The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing

Paula Moolhuijzen,Caroline S Moffat,Pao Theen See

doi:10.1186/s13104-021-05751-0

Abstract

ObjectivesThe assembly of fungal genomes using short-reads is challenged by long repetitive and low GC regions. However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented genome assemblies derived from short reads only. Here, a necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) isolate 134 (Ptr134), which causes tan spot disease on wheat, was sequenced on a MinION using Oxford Nanopore Technologies (ONT), to improve on a previous Illumina short-read genome assembly and provide a more complete genome resource for pan-genomic analyses of Ptr.ResultsThe genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%. The long-read assembly provided 6.79 Mb of new sequence and 2846 extra annotated protein coding genes as compared to the previous short-read assembly. This improved genome sequence represents near complete chromosomes, an important resource for large scale and pan genomic comparative analyses.

Highlights

The necrotrophic fungal pathogen Pyrenophora triticirepentis (Ptr) is the causal agent of tan spot a major disease of wheat (Triticum aestivum) [1]
The Oxford Nanopore Technologies (ONT) Ptr isolate 134 (Ptr134) annotated genome has been deposited with DNA Data Bank of Japan (DDBJ)/European Nucleotide Archive (ENA)/GenBank under the updated accession MVBF02000000
Genome assembly and annotation of Ptr134 The Ptr134 genome assembled into 28 contiguous sequences with of total length 40.79 Mega bases (Mb) and GC content of 50.81% (Table 1)

Summary

Results

The genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%. The long-read assembly provided 6.79 Mb of new sequence and 2846 extra annotated protein coding genes as compared to the previous short-read assembly. This improved genome sequence represents near complete chromosomes, an important resource for large scale and pan genomic comparative analyses

Introduction

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Results and discussion

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