Category Archives: pathogens

2012 Fungal Genomes: a review of mycological genomic accomplishments

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

There were also several new insights into the evolution of wood decay fungi derived from new genomes of basidiomycete fungi. This includes

(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.

Recent animal-associated fungal genome papers

The genomes of five dermatophyte fungi were sequenced and the analyses of their lifestyles presented in a new paper out in mBio in Martinez et al. 2012. The authors were able to identify gene family changes that associate with lifestyle changes including proteases that can degrade keratin suggesting how these species have adapted to obtaining nutrients from an animal host. The continued finding of fungal-specific kinase families in these fungi, extending the observations from previous studies in Coprinopsis and Paracoccidioides on the FunK1 kinase family, makes me hope we will some day get some molecular information on the specificity of these families in addition to these copy number observations.
Another paper published in Genome Research this summer from Emily Troemel‘s lab and the Broad Institute describes the sequencing of two microsporidia species that are natural parasites of Caenorhabditis.The paper reveals some suprising things about Microsporidia evolution including the presence of a clade-specific nucleoside H+ symporter which is only found in bacteria and some eukaryotes and not in any Fungi. The phyletic distribution suggested it was acquired more recently and couple from lateral gene transfer. This acquisition likely helps the microsporidia cells obtain nucleosides from the host since the parasite cannot synthesize these. There is also evidence of evolution of microsporidia-specific secretion signals in the hexokinases which may be a mechanism for delivery of these enzymes into host cells to catalyze rapid growth once inside the host. Many more gems in this paper including phylogenetic placement of the microsporidia from phylogenomic approaches (also see related recent work from Toni Gabaldon‘s lab).

Few fungi+host papers

Three papers on some cool fungi that interact with hosts and I recommend them for a good read.

One is coverage of by Ed Yong on rice blast (Magnaporthae orzyae) on paper from Nick Talbot and Gero Steinberg‘s lab on appressorium development in Science this week.

A paper from my lab on role of an expansion of copy number of a chitin-binding domain in the amphibian pathogen B. dendrobatidis.

New Scientist also provides a nice summary of tripartite symbiosis paper on Metarhizium, insects, and plants from Mike Bidochka’s lab.

Eastern hemlocks and citizen science

If you live on the east coast and are interested in a citizen science project or an outreach project through your classes check out this post from Cyme & Cystidium. Especially if you like to tromp around the woods and can help find fungi associated with Eastern Hemlock trees which are undergoing a serious die-off due to an insect called the Woolly Adelgid. Cyme is interested in finding what happens to the mycorrhizal fungi associated with trees undergoing this massive die-off so collecting what fungal species fruit under these trees will help answer questions as to what kinds of shifts in populations occur when the host species are lost.

Vote for your favorite plant pathogenic fungus

Molecular Plant Pathology (twitter: MPPjournal) is engaging the community to vote for their favorite plant pathogenic fungus. Below is info requesting your vote.

As a member of the MPP community we would like you to take part in a fun but informative vote.

We aim to publish a Review detailing the top 10 plant pathogenic fungi worldwide, and we need your help.

Please could you list 3 fungi you feel should be in the top 10.
There is no need to rank them. Please state after the name whether it is for
scientific impact (SI) or economic impact (EI).

An example might be…

Magnaporthe grisea (SI/EI)
Melampsora lini (SI)
Botrytis cinerea (EI)

We will rank all the entries to compile a list. We will then find authors to write a short piece (1/2 page or so) on each one, introducing the pathogen and explaining its importance. This Review will be published in MPP for people to use, comment upon and discuss.

We hope you will take part, it will only take a few seconds of your time.

Please send your vote to diane.hird[AT]bristol.ac.uk by 11th February at the latest.

Feel free to pass on this email to any colleagues or co-workers as the more votes we get the better. Many thanks

Best wishes
Diane

-------------------------------
Dr Diane Hird
Journal Administrator
Molecular Plant Pathology
School of Biological Sciences
University of Bristol
Woodland Road
Bristol, BS8 1UG, UK

Tel/Fax: +44 (0)117 331 7021
Email: diane.hird[AT]bristol.ac.uk

Microsporidia genomes on the way

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.

Presents for the holidays – Plant pathogen genomes

Though a bit cliche, I think the metaphor of “presents under the tree” of some new plant pathogen genomes summarized in 4 recent publications is still too good to resist.  There are 4 papers in this week’s Science that will certainly make a collection of plant pathogen biologists very happy. There are also treats for the general purpose genome biologists with descriptions of next generation/2nd generation sequencing technologies, assembly methods, and comparative genomics. Much more inside these papers than I am summarizing so I urge you to take look if you have access to these pay-for-view articles or contact the authors for reprints to get a copy.

