Tag Archives: genome

Postdoc: genome evolution of mycoheterotrophic plants.

 Naturalis has a position for a Postdoctoral researcher in the laboratory of Vincent Merckx

 We seek a postdoctoral fellow for a 12-month project on the genome evolution of mycoheterotrophic plants. The project will employ next-generation sequencing techniques for de novo  genome and transcriptome assembly of achlorophyllous mycoheterotrophic flowering plants. There will be a strong focus on genome assembly and genome comparison to dectect common genetic patterns in the evolution of mycoheterotrophy.

Full advert is here: Postdoc_Merckx

More information: mycoheterotrophy.com
Twitter: @VMerckx
YouTube: youtube.com/vincentmerckx

Basidiobolus! – genus of the month at ATCC

ATCC sent out this email with the Genus of the month as Basidiobolus. It is worth noting they call out B. ranarum as inhabitant of bat and rodent guts but it is mainly known (and named) for being associated with frogs (hence the ‘rana’). It has some quite cool biology, it grows dimorphically as a yeast or hyphae, and is reported to have a large genome (Henk and Fisher PLoS One 2012).
Note that the genome and transcriptome of B. meristosporus is being sequenced as part of the 1000 Fungal genomes project from samples Andrii Gryganski prepared. Don’t forget that YOU can propose genomes to this project by logging in here and submitting a proposed species in a family that is not sufficiently sampled (2 per Family).

The info below is from ATCC®. I couldn’t find a link to the on their site so I am copying the email text in.

There is nothing more fascinating than when a microbial species begins popping up in the literature as a true pathogen. Basidiobolus ranarum, which typically inhabits the guts of bats and small rodents, has been recently tagged as an emerging human pathogen that may have previously been unrecognized.1

       B. ranarum was first added to the CDC’s Morbidity and Mortality Weekly Report (MMWR)1 in 1999 after 6 immunocompetent individuals tested positive for gastrointestinal basidiobolomycosis over a 5-year period. The most interesting aspect of this study, however, was the fact that each patient was originally misdiagnosed with some other intestinal ailment, ranging from diverticulitis to cancer.

While many of the Zygomycetes, including Basidiobolus, have been implicated in subcutaneous human diseases, it is still relatively uncommon for Basidiobolus to colonize the human intestine. This new development piqued the interest of several researchers at the Mayo Clinic in Scottsdale, Arizona, a region of the U.S. where the majority of such cases have been reported.  Following an in-depth analysis of all known case records, they discovered a total of 44 cases of gastrointestinal basidiobolomycosis worldwide; 19 of which occurred in the southwestern U.S., 11 in Saudi Arabia, and 14 in other arid regions of the globe.2

Symptoms displayed in each case were similar, with complaints ranging from abdominal distention and pain to a palpable abdominal mass. Of particular interest was a patient originally treated for Clostridium difficile colitis. This patient underwent several surgeries and treatment with oral vancomycin before a stool fungal culture revealed the presence of B. ranarum. While this patient was successfully treated with a 3-month course of voriconazole, repeated at 1-year follow-up, the investigators cautioned that antifungal resistance may pose a problem in the future. Earlier work performed by the same group revealed uniform resistance to amphotericin B and flucytosine in four  B. ranarum isolates, as well as mixed resistance to several other azoles.2

The source of B. ranarum infection leading to gastrointestinal disease is still not understood, but the fecal-oral route has been suggested. Pathologists and clinicians should be aware of this potential new threat, and additional work to understand the pathogenesis and antifungal susceptibility/resistance of B. ranarum should be an on-going effort among the research and medical communities.

ATCC® Basidiobolus Strains
Want to learn more about ATCC Basidiobolus strains available from ATCC? View a list of Basidiobolus spp. online.

References

1. Centers for Disease Control and Prevention (CDC). MMWR: Gastrointestinal Basidiobolomycosis – Arizona, 1994-1999. August 20, 1999.

2. Vikram, et al. Emergence of Gastrointestinal Basidiobolomycosis in the United States, with a Review of Worldwide Cases. Clinical Infectious Diseases Advance Access published on March 22, 2012.

Nominate genomes for F1000 project

I posted over in the 1000 Fungal genomes blog, as well as a post by Francis Martin, about details for nominating your fungus for the F1000 project. You have to be able to supply DNA and RNA and justify the project under DOE/JGI mission, but we are looking for contributors to help fill in all the gaps in the diversity of sampled fungal genomes.

There might even be a way to use these projects to support mycology or genomics classes. For example one part of a class could work on isolation and growth of the fungi, obtaining RNA and DNA and sending this off to to the sequencing center. The rest of the class would be spent analyzing existing fungal genomes. In the subsequent year the nominated genome would likely be completed and the next year’s class could work on processing it.

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.

Cordyceps on the brain

Cordyceps militaris (Ryan Kepler)I gave a lecture on animal-fungal symbionts and parasites this week so was doing more reading of recent literature on insect-fungi associations. A couple of quick notes worth sharing.

