The cover of Nature today highlights an article from Matthew Fisher and colleagues on the major impact that Fungi as emerging infectious diseases are playing on threatening diversity of ecosystems and agricultural productivity.
Fisher, M., Henk, D., Briggs, C., Brownstein, J., Madoff, L., McCraw, S., & Gurr, S. (2012). Emerging fungal threats to animal, plant and ecosystem health Nature, 484 (7393), 186-194 DOI: 10.1038/nature10947
New genomes from Microsporidia are on the way from the Broad Institute and other groups, and will be a boon to those working on these fascinating creatures. Microsporidia are obligate intracellular parasites of eukaryotic cells and many can cause serious disease in humans. Some parasitize worms and insects too. The evolutionary placement of these species in the fungi is still debated with recent evidence placing them as derived members of the Mucormycotina based on shared synteny (conserved gene order), in particular around the mating type locus. There is still some debate as to where this group belongs in the Fungal kingdom, with their highly derived characteristics and long branches they are still make them hard to place. The synteny-based evidence was another way to find a phylogenetic placement for them but it would be helpful to have additional support in the form of additional shared derived characteristics that group Mucormycotina and Microsporidia. There is hope that increased number of genome sequences and phylogenomic approaches can help resolve the placement and more further understand the evolution of the group.
For data analysis, a new genome database for comparing these genomes is online called MicrosporidiaDB. This project has begun incorporating the available genomes and providing a data mining interface that extends from the EuPathDB project.
An article in PLoS Pathogens by Morris et al describe a hypothesis about the evolution and origins of plant pathogens applying the parallel theories to the emergence of medically relevant pathogens. The authors highlight the importance of understanding the evolution of organisms in the context of emerging pathogens like Puccinia Ug99 for our ability to design strategies to protect human health and food supplies. Both bacterial and fungal pathogens of plants are discussed but I (perhaps unsurprisingly) focus on the fungi here. Continue reading Origins and evolution of pathogens
A new and improved annotation of Cryptococcus neoformans var grubii strain H99 (serotype A) has been made available in GenBank and the Broad Institute website. This update is collaboration between several groups providing data and analyses and the genome annotation team at the Broad Institute.
Some changes noted by the Broad Institute include:
“This release of gene predictions for the serotype A isolate Cryptococcus neoformans var. grubii H99 is based on a new genomic assembly provided by Dr. Fred Dietrich at the Duke Center for Genome Technology. The new assembly consists of 14 nuclear chromosomes and a single 21 KB mitochondrial chromosome, and has resulted in a reduction of the estimated genome size from 19.5 to 18.9 Mb. Improvements in the assembly and in our annotation process have resulted in a set of 6,967 predicted protein products, 335 fewer than the previous release.”