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

Abstract

The fungal plant pathogen Austropuccinia psidii is spreading globally and causing myrtle rust disease symptoms on plants in the family Myrtaceae. A. psidii is dikaryotic, with two nuclei that do not exchange genetic material during the dominant phase of its life-cycle. Phased and scaffolded genome resources for rust fungi are important for understanding heterozygosity, mechanisms of pathogenicity, pathogen population structure and for determining the likelihood of disease spread. We have assembled a chromosome-level phased genome for the pandemic biotype of A. psidii and, for the first time, show that each nucleus contains 18 chromosomes, in line with other distantly related rust fungi. We show synteny between the two haplo-phased genomes and provide a new tool, ChromSyn, that enables efficient comparisons between chromosomes based on conserved genes. Our genome resource includes a fully assembled and circularised mitochondrial sequence for the pandemic biotype.

Haplotype-phased and chromosome-level genome assembly ofPuccinia polysora, a giga-scale fungal pathogen causing southern corn rust

“…This overall chromosome synteny was consistent with the dominant synteny detected by comparing BUSCO genes (Henningsen et al 2022). In addition, this conservatism of chromosome synteny was also detected between species from different genera (Edwards et al 2022).…”

“…This overall chromosome synteny was consistent with the dominant synteny detected by comparing BUSCO genes (Henningsen et al 2022). In addition, Edwards et al (2022) reported that Austropuccinia psidii (Sphaerophragmiaceae, Pucciales), was in parallel with species in Pucciniaceae, Pucciales, indicating that conservatism of chromosomal synteny can exist at a family level.…”

“…In this study, we assembled the genome of P. polysora to haplotype-resolved and chromosome-scale levels using a modified haplotype-phasing assembly pipeline. To our knowledge, the current study and the report on the myrtle rust pathogen, Austropuccinia psidii (Edwards et al 2022) provide the first giga-scale fungal genome ever assembled to complete-chromosome level. The P. polysora genome was annotated by fine-time-point gene expression data from germinated spores and infected issues, which supplied robust data for coexpression analyses of secreted proteins and prediction of candidate secreted effectors.…”

A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix

“…While several distantly related rust fungi within the Pucciniamycotina subdivision are known to have 18 haploid chromosomes (Schwessinger et al . 2020; Wu et al 2021; Edwards et al . 2022), a much greater variation in chromosome number may be expected among the Pucciniales, particularly in ancient rusts.…”

“…More recently, Tavares et al (2013) determined between 7-13 chromosomes using both electrophoretic and cytological karyotyping, as well as fluorescence in-situ hybridization of two races of H. vastatrix (race II -isolate 1065 and race VI -isolate 71) from the CIFC/ISA collection. While several distantly related rust fungi within the Pucciniamycotina subdivision are known to have 18 haploid chromosomes (Schwessinger et al 2020;Wu et al 2021;Edwards et al 2022), a much greater variation in chromosome number may be expected among the Pucciniales, particularly in ancient rusts.…”