Reference Assembly and Annotation of the Pyrenophora teres f. teres Isolate 0-1

Abstract

Pyrenophora teres f. teres, the causal agent of net form net blotch (NFNB) of barley, is a destructive pathogen in barley-growing regions throughout the world. Typical yield losses due to NFNB range from 10 to 40%; however, complete loss has been observed on highly susceptible barley lines where environmental conditions favor the pathogen. Currently, genomic resources for this economically important pathogen are limited to a fragmented draft genome assembly and annotation, with limited RNA support of the P. teres f. teres isolate 0-1. This research presents an updated 0-1 reference assembly facilitated by long-read sequencing and scaffolding with the assistance of genetic linkage maps. Additionally, genome annotation was mediated by RNAseq analysis using three infection time points and a pure culture sample, resulting in 11,541 high-confidence gene models. The 0-1 genome assembly and annotation presented here now contains the majority of the repetitive content of the genome. Analysis of the 0-1 genome revealed classic characteristics of a “two-speed” genome, being compartmentalized into GC-equilibrated and AT-rich compartments. The assembly of repetitive AT-rich regions will be important for future investigation of genes known as effectors, which often reside in close proximity to repetitive regions. These effectors are responsible for manipulation of the host defense during infection. This updated P. teres f. teres isolate 0-1 reference genome assembly and annotation provides a robust resource for the examination of the barley–P. teres f. teres host–pathogen coevolution.

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

“…Consistent with total genome sizes, the chromosomes ranged in size from 1.99 to 7.22 Mbp in PTT W1-1 and 1.56–5.43 Mbp for PTM SG1. Chromosomes were numbered to match the PTT 0-1 chromosomes ( Wyatt et al, 2017 ).…”

“…Scaffolds were manually merged using Geneious 8.1.8 ( Kearse et al, 2012 ). PTM FGO was assembled as described by Wyatt et al (2017) for PTT 0-1.…”

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

“…Ptr race 1 isolates M4 (NQIK01000000.1) [29], V1 (SAXQ00000000) [66], Pt-1C-BFP (AAXI01000000.1) [28]. Ptt isolates included Beecher virulent W1-1 (OCTH01000000.1), Harbin virulent 0-1 (NPOS01000000.1) [31], FGOH04Ptt-21 (VBVN01000000.1), 6A (VFEN01000000.1), 15A (VBVL01000000.1) [32], Beecher virulent BB25 (VBVM01000000.1), Yeong, Maritime and Kombar virulent NB29 (WJSO01000000.1), Shepherd virulent NB73 (WJSN01000000.1) and Prior, Corvette and Gilbert virulent NB85 (WJSM01000000.1) [30]. Ptm isolates included SG1 (OCTF01000000.1) [30] and FGOB10 (PRJNA417860) (unpublished).…”

“…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.…”

Expression Analysis of Cell Wall-Related Genes in the Plant Pathogenic Fungus Drechslera teres

“…In light of the crucial role played by the fungal cell walls as targets in the development of effective drugs to inhibit pathogens' growth, we here mine the genome of D. teres to identify key genes involved in cell wall biosynthesis [12,13]. The goal is to analyze their expression pattern in the spores and the mycelium grown on different media and in the presence/absence of the plant growth-promoting bacterium (PGPB) Paraburkholderia phytofirmans, strain PsJN [14][15][16].…”