Hyaloperonospora

These include the genome of biotrophic oomycete and Arabidopsis pathogen Hyaloperonospora arabidopsidis (Baxter et al). While preserving the health of Arabidopsis is not a major concern of most researchers, this is an excellent model system for studying plant-microbe interaction.  The genome sequence of Hpa provides a look at specialization as a biotroph. The authors found a reduction (relative to other oomycete species) in factors related to host-targeted degrading enzymes and also reduction in necrosis factors suggesting the specialization in biotrophic lifestyle from a necrotrophic ancestor. Hpa also does not make zoospores with flagella like its relatives and sequence searches for 90 flagella-related genes turned up no identifiable homologs.

While the technical aspects of sequencing are less glamourous now the authors used Sanger and Illumina sequencing to complete this genome at 45X sequencing coverage and an estimated genome size fo 80 Mb. To produce the assembly they used Velvet on the paired end Illumina data to produce a 56Mb assembly and PCAP (8X coverage to produce a 70Mb genome) on the Sanger reads to produce two assemblies that were merged with an ad hoc procedure that relied on BLAT to scaffold and link contigs through the two assembled datasets. They used CEGMA and several in-house pipelines to annotate the genes in this assembly. SYNTENY analysis was completed with PHRINGE. A relatively large percentage (17%) of the genome fell into ‘Unknown repetitive sequence’ that is unclassified – larger than P.sojae (12%) but there remain a lot of mystery elements of unknown function in these genomes.  If you jump ahead to the Blumeria genome article you’ll see this is still peanuts compared to that Blumeria’s genome (64%). The largest known transposable element family in Hpa was the LTR/Gypsy element. Of interest to some following oomycete literature is the relative abundance of the RLXR containing proteins which are typically effectors – there were still quite a few (~150 instead of ~500 see in some Phytophora genomes).

Blumeria

 

A second paper on the genome of the barley powdery mildew Blumeria graminis f.sp. hordei and two close relatives Erysiphe pisi, a pea pathogen, and Golovinomyces orontii, an Arabidopsis thaliana pathogen (Spanu et al).  These are Ascomycetes in the Leotiomycete class where there are only a handful of genomes Overall this paper tells a story told about how obligate biotrophy has shaped the genome. I found most striking was depicted in Figure 1. It shows that typical genome size for (so far sampled) Pezizomycotina Ascomycetes in the ~40-50Mb range whereas these powdery mildew genomes here significantly large genomes in ~120-160 Mb range. These large genomes were primarily comprised of Transposable Elements (TE) with ~65% of the genome containing TE. However the protein coding gene content is still only on the order of ~6000 genes, which is actually quite low for a filamentous Ascomycete, suggesting that despite genome expansion the functional potential shows signs of reduction.  The obligate lifestyle of the powdery mildews suggested that the species had lost some autotrophic genes and the authors further cataloged a set of ~100 genes which are missing in the mildews but are found in the core ascomycete genomes. They also document other genome cataloging results like only a few secondary metabolite genes although these are typically in much higher copy numbers in other filamentous ascomycetes (e.g. Aspergillus).  I still don’t have a clear picture of how this gene content differs from their closest sequenced neighbors, the other Leotiomycetes Botrytis cinerea and Sclerotinia sclerotium, are on the order of 12-14k genes. Since the E. pisi and G. orontii data is not yet available in GenBank or the MPI site it is hard to figure this out just yet – I presume it will be available soon.

More techie details — The authors used Sanger and second generation technologies and utilized the Celera assembler to build the assemblies from 120X coverage sequence from a hybrid of sequencing technologies.  Interestingly, for the E. pisi and G. orontii assemblies the MPI site lists the genome sizes closer to 65Mb in the first drafts of the assembly with 454 data so I guess you can see what happens when the Newbler assembler which overcollapses repeats. They also used a customized automated annotation with some ab intio gene finders (not sure if there was custom training or not for the various gene finders) and estimated the coverage with the CEGMA genes. I do think a Fungal-Specific set of core-conserved genes would be in order here as a better comparison set – some nice data like this already exist in a few databases but would be interesting to see if CEGMA represents a broad enough core-set to estimate genome coverage vs a Fungal-derived CEGMA-like set.

