2012 was certainly a banner year in genome sequence production and publications. The cost of generating the data keeps dropping and the automation for assembly and annotation continues to improve making it possible for a range of groups to publish genomes.
I made a NCBI PubMed Collection of these here Fungal Genomes 2012
Some notable fungal genome publications include
- the button mushroom Agaricus bisporus (your pizzas would never be the same without it)
- plant pathogens Colletotrichum
- comparative analyses of 18 genomes from plant associated Dothideomycetes
- new microsporidian genomes including two new Encephalitozoon and C. elegans parasites helping resolve some phylogenetic position of these fungi also explored in another paper.
- multiple genomes of the wine spoilage yeast Dekkera
- the Chinese medicinal mushroom Ganoderma
- the barley pathogen Ustilago hordei and comparison with maize pathogens U. maydis and Sporisorium reilianum
- human pathogen Candida orthopsilosis and comparison with its close relative C. parapsilosis.
- the basal basidiomycete and xerotolerant Wallemia sebi
- The transcriptome of Glomus intraradices
There were also several new insights into the evolution of wood decay fungi derived from new genomes of basidiomycete fungi. This includes
- the tree pathogen Heterobasidion annosum
- the white rot fungus Ceriporiopsis subvermispora
- a draft of the brown rotter Fibroporia radiculosa
- a magnum opus reconstructing the evolution history of lignin degradation in basidiomycete fungi in “The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes“.
(Now I might have missed a few in my attempt to get this done before holidays overtake me – if so, please post comments or tweets and I’ll be sure to amend the list on pubmed and here.)
A new trend for fungal genome papers can be seen now in the Genome Announcements of Eukaryotic Cell which aim to get the genome data out quickly with a citateable reference. These are short descriptions which I expect will become more popular ways to insure data made public can also be cited. I only counted about 5 published in 2012 but I expect to see a lot more of these in the 2013 either at EC or other journals. I’m sure there will still be some tension between providers making data public as soon as possible and the sponsoring authors’ desire to have first crack at analyzing and publish interpretations and comparison of the genome(s). The bacterial community has been doing this for Genome Reports in the SIGS journal and the Journal of Bacteriology so will see what happens as these small eukaryotic genomes become even easier to produce.
I look forward to exciting year with more of the 1000 Fungal genomes and other JGI projects start to roll out more genomes. I also predict there will be many more resequencing datasets published as functional and population genomics. It will also probably be a countdown for what are the last Sanger sequenced genomes and how the many flavors of next generation sequencing will be optimized for generation. I am hopeful work on automation of annotation and comparisons will be even easier for more people to use and that we start to provide a shared repository of gene predictions. I’ve just launched the latter and look forward to engaging more people to contribute to this.