De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae , the Causal Agent of Oat Crown Rust

MBio
Marisa E MillerMelania Figueroa

Abstract

Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effecto...Continue Reading

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Nov 6, 2018·BioTechniques·Alistair R McTaggartBrenda D Wingfield
Dec 5, 2019·Phytopathology·Guus Bakkeren, Les J Szabo
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Mar 19, 2021·Phytopathology·Daniela E CardenasLiliana M Cano
Oct 21, 2020·Microbiological Research·Rajdeep JaswalT R Sharma

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Datasets Mentioned

BETA
PGCI00000000

Methods Mentioned

BETA
RNA-seq
electrophoresis
Illumina sequencing

Software Mentioned

CAZymes
ggjoy
HPCdaligner
BEDtools
Proteinortho
RepeatMasker
HISAT2
Quiver
SignalP
Funannotate

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