Ophiocordyceps unilateralis was the parasite of the day last week and includes a description of an interesting recent paper looking at the consistency of the symptoms of zombie ants. The article also mentions Carl Zimmer’s post on the same paper in more detail.

You of course have seen the very cool electronic/online Cordyceps monograph at cordyceps.us from Joey Spatafora’s lab?

The genome of Cordyceps militaris was sequenced by researchers at the Chinese Academy of Sciences. They find a reduced copy numbers of many gene families suggesting to the authors that the specialized ecology of the fungus may have limited the need for expanded gene families. The do find expanded copy numbers of metalloproteases – a finding we have also seen in human and amphibian associated pathogens as well as by the authors who looked at the insect associated fungus Metarhizium. There is also a reduction in cutinases and genes related to degrading plant cell walls similar to findings in the human associated pathogens Coccidioides suggesting similar genomic routes to specializing on an animal host from a generalist. They also found that this fungus is heterothallic based on genomic identification of the MAT1-1 locus. There are several more interesting findings in the paper including expression profiling of fruiting body via RNA-Seq.
Zheng, P., Xia, Y., Xiao, G., Xiong, C., Hu, X., Zhang, S., Zheng, H., Huang, Y., Zhou, Y., Wang, S., Zhao, G., Liu, X., St Leger, R., & Wang, C. (2011). Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine Genome Biology, 12 (11) DOI: 10.1186/gb-2011-12-11-r116

Schizophyllum genome update

Robin Ohm at the JGI has announced the release of version 2 of the Schizophyllum commune genome. This is great news on the heels of the announcement that one of the funded 2012 CSPs will include detailed functional genomics experiments in this mushroom.

I am pleased to announce the public release of the JGI annotation and portal for the improved assembly of Schizophyllum commune.  Annotations of the assembly are now publicly visible at http://jgi.doe.gov/Scommune2 .  Annotation and editing privileges remain password-protected but all other tools are now available to the general public.

A detailed set of statistics on the assembly and annotation can be found on the Info page of that portal:  http://genome.jgi-psf.org/Schco2/Schco2.info.html

 

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

Genome sequence of mushroom Schizophyllum commune

Schizophyllum CommuneI am excited to announce the publication of another mushroom genome this week. The mushroom Schizophyllum commune is an important model system for mushroom biology, development of genome was sequenced as part of efforts at the Joint Genome Institute and a collection of international researchers.  The data and analyses from these efforts are presented in a publication appearing in Nature Biotechnology today.

Studies in mushrooms can have important impact on other research areas.  They can be useful in biotechnology as protein biosynthesis factories for producing compounds or even as an edible delivery mechanism for new drugs.  What we found in the analysis of this genome include clues to mechanisms of how white rotting fungi degrade lignin through analysis of enzyme families.  We also saw evidence for extensive antisense transcription during different developmental stages suggesting some important clues as to how some gene regulation could impact or control developmental progression.  Through gene expression comparison (by MPSS) a large number of transcription factors were shown to be differentially regulated during sexual development.  A knockout out two of these (fst3 and fst4) resulting in changes in ability to form mushrooms (fst4) or smaller mushrooms (fst3).

Several more interesting findings in this work that I hope to add back to this post when there is a little more time –

Ohm, R., de Jong, J., Lugones, L., Aerts, A., Kothe, E., Stajich, J., de Vries, R., Record, E., Levasseur, A., Baker, S., Bartholomew, K., Coutinho, P., Erdmann, S., Fowler, T., Gathman, A., Lombard, V., Henrissat, B., Knabe, N., Kües, U., Lilly, W., Lindquist, E., Lucas, S., Magnuson, J., Piumi, F., Raudaskoski, M., Salamov, A., Schmutz, J., Schwarze, F., vanKuyk, P., Horton, J., Grigoriev, I., & Wösten, H. (2010). Genome sequence of the model mushroom Schizophyllum commune Nature Biotechnology DOI: 10.1038/nbt.1643

A mushroom on the cover

I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus.  You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some of the high points in the paper.

Coprinopsis cover

Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C., Deng, J., Dietrich, F., Fargo, D., Farman, M., Gathman, A., Goldberg, J., Guigo, R., Hoegger, P., Hooker, J., Huggins, A., James, T., Kamada, T., Kilaru, S., Kodira, C., Kues, U., Kupfer, D., Kwan, H., Lomsadze, A., Li, W., Lilly, W., Ma, L., Mackey, A., Manning, G., Martin, F., Muraguchi, H., Natvig, D., Palmerini, H., Ramesh, M., Rehmeyer, C., Roe, B., Shenoy, N., Stanke, M., Ter-Hovhannisyan, V., Tunlid, A., Velagapudi, R., Vision, T., Zeng, Q., Zolan, M., & Pukkila, P. (2010). Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) Proceedings of the National Academy of Sciences, 107 (26), 11889-11894 DOI: 10.1073/pnas.1003391107