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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #407438
Research Project: Improvement of Biotic Stress Resistance in Durum and Hard Red Spring Wheat Using Genetics and Genomics

Location: Cereal Crops Research

Title: A telomere-to-telomere genome assembly resource of Bipolaris sorokiniana, the fungal pathogen causing spot blotch and common root rot diseases in barley and wheat

Author
item LENG, YUEQIANG - North Dakota State University
item DU, YANG - Valley City State University
item Fiedler, Jason
item HARIDAS, SARJEET - US Department Of Energy
item GRIGORIEV, IGOR - University Of California Berkeley
item ZHONG, SHAOBIN - North Dakota State University

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/22/2023
Publication Date: 1/17/2024
Citation: Leng, Y., Du, Y., Fiedler, J.D., Haridas, S., Grigoriev, I., Zhong, S. 2024. A telomere-to-telomere genome assembly resource of Bipolaris sorokiniana, the fungal pathogen causing spot blotch and common root rot diseases in barley and wheat. PhytoFrontiers. 4(2):247-250. https://doi.org/10.1094/PHYTOFR-08-23-0108-A.
DOI: https://doi.org/10.1094/PHYTOFR-08-23-0108-A

Interpretive Summary: The fungal pathogen that causes spot blotch, common root rot, and kernel blight is a large problem for barley and wheat production. Different strains of the pathogen were previously discovered based on their ability to infect various crop varieties. In this study, we have assembled the genome sequence of one of these strains by combining two different next-generation long-read technologies. For the first time with this pathogen, we have uncovered the entire end-to-end genome with all its associated genes and have identified the 473 potential effector genes that may be influencing the disease. This will be a valuable resource for future comparative fungal genomics studies and will assist in the determining what genes the pathogen is using to infect the host and cause disease. With a better understanding of this system, we will be able to counteract it through fungicide applications or molecular breeding to build genetic control.

Technical Abstract: Bipolaris sorokiniana (=Cochliobolus sativus) is a fungal pathogen that causes spot blotch, common root rot, and kernel blight in barley and wheat. Four pathotypes (0, 1, 2, 7) of the fungus were previously identified based on their virulence on three barley differential lines (Bowman, ND 5883 and NDB 112). Although several genome assemblies have been reported for B. sorokiniana, they are at the chromosome level and a telomere-to-telomere genome assembly is still lacking for this fungus. In this study, we assembled the genome of a pathotype 0 isolate (ND93-1) of B. sorokiniana using both PacBio HiFi reads and ultralong Oxford Nanopore Technology (ONT) reads. The genome assembly of ND93-1 has an estimated size of 35.7 Mb and consists of 16 scaffolds with telomere at both ends. A total of 11,564 protein-coding genes were predicted, including 1633 genes encoding for secretory proteins and 473 genes for effectors. This chromosome-level genome assembly provides an important resource for comparative genomics and understanding molecular biology of B. sorokiniana and the Bipolaris species.