 

A third paper in this issue covers the genome evolution in the massively successful pathogen Phytophora infestans through resequencing of six genomes of related species to track recent evolutionary history of the pathogen (Raffaele et al). The authors used high throughput Illumina sequencing to sequence genomes of closely related species. They found a variety differences among genes in the pathogen among the findings “genes in repeat-rich regions show[ed] higher rates of structural polymorphisms and positive selection”. They found 14% of the genes experienced positive selection and these included many (300 out of ~800) of the annotated effector genes. P. infestans also showed high rates of change in the repeat rich regions which is also where a lot of the disease implicated genes are locating supporting the hypothesis that the repeat driven expansion of the genome (as described in the 2009 genome paper). The paper generates a lot of very nice data for followup by helping to prioritize the genes with fast rates of evolution or profiles that suggest they have been shaped by recent adaptive evolutionary forces and are candidates for the mechanisms of pathogenecity in this devastating plant pathogen.

 

A fourth paper describes the genome sequencing of Sporisorium reilianum, a biotrophic pathogen that is closely related species to corn smut Ustilago maydis (Schirawski et al). Both these species both infect maize hosts but while U. maydis induces tumors in the ears, leaves, tassels of corn the S. reilianum infection is limited to tassels and . The authors used comparative biology and genome sequencing to try and tease out what genetic components may be responsible for the phenotypic differences. The comparison revealed a relative syntentic genome but also found 43 regions in U. maydis that represent highly divergent sequence between the species. These regions contained disproportionate number of secreted proteins indicating that these secreted proteins have been evolving at a much faster rate and that they may be important for the distinct differences in the biology. The chromosome ends of U. maydis were also found to contain up to 20 additional genes in the sub-telomeric regions that were unique to U. maydis. Another fantastic finding that this sequencing and comparison revealed is more about the history of the lack of RNAi genes in U. maydis. It was a striking feature from the 2006 genome sequence that the genome lacked a functioning copy of Dicer. However knocking out this gene in S. reilianum failed to show a developmental or virulence phenotype suggesting it is dispensible for those functions so I think there will be some followups to explore (like do either of these species make small RNAs, do they produce any that are translocated to the host, etc).  The rest of the analyses covered in the manuscript identify the specific loci that are different between the two species — interestingly a lot of the identified loci were the same ones found as islands of secreted proteins in the first genome analysis paper so the comparative approach was another way to get to the genes which may be important for the virulence if the two organisms have different phenotypes. This is certainly the approach that has also been take in other plant pathogens (e.g. Mycosphaerella, Fusarium) and animal pathogens (Candida, Cryptococcus, Coccidioides) but requires a sampling species or appropriate distance that that the number of changes haven’t saturated our ability to reconstruct the history either at the gene order/content or codon level.

Without the comparison of an outgroup species it is impossible to determine if U. maydis gained function that relates to the phenotypes observed here through these speculated evolutionary changes involving new genes and newly evolved functions or if S. reilianum lost functionality that was present in their common ancestor. However, this paper is an example of how using a comparative approach can identify testable hypotheses for origins of pathogenecity genes.

 

Hope everyone has a chance to enjoy holidays and unwrap and spend some time looking at these and other science gems over the coming weeks.

 

Baxter, L., Tripathy, S., Ishaque, N., Boot, N., Cabral, A., Kemen, E., Thines, M., Ah-Fong, A., Anderson, R., Badejoko, W., Bittner-Eddy, P., Boore, J., Chibucos, M., Coates, M., Dehal, P., Delehaunty, K., Dong, S., Downton, P., Dumas, B., Fabro, G., Fronick, C., Fuerstenberg, S., Fulton, L., Gaulin, E., Govers, F., Hughes, L., Humphray, S., Jiang, R., Judelson, H., Kamoun, S., Kyung, K., Meijer, H., Minx, P., Morris, P., Nelson, J., Phuntumart, V., Qutob, D., Rehmany, A., Rougon-Cardoso, A., Ryden, P., Torto-Alalibo, T., Studholme, D., Wang, Y., Win, J., Wood, J., Clifton, S., Rogers, J., Van den Ackerveken, G., Jones, J., McDowell, J., Beynon, J., & Tyler, B. (2010). Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome Science, 330 (6010), 1549-1551 DOI: 10.1126/science.1195203

