There have been several manuscripts are now out from work that was done over the last few years. It has been great to be able to collaborate with many research teams as part of this work.
Been slow to mention these but wanted to make sure and call out the hard work from everyone. A long term collaboration lead by Cene Gostinčar on population genomics in Hortaea, a ascomycete black yeast, complemented some reference genome work we published last year . Former postdoc Ousmane Cissé published his work on Pneumocystis at the NIH in his current postdoc . Current postdoc Yan Wang published part of his thesis work and we worked on these data a bit as part of the zygolifeproject here . Graduate students Nat Pombubpa collaborated with Plant Sciences and Jeff Diez lab graduate student Courtney Collins on her thesis work looking at the mycobiome differences of soils in an alpine gradient with and without invasive shrub introduction . Andrii Gryganskyi’s work on Rhizopus phylogeny with some of the first multi-genome work on this genus that was one of the earliest collaborations on some ZyGoLife questions questions . Work exploring whether Transposable elements have a role in stage-specific gene expression in Coccidioides with Theo Kirkland and Anna Muszewska . A collaboration lead by Tom Richard’s lab and Guy Leonard sequence and assembled and annotated a genome of a ‘pseudofungus’ hyphochytriomycete called Hyphochytrium catenoides . I think I forgot to also call out that last year postdoc Jinfeng Chen published work collaboratively with postdocs Lu Lu and Sofia Robb on the active Rice transposable element system mPing and Ping .
Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM. Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient. Mol Ecol.2018 Apr 19. doi: 10.1111/mec.14694.
We published a paper on the manual curation of the literature for the Cryptococcus complex of species (C. neoformans var neoformans, C. neoformans var grubii, and C. gattii) this includes associated gene names with systematic locus names, something that was not easy to lookup without reading the published literature. In all more than 600 loci had gene names associated with them and include updated Gene Ontology associations, gene product names and descriptions and a table of orthology relationships between the genes in the different species genomes.
The early access to the paper is available was released at Eukaryotic Cell in May and includes guidelines of how the community can go forward naming genes in these species. In addition we make available a table of these names available at FungiDB at this link. And future updates are being posted through GitHub so that community contributions can happen directly through edits to the file or through the comments section at FungiDB where comments can be added by any user indicating a gene name and these will be evaluated and curated by a Scientific Curator.
This work was done my a lot of hard work from Diane Inglis and Marek Skrzypek who are scientific curators at (Stanford University) under the direction of Gavin Sherlock and the gene names and descriptions are loaded and available in FungiDB through the work of Ed Liaw and Venky Moktali at UC Riverside. We were able to do this work through an NIH R03 grant and look forward to finishing the complete literature curation by the end of this year.
We’re excited that several manuscripts were published in the last month.
One presents the first genome from the Cryptomycota, Rozella allomycis, in a manuscript published in Current Biology along with a nice companion piece from Mark van der Giezen about the work. Steven and Divya participating in this project in collaboration with Tim James at Michigan and Nico Corradi in Montreal. Some of the scripts used for this project are available as well here on github and other associated genome data are available here. We are working to get this into the next FungiDB release as well.
A paper on the population genomics of amphibian killing chytrid fungus B. dendrobatidis that culminated several years of work and large collection of researchers was published in PNAS at the beginning of the summer.
Here’s our 2010 publications wordle made with pubmed2wordle using this query that includes paper co-authored by Jason, Divya, and John with this search. [h/t to Kevin’s blog for showing this easy app – had done this previously with a cmdline bioperl script]
We had a productive period over the last year and finally saw set of papers representing this work come out in the last month. This represents great collaborations with several different groups. In addition to the Coprinus genome, we were involved in the publication of two other genome sequences thus summer. One a basidiomycete mushroom and one for an oomycete and pathogen of plants, both with a host of collaborating labs. Two papers on Neurospora also appeared as part of collaborations with Hanna Johannesson‘s group and Michael Freitag, Michael Brunner, and Deb Bell-Pedersen. A fifth paper on Coprinopsis meiotic genes is in press but will post about it when it appears.
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR. Genome Biol. 2010;11(7):R73. Epub 2010 Jul 13.
Genome sequence of the model mushroom Schizophyllum commune. Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, Vankuyk PA, Horton JS, Grigoriev IV, Wösten HA. Nat Biotechnol. 2010 Jul 11.
The work highlights the important aspect of how pathogenicity factors can be exchanged via mobile chromosomes and can be an important pathway for adaptive evolution and acquisition of new function through whole chromosome exchange between strains.