Reference assembly and annotation of the Pyrenophora teres f. teres isolate 0-1

Authors: WYATT, NATHAN - North Dakota State University; BRUEGGEMAN, R - North Dakota State University; Friesen, Timothy

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/20/2017
Publication Date: 1/1/2018
Citation: Wyatt, N.A., Brueggeman, R.S., Friesen, T.L. 2018. Reference assembly and annotation of the Pyrenophora teres f. teres isolate 0-1. G3, Genes/Genomes/Genetics. 8:1-8.

Interpretive Summary: The fungal pathogen Pyrenophora teres f. teres (P. teres f. teres) causes the destructive disease net form net blotch (NFNB) of barley. NFNB typically results in 10-40% losses, but can result in complete crop loss when susceptible barley cultivars are grown under cool wet conditions. A significant amount of research has been done to identify and characterize the genetics of resistance to this destructive pathogen in barley, but this resistance is often overcome by the pathogen. Little is known about how the pathogen causes disease in barley, yet this is critical to our understanding of not only the pathogen but also of how to overcome this disease through breeding for durable resistance. Therefore, we have developed tools to investigate the P. teres f. teres-barley interaction by focusing on the genetics of the pathogen. Here we present a reference quality genome sequence assembly of P. teres f. teres in which we have annotated the genes, making it possible to identify the pathogen genes that ultimately lead to economic losses for growers.

Technical Abstract: Pyrenophora teres f. teres, the causal agent of net form net blotch (NFNB) of barley, has become a prevalent pathogen in barley growing regions of the world. Typical yield losses due to NFNB range from 10-40%, however, complete loss has been observed on 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 and annotation provides a robust resource for the examination of the barley-P. teres f. teres host-pathogen co-evolution.