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

Abstract

Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.

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

“…These reads were assembled, polished and circularised into a contiguous 94,553 bp circular mtDNA genome (37.42% GC), APSIMTv2. The previously published mtDNA genome from the MF-1 isolate of A. psidii was assembled with a combination of sequence read-types (NC_044121.1) and is 93,299 bp (de Almeida et al . 2021).…”

“…This subset was reassembled with Hifiasm and a new 94.5 kb circular contig representing the mtDNA was identified. A double-copy version of this contig was polished with Hypo v1.0.3 using only the “pure” 10 kb reads and re-circularised to have the same starting position as published A. psidii mtDNA sequence NC_044121.1 (de Almeida et al . 2021).…”

In Planta Study Localizes an Effector Candidate from Austropuccinia psidii Strain MF-1 to the Nucleus and Demonstrates In Vitro Cuticular Wax-Dependent Differential Expression

“…In comparison to Au-3 and PREM, this strain has a smaller predicted genome size (650 Mbp), though this could be due to differences in the sequencing technologies used (GenBank accession number GCA_000469055.1). The MF-1 mitochondrial genome is also available [ 27 ] and meiotic spores have been observed in older infections on E. grandis [ 26 ]. Due to the complexity of A. psidii host interactions, in particular the numerous pathogen strains, as well as different host genotypes, much remains to be understood about this important plant pathogen.…”

Exploring Mitogenomes Diversity of Fusarium musae from Banana Fruits and Human Patients

“…Mitochondrial genomes evolve independently of and faster than the nuclear genome [10]. Mitogenomes have also been proposed as a useful tool for diagnostic purposes in Fusarium species [11].…”