Category Archives: evolution

Postdoc & PhD positions in Evolutionary Biology – Genome organization of AM fungi

Postdoc & PhD positions in Evolutionary Biology – Genome organization of AM fungi

At the Department of Evolutionary Biology, Uppsala University, Sweden.

Description

Arbuscular mycorrhizal (AM) fungi form symbiotic interactions with almost all terrestrial plants and have done so since plants first colonized land. The postdoc and PhD position are both part of a newly funded ERC research program aimed at understanding the ecology and evolution of these widespread and important organisms. Using state-of-the art technology, e.g., PacBio long read sequencing and single nucleus genomics methods, the research program seeks to resolve the genome organization of AM fungi so that the evolutionary consequences of their genome organization can be studied. Specifically, the project aims at testing the hypothesis that genetically distinct nuclear genotypes coexist within AM fungi. The project involves culturing of AM fungi, sorting and genotyping of nuclei from individual fungal isolates, genome and meta-genome sequencing and assembly, as well as genome size estimation. Based on the outcome of this first part, the project will be developed to connect genotype and phenotype to mycorrhizal activity.

The postdoc and PhD student will work close together and be part of an expanding research team led by Anna Rosling (http://www.ieg.uu.se/evolutionary-biology/rosling/research/) in collaboration with Hanna Johannesson (http://www.iob.uu.se/research/systematic-biology/johannesson/) at the Evolutionary Biology Centre (EBC), Uppsala University. EBC constitutes an exciting arena for multidisciplinary research in evolutionary biology in a broad sense, housing some 300 scientists and graduate students. The scientific environment with numerous seminars, journal clubs and social activities offer excellent possibilities for contacts and collaborations. Local platforms for high-performance computational analyses (https://www.uppmax.uu.se/uppnex), NGS, SNP genotyping and proteomic analyses (http://www.scilifelab.se) ensure immediate access to state-of-the-art technology. This project will utilize several of the technological platforms at SciLifeLab in Uppsala, in particular the Microbial Single Cell Genomics Platform (https://www.scilifelab.se/facilities/single-cell/).

Qualifications

Experience in bioinformatics and genome analysis is necessary and experience in mycology is a merit. The ideal candidate is scientifically motivated and can work both independently and as part of a team. High standard of spoken and written English is required.

To apply for the PhD position you must have a Master Degree in Bioinformatics, Evolutionary Biology, Microbiology, Mycology or equivalent. Attach a copy of your diploma and your master thesis with the application.

To apply for the Post Doc position you must have acquired a PhD in Bioinformatics, Evolutionary Biology, Microbiology, Mycology or equivalent. Attach a copy of your PhD degree with the application.

Information about the position will be given by Anna Rosling tel +46 18-471 64 44, Anna.Rosling@ebc.uu.se.

Application: The application should include a letter with a short motivation of your interest in the position (one A4 page) and name and contact information to at least three reference persons and your CV. Use the link below to access the application form.

PhD candidates are welcome to submit their application using the link below no later than February 29, 2016. http://www.uu.se/en/about-uu/join-us/details/?positionId=88336

Post Doc candidates are welcome to submit their application by email to Anna.Rosling@ebc.uu.se no later than February 15, 2016

Postdoctoral Position in Bioinformatics – University of Ottawa

The Corradi Lab is currently seeking a postdoctoral fellow in Bioinformatics to work on projects related to Comparative and Population Genomics. The research will be led by Dr. Nicolas Corradi and carried out in a CIFAR (Canadian Institute for Advanced Research) – affiliated laboratory located in the Department of Biology of the University of Ottawa, Canada.

