“…Sequences were assembled using Geneious 6.1.8 (Biomatters, Auckland, New Zealand) and aligned with ClustalW algorithm (Thompson, Higgins, and Gibson 1994) with the following parameters: IUB scoring matrix, gap opening penalty 15, gap extension penalty 6.66 and free end gaps. Insertion sequences were analysed using BLASTN 2.10.0+ algorithm (Altschul et al 1990) against Ptm isolate SG1 reference genome (GenBank BioProject number PRJEB18107) (Syme et al 2018). Prediction of promoter sequences within the upstream regulatory regions performed using Neural Network Promoter Prediction 2.2 software (http://www.fruitfly.org/seq_tools/promoter.html) with a cutoff score of 0.8 (Reese 2001).…”

Expansion and Conservation of Biosynthetic Gene Clusters in Pathogenic Pyrenophora spp.

“…Two new Australian Ptt isolates with differing pathotypes were sequenced to add to existing genome assemblies for four pathotypes [30] (Table 1). As Ptt has a comparatively large and variable genome size compared to Ptm and Ptr, these isolates were included to increase the potential to detect isolate-specific differences in BGCs.…”

“…Previous PacBio genome sequencing projects for Ptr, Ptt and Ptm [28][29][30][31][32] have provided an opportunity to explore the genetic capacity of these taxa to produce specialised metabolites and explore gene cluster conservation within the three different species. To date, whole genome-based comparative investigation into specialised metabolite BGCs in Ptr, Ptt and Ptm has not been undertaken.…”

“…Initial investigations into Ptr found that not all backbone biosynthetic genes were conserved between the different races of Ptr [28,29]. In Ptt, a genome expansion of low complexity (low GC) regions and NRPS genes was identified when comparatively analysed to Ptm and Ptr, and many predicted NRPSs were found to be non-canonical, with some of their main enzymatic domains missing (e.g., adenylation, peptidyl carrier protein, condensation and/or thioesterase domains) [30]. This study investigates the genome SM landscape for three important fungal diseases that have a direct negative impact on global barley and wheat yields.…”

Genetic variation of Pyrenophora teres f. teres isolates in Western Australia and emergence of a Cyp51A fungicide resistance mutation

“…To investigate genetic variation of PTT in WA, genetically unlinked and neutral SSR markers were selected from a genome assembly composed of whole chromosomes, based on PacBio single molecule long-read DNA sequencing with optical mapping (Syme et al, 2018). The markers were intended to provide unbiased estimates of allelic variability of isolates from across the main WA barley-growing area in the southwest of the state.…”