De novoassembly and phasing of dikaryotic genomes from two isolates ofPuccinia coronataf. sp.avenae, the causal agent of oat crown rust

Abstract

21Word count for abstract: 348 22Word count for text (excluding references, table footnotes, and figure legends): 7,321 23 24 peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/179226 doi: bioRxiv preprint first posted online affecting production in nearly every oat growing region worldwide (2, 3) with yield losses due to 64 infection reaching 50% (4). 65Pca is a macrocyclic and heteroecious rust fungus (Puccinales, Basidiomycota) (2). 66Asexual or clonal reproduction of Pca occurs in oat, and its wild relatives, and involves repeated Disease management strategies for oat crown rust rely heavily on breeding for race- contrasting virulence profiles on an oat differential set ( Figure 1A and B). Isolate 12SD80 is 128 virulent on a broader range of oat differentials than isolate 12NC29, although recently released were detected by 5 days post infection (dpi) and 40-50% of infection sites displayed sporulation 135 by 7 dpi. Thus, both Pca isolates were equally aggressive in the absence of effective Pc genes.peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/179226 doi: bioRxiv preprint first posted online Aug. 25, 136De novo genome assembly and haplotype-phasing of Pca isolates. High molecular weight 137 DNA (>50 kbp) was extracted from germinated urediniospores of 12SD80 and 12NC29, and 138 long-read sequence data was generated using SMRT sequencing. This yielded approximately 139 20.9 and 25.9 Gbp of filtered subreads for 12SD80 and 12NC29, respectively. The mean and 140

A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii

“…Predicted effector genes between the haploid genomes indicate high levels of heterozygosity, as previously determined for oat crown rust and stripe rust isolates (Miller et al . 2018; Schwessinger et al .…”

A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution

“…For example, several LRS-based genome assemblies have been released for rust fungi, such as those for Pst isolates 104E 137 A- and 11-281 ( Schwessinger et al, 2018 ; Li et al, 2019b ), the Australian Pt isolate Pt104 ( Wu et al, 2020 ), and two isolates of the oat crown rust pathogen Puccinia coronata f. sp. avenae ( Miller et al, 2018 ). Recently, the LRS-based Pgt21-0 assembly was combined with Hi-C scaffolding data to yield the first chromosome-scale assembly for Pgt ( Li et al, 2019a ).…”

Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

“…Plant pathogenic fungi can secrete a series of proteins that are deployed to the host–pathogen interface during infection, including enzymes interacting with plant substrates (CAZymes, peptidases and lipases), together with proteins of unknown function [ 61 ]. Necrotrophic and hemibiotrophic plant pathogenic fungi usually secrete a larger number of enzymes that are more important for host invasion than biotrophs [ 62 , 63 ]. Our results showed that all three tested C. cassiicola strains possess a large number of secreted protein-coding genes in their genomes.…”

“…Numerous C. cassiicola strains do not encode the cassicolin toxin, and some can still cause CFL disease in rubber trees in many areas, including China, India and Thailand [ 8 , 62 ]. Similarly, serval Cas0 isolates were found to infect cucumber [ 15 ].…”