Spanu, P., Abbott, J., Amselem, J., Burgis, T., Soanes, D., Stuber, K., Loren van Themaat, E., Brown, J., Butcher, S., Gurr, S., Lebrun, M., Ridout, C., Schulze-Lefert, P., Talbot, N., Ahmadinejad, N., Ametz, C., Barton, G., Benjdia, M., Bidzinski, P., Bindschedler, L., Both, M., Brewer, M., Cadle-Davidson, L., Cadle-Davidson, M., Collemare, J., Cramer, R., Frenkel, O., Godfrey, D., Harriman, J., Hoede, C., King, B., Klages, S., Kleemann, J., Knoll, D., Koti, P., Kreplak, J., Lopez-Ruiz, F., Lu, X., Maekawa, T., Mahanil, S., Micali, C., Milgroom, M., Montana, G., Noir, S., O’Connell, R., Oberhaensli, S., Parlange, F., Pedersen, C., Quesneville, H., Reinhardt, R., Rott, M., Sacristan, S., Schmidt, S., Schon, M., Skamnioti, P., Sommer, H., Stephens, A., Takahara, H., Thordal-Christensen, H., Vigouroux, M., Wessling, R., Wicker, T., & Panstruga, R. (2010). Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism Science, 330 (6010), 1543-1546 DOI: 10.1126/science.1194573

Raffaele, S., Farrer, R., Cano, L., Studholme, D., MacLean, D., Thines, M., Jiang, R., Zody, M., Kunjeti, S., Donofrio, N., Meyers, B., Nusbaum, C., & Kamoun, S. (2010). Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage Science, 330 (6010), 1540-1543 DOI: 10.1126/science.1193070

Schirawski, J., Mannhaupt, G., Munch, K., Brefort, T., Schipper, K., Doehlemann, G., Di Stasio, M., Rossel, N., Mendoza-Mendoza, A., Pester, D., Muller, O., Winterberg, B., Meyer, E., Ghareeb, H., Wollenberg, T., Munsterkotter, M., Wong, P., Walter, M., Stukenbrock, E., Guldener, U., & Kahmann, R. (2010). Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison Science, 330 (6010), 1546-1548 DOI: 10.1126/science.1195330

Dynamics of amphibian pathogen infection cycles

ResearchBlogging.org
Two papers out this week on the population dynamics and epidemiology of the chytrid pathogen of amphibians, Batrachochytrium dendrobatidis (Bd). This is work from the Vredenburg and Briggs labs that includes several decade-long studies of frog declines and the prevalence of Bd.

See Vance in action swabbing a frog

In the Briggs et al paper, they describe a 5-year study on the fungal load in surviving populations of frogs in Sierra Nevada mountain lakes.  They find that adult frogs that have low enough fungal load escape chytridiomycosis and can actually lose and regain infection. They propose that fungal load dynamics are the reason behind differential survival of various populations of mountain frogs. They conclude that:

“Importantly, model results suggest that host persistence versus extinction does not require differences in host susceptibility, pathogen virulence, or environmental conditions, and may be just epidemic and endemic population dynamics of the same host–pathogen system.”

So they propose that differences in the populations that are coming down with the disease is due only to “density-dependent host–pathogen dynamics” not that some populations are resistant. They go on to provide a detailed model of persistence if the host and pathogen, chance of reinfection, and survival of the host which is derived from the long-term study data.  There are many more interesting findings and models proposed in the paper. It also further reinforces (for me) the need to know more about the molecular basis of the host-pathogen interactions and more about how the fungus persists without a host, lifestyle of how it overwinters, and the details of the microbe-host interactions, and the infection dynamic when zoospores disperse from infected frogs.

The Vrendenburg et al paper adresses the dynamics of population decline in the mountain yellow-legged frogs over a periods of 1-5 and 9-13 year study in 3 different study sites at different sampling intervals.  The authors were able to catalog the species decline and conduct skin swabbing to assess Bd prevalence. They found that the fungus spread quickly as it could detected in virtually all the lakes over the course of a year starting with a 2004 survey. The dramatic declines of frog populations in these lakes followed in the years subsequent to the initial detection. This sadly predicts that most if not all of the mountain lakes will go extinct for the frogs as the current tadpoles develop into frogs in the next 3 years and then fall victim to Bd. Based on their sampling work, the authors were also able to correlate what fungal burden predicted a subsequent decline – in populations where more the ~10,000 zoospores were detected in a swab from frog skin, then the frog population was about to experience a sharp decline.  The take-home from this work is that finding ways to keep the intensity of fungal infections down could provide a meaningful intervention that could prolong the viability of the population.

Briggs, C., Knapp, R., & Vredenburg, V. (2010). Enzootic and epizootic dynamics of the chytrid fungal pathogen of amphibians Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0912886107


Vredenburg, V., Knapp, R., Tunstall, T., & Briggs, C. (2010). Dynamics of an emerging disease drive large-scale amphibian population extinctions Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0914111107

Origins and evolution of pathogens

ResearchBlogging.org 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