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.

Keywords: Hordeum vulgare; barley net blotch; optical mapping; repeat annotation; single molecule sequencing DNA; synteny; transposable element.

FIGURE 1

Net blotch field symptoms on barley leaves. (A) Net form net blotch (NFNB) caused by Pyrenophora teres f. teres with lesions along leaf veins containing longitudinal and transverse striations and (B) ovoid lesions in spot form net blotch (SFNB) caused by P. teres f. maculata.

FIGURE 2

Large scale inter- and intra-chromosomal rearrangements between P. teres and P. tritici-repentis. Two major rearrangements were detected between both forms of P. teres and P. tritici-repentis. Nucmer matches (Kurtz et al., 2004) were filtered to show regions longer than 1 kb.

FIGURE 3

Whole genome macrosyntenic comparison of P. teres f. teres and P. teres f. maculata. Nucmer matches (Kurtz et al., 2004) show high conservation of synteny between the two forms, represented here by strains PTM SG1 (chromosomes depicted on the left-hand side of each alignment) and PTT W1-1 (chromosomes depicted on the right-hand side). Collinear syntenic blocks >1 kb in length are shown in blue. Gaps between syntenic blocks are composed of low GC, repetitive, and transposon-rich regions. Similarly, matches to the reverse strand shown in red are repetitive transposon-rich regions rather than genic translocations or inversions.

FIGURE 4

Whole-genome histogram of GC-content for all P. teres PacBio genome assemblies generated by OcculterCut (Testa et al., 2016). In both P. teres f. teres (PTT) and P. teres f. maculata (PTM), in all genomes, the bulk of the genome is GC-equilibrated to just over 50%. Secondary bands with approximately 30% GC content are stronger in PTT than PTM. GC content of DNA sequencing reads are shown in Supplementary Figure 4. The intensity of secondary bands vary between PTT isolates consistent with genome size.

FIGURE 5

Total repeat length of each repeat element type. The difference in genome size between P. teres f. teres (PTT) and P. teres f. maculata (PTM) is due to a relatively larger length of low-GC regions in PTT. In both forms, long terminal repeats (LTRs) comprise the bulk of the repeats. The DNA transposable Tcl-Mariner-like elements are consistently more abundant in PTT than PTM. A table of repeat lengths for two isolates is available in Supplementary Table 1 and a log-transformed version or this figure presented in Supplementary Figure 3 to show low abundance families.