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

Fungal conferences abstract wordle

I am preparing to read through the abstracts submitted for the 26th Fungal Genetics Conference in choosing talks for my session and I wondered if there were any changing trends in the topics over the years. While I won’t put up the Wordle for this year’s abstracts till the booklet is published, I thought I’d see how the topics trended in the last few years for some of these meetings. Will be fun to do this for a few more years back to see whether real trends emerge.

The data is a little cleaned up but the text included institution and individual names so things like university and department show up as prominent in some of these graphs.

Here is the Neurospora 2010 meeting (wordle page)

Neurospora 2010 abstracts Wordle
2010 Neurospora abstracts Wordle

 

Neurospora 2008 (wordle page)

2008 Neurospora conference abstracts Wordle

25th (2009) Fungal Genetics Conference (wordle page)

25th Fungal Genetics Abstracts
25th Fungal Genetics Wordle

24th (2007) Fungal Genetics Conference (wordle page)

24th Fungal Genetics abstracts Wordle

 

The roundup of twittered updates for 2010-12-21

  • A new oomycete genome:Signatures of adaptation to obligate biotrophy in the H. arabidopsidis genome. http://bit.ly/hGwHVq #
  • Characterization of the meiosis-specific recombinase Dmc1 of pneumocystis. http://bit.ly/enwyc7 #
  • FTIR spectroscopic discrimination of Saccharomyces cerevisiae and Saccharomyces bayanus strains. http://bit.ly/fLP0QH #
  • Global gene expression analysis of A. nidulans reveals metabolic shift and transcription suppression under hypoxia. http://bit.ly/aSgbBr #
  • Ime1 and Ime2 are required for pseudohyphal growth of Saccharomyces cerevisiae on nonfermentable carbon sources. http://bit.ly/hfadNF #
  • Identification & functional characterization of genes inv in the sexual reproduction of the ascomycete fungus G. zeae http://bit.ly/f1kO0D #
  • Laser capture disc of M. larici-populina uredinia revealed a transcriptional switch btw biotrophy & sporulation. http://bit.ly/gmZIWi #
  • Adaptation of yeasts S.cerevisiae & B.bruxellensis to winemaking conditions: a cmp study of stress genes expression http://bit.ly/dQTHTR #
  • Identification of transcripts upregulated in asexual & sexual fruiting bodies of Dutch elm disease Ophiostoma novo-ulmi http://bit.ly/fchmje #
  • The transcription factor Rbf1 is the master regulator for b-mating type controlled pathogenic development in U maydis http://bit.ly/hDHQjY #
  • Role of Individual Subunits of the N.crassa CSN Complex in Regulation of Deneddylation and Stability of Cullin Proteins http://bit.ly/gz055z #
  • Structure, Function, and Phylogeny of the Mating Locus in the Rhizopus oryzae Complex http://bit.ly/gIIAum #
  • LaeA Control of Velvet Family Regulatory Proteins for Light-Dependent Development and Fungal Cell-Type Specificity. http://bit.ly/dUZomH #
  • Pathogenicity determinants in smut fungi revealed by genome comparison. http://bit.ly/gnuXIP #
  • Genome evolution following host jumps in the Irish potato famine pathogen lineage. http://bit.ly/gHWgTC #
  • Blumeria genome: Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. http://bit.ly/gT5zOq #

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3 faculty jobs in fungal biology at U Georgia

This came across EvolDir today.

The University of Georgia invites applications for three tenure-track positions in the biology of fungi and fungus-like organisms to join a highly interactive multi-departmental group of plant and microbial biologists.

1) The Department of Plant Biology in the Franklin College of Arts and Sciences seeks applicants at the level of assistant professor, though candidates may also be considered at the level of early associate professor. We are especially interested in applicants studying the biology, genetics, cellular biology, functional genomics, phylogenomics or ecology of plant-associated fungi, including mycorrhizal fungi.

2) The Department of Microbiology in the Franklin College of Arts and Sciences seeks applicants at the level of assistant professor, though candidates may also be considered at the level of early associate professor. We are especially interested in applicants studying fungal diversity and ecology; fungal interactions with plants, animals or other microbes; fungal natural products and their impact on the environment, food or human health; manipulation of fungi for industrial and environmental applications, such as biofuel production and bioremediation; and other areas in basic and applied fungal biology.

3) The Department of Plant Pathology in the College of Agricultural and Environmental Sciences seeks applicants at the assistant or associate professor level. We are especially interested in applicants studying plant-fungal interactions to facilitate management of economically important plant diseases, understanding the ecological and genetic dynamics of host-pathogen resistance, and using contemporary approaches to elucidate the phylogeny of plant-pathogenic fungal species. Applicants at the assistant professor level should have a Ph.D. degree and postdoctoral research experience.

Applicants at the associate professor level should also have a record of independent scientific productivity. Successful applicants will be expected to establish (assistant professor) or continue and expand (associate professor) a vigorous externally-funded research program and to instruct and mentor undergraduate and graduate students. To apply, the following should be submitted at https://www.plantbio.uga.edu/positions/ :

(1) a single PDF containing a cover letter which includes a statement of the position(s) the candidate is applying for, a curriculum vitae, and 1-2 page statements of research interests and teaching philosophy; (2) a single PDF containing reprints of three research papers; (3) three letters of recommendation submitted directly by the references. For questions, please contact Stephanie Chirello at schirello@plantbio.uga.edu or 706-542-1820. Review of applications will begin February 7, 2011, and the search will remain open until the positions are filled. The Franklin College of Arts and Sciences, the College of Agricultural and Environmental Sciences, their many units and the University of Georgia are committed to increasing the diversity of faculty and students and sustaining a work and learning environment that is inclusive. Women, minorities and people with disabilities are encouraged to apply. The University of Georgia is an EEO/AA institution.

Jim Leebens-Mack
4505 Miller Plant Sciences
Department of Plant Biology
University of Georgia
Athens, GA 30602-7271
Phone: 706-583-5573
Fax: 706-542-1805
email: jleebensmack@plantbio.uga.edu
url: http://www.plantbio.uga.edu/~jleebensmack/JLMmain.html

Genetics, Epigenetics and Evolution of Sex Chromosomes

[Save the date] On 9-10 June 2011, the French Genetics Society (SFG) is organising a meeting “Genetics, Epigenetics and Evolution of Sex Chromosomes” in Paris. Sessions will cover evolution, sex determination, meiosis, dosage compensation and epigenetics. The meeting will include invited talks, talks to be chosen from submitted abstracts and poster sessions. Registration and abstract submission will open in February, on the web site of the SFG.

Les 9-10 juin 2011, la Société Française de Génétique (SFG) organise un colloque “Génétique, Epigénétique et Evolution des Chromosomes Sexuels” à Paris. Les thèmes abordés lors des sessions incluront l’évolution, la détermination du sexe, la méïose, la compensation de dose et l’épigénétique. Le colloque comprendra des présentations orales invitées, mais aussi des présentations orales choisies parmi les résumés soumis, ainsi que des présentations par affiches. Les inscriptions et la soumission de résumés seront ouverts en Février sur le site de la SFG