Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Abstract

Austropuccinia psidii, originating in South America, is a globally invasive plant pathogen causing rust disease on Myrtaceae. Several biotypes are recognized with the most widely distributed pandemic strain spreading throughout the Asia-Pacific and Oceania regions within the last decade. Austropuccinia psidii has a broad host range (currently 480 myrtaceous species), making it a particularly dangerous plant pathogen. In the nine years since the pandemic biotype was first found in Australia in 2010, the pathogen has caused the near extinction of at least three species, the decline of at least one keystone species, and negatively affected commercial production of several Myrtaceae. To enable molecular and genomic studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype based on PacBio sequence data and scaffolding with Hi-C technology. With an estimated haploid genome size of just over 1 Gbp, it is the largest assembled fungal genome to date. We found the A. psidii genome to have a lower GC content (33.8 %), greatly expanded telomeric and intergenic regions and more repetitive regions (> 90 %) compared to other genomes of species in the Pucciniales, however numbers of predicted coding regions (18,875) are comparable. Most of the increase in genome size is caused by a recent expansion of transposable elements belonging to the Gypsy superfamily. Post-inoculation mRNA sequence capture from a susceptible host provides expression evidence for 10,613 predicted coding genes, including 210 of the 367 putative effectors. The completeness of the genome provides a greatly needed resource for strategic approaches to combat disease spread.3

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

“…After converting RSII data to subreads.bam, we obtained 162 GB of data. Details on data preprocessing and assembly are available at the myrtle-rust-genome-assembly github repository ( Tobias 2019 ). In brief, RSII bax.h5 files were converted to subreads.bam before fasta files were extracted from all datasets.…”

“…After extracting fasta files for assembly, we had approximately 72X raw sequence coverage (7.24E + 10 bases and 5.80E + 06 reads). The reads were then mapped to an in-house A. psidii mitochondrial sequence to retain only genomic DNA sequence data (APSI_mitochondria.fa available on the github repository) ( Tobias 2019 ). Canu v1.6 long-read assembly software ( Koren et al 2017 ) was used to assemble the genome with correctedErrorRate = 0.040, batOptions = “-dg 3 -db 3 -dr 1 -ca 500 -cp 50” and predicted genome size of 1 Gb.…”

A new, highly aggressive race of Austropuccinia psidii infects a widely planted, myrtle rust‐resistant, eucalypt genotype in Brazil

“…Unpublished data by Santos, S.A., DFP/UFV; Tobias et al, 2020). TEs play multiple roles in genome plasticity, pathogenicity, and evolution in fungal phytopathogens (Razali et al, 2019).…”

“…production of powdery, bright-yellow urediniospores associated with shoot dieback that may ultimately result in plant mortality (Alfenas et al, 2009;Coutinho et al, 1998). MR has significant economic importance in eucalypt plantations (Alfenas et al, 2003(Alfenas et al, , 2009Carvalho et al, 1998;Glen et al, 2007;Graça et al, 2011;Silva et al, 2017;Zauza et al, 2015), especially during the first year after planting when trees are 0.5-to 3.0-m tall (Zauza et al, 2010). In eucalypt plantations, MR can cause a 23%-35% reduction in wood volume, as determined in a study conducted by the Company Votorantim Celulose e Papel covering five plantations of 6-year-old E. grandis, distributed in the regions of Guararema, São José dos Campos, and Taubaté in São Paulo state, Brazil (Santos, Gomes et al, 2020).…”

Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

“…To date, 358 native species from 49 genera identified in Australia were susceptible to rust [9]. There are several efforts to improve knowledge about the biology of A. psidii, such as the sequencing of its nuclear genome [10][11][12][13]; proteomic of urediniospores [14]; effects of cuticular waxes on fungal germination [15]; confirmation of its sexual life cycle [12,16]; among others. Recently, taxonomic studies have led to the reclassification of A. psidii.…”