Genomes of tropical rust fungi (Araucariomyces, Coleosporium, Hamaspora, Puccinia paululla, Skierka, and Sphaerophragmium)

Hi, 

Everyone is welcome to use the assemblies shared here.

The catch is they are not perfect. The DNA was extracted from environmental samples and has contaminant contigs from hosts, bacteria and endophytic or saprophytic fungi. I've run Kraken2 to remove most host and bacterial contigs, but there are no doubt some remaining. The genomes were sequenced in the same run and the mitochondrion of Sphaerophragmium is present in all genomes.

The taxa are selected for their evolutionary relationships in the Pucciniales (see Aime and McTaggart 2021, A familial rank classification of rust fungi, with notes on genera). More about each taxon is available below.
Araucariomyces fragiforme: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/aecidiumfragiforme.html
Coleosporium plumeriae: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/coleosporiumplumeriae.html
Hamaspora acutissima: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/hamasporaacutissima.html
Puccinia paullula: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/pucciniapaullula.html
Skierka agallocha: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/skierkaagallocha.html
Sphaerophragmium acaciae: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/sphaerophragmiumacaciae.html

The raw sequencing data are available either in this Google Drive folder https://drive.google.com/drive/folders/1nDRWYLEO80R6CCxdnMzkaFY3DqUKn6Vo?usp=sharing, or contact me ([e-mail]) if you need another option.

If you have the fortitude to clean up these genomes, let's get them on to GenBank. I'd be delighted to collaborate on anything and currently am working on mating genes and mitochondria.

All genomes were assembled with the below commands for Supernova. The assembly reports have also been provided.

supernova run --id RustName --accept-extreme-coverage --localmem 350 --fastqs=$PATH/reads --maxreads=2140000000
supernova mkoutput --style=megabubbles --asmdir=$PATH/RustName/outs/assembly --outprefix=RustName_mkoutput

There are more raw sequencing data for Uromycladium and Ravenelia, but nothing assembled from these yet. You're welcome to use them if you need.

You could do me a solid and cite: McTaggart et al. (2022) Sexual reproduction is the null hypothesis in life cycles of rust fungi. PLoS Pathogens 18(5):e1010439. DOI: 10.1371/journal.ppat.1010439. We released the MAT loci based on the genomes in there, more work on RNAi pathway genes coming that can be cited as an alternative to reference these assemblies when published.

Enjoy and keep smiling,
Alistair