Website: http://corradilab.weebly.com/

The position is initially funded for one year, with the possibility of renewal for up to three years, depending on performance. The candidate is expected to work on two ongoing lab projects:

  1. Populations genomics of global samples of the bee-pathogen Nosema ceranae

    The recent decline in global populations of honey-bees has been attributed to a many factors, including infections from the microsporidian pathogen Nosema ceranae. Despite the potential threat that this parasite may have on global bee populations, the basic biology of this species is not well understood.
    The present project aims to increase our knowledge of the N. ceranae’s biology by exploring the extent, nature and function of genome diversity that exist both within and between dozens of parasite samples isolated globally (i.e. Spain, France, Turkey, Thailand, USA..etc…).
  2. Population genomics of global isolates of the model plant symbiont, Rhizophagus irregularis

    The Arbuscular Mycorrhizal Fungi (AMF) are ubiquitous plant symbionts that improve the ability of roots to uptake nutrients from soil and provide protection against plant pathogens. These organisms are intriguing as they harbor many nuclei within one cytoplasm throughout their entire life cycle. The genetic organization of these nuclei has been debated for years, but recent genome analyses in our lab are providing essential insights to this debate.

    The proposed projects aims to increase our knowledge of biology and evolution of these curious fungi and critical symbionts by investigating the genome diversity within and across different strains of the model AMF R. irregularis sampled globally.

For specific enquiries please contactDr. Nicolas Corradi (ncorradi@uottawa.ca).

Applicants are expected to have a strong background in either comparative genomics or populations genomics. Experience in either population genetics, environmental genomics, metagenomics, or ab-initio gene annotation and programming will be seen as an asset for the final selection of the candidate. Some basic training in bioinformatics (Perl, Python, or R) is desired.

A complete application package includes a CV, a one-page description of past research accomplishments and future goals, and the names and e-mail addresses of at least 2 references. The position opens immediately, and evaluation of applications will continue until a suitable candidate is found.

The University of Ottawa is a large, research-intensive university, hosting over 40,000 students and located in the downtown core area of Canada’s capital city. Ottawa is a vibrant, multicultural city with a very high quality of life.

Applications can be sent to Dr. Nicolas Corradi (ncorradi@uottawa.ca).

Representative publications:

  • Pelin A., Selman M., Laurent Farinelli, Aris-Brosou S. and N. Corradi. 2015. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae. Environmental Microbiology
  • Ropars J. and N. Corradi. 2015. Heterokaryotic vs Homokaryotic Mycelium in the Arbuscular Mycorrhizal Fungi: Different Techniques, Different Results? New Phytologist
  • Corradi, N. 2015. Microsporidians: Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfer. Annual Review of Microbiology
  • Riley R., Charron P., Idnurm A., Farinelli F., Yolande D. , Martin F. and N. Corradi. 2014. Extreme diversification of the mating type–high?mobility group (MATA?HMG) gene family in a plant?associated arbuscular mycorrhizal fungus. New Phytologist
  • Tisserant E., Malbreil M. et al. 2013. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. PNAS

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).

Fear of Fungi!

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

One Fungus, One Name

The naming of organisms is an important part of how we communicate. When a fungus is found, be it a mycelium from a rotting fruit, a mushroom from the forest, or something growing on a petri dish, we have used morphological and other phenotypic characteristics to group them together and identify if it is an already known species or a new one. However, some fungi have very different shapes and forms that occur during asexual and sexual (after mating with a partner) stages, some incredible elaborate and even (to some people) beautiful. Because these stages mean that fungi can look very different, and often these fungi are not amenable to life in the laboratory (e.g. we can’t get it to complete the lifecycle in an petri dish in the lab), it was the case that observed asexual (or anamorphic) and sexual (teleomorphic) forms of a species get different names. For some species, connecting the two forms has eluded mycologists, and those which had a lack of a sexual stage were called Fungi Imperfecti. Some fungi are only thought to have an asexual stage, though that may change as more molecular and other data is developed.

If we don’t share names that refer to the same thing, how do I know the mushroom you found in Alaska is the same as the one from North Carolina?  Enter molecular identification of species by genotyping a common marker sequence such as the ITS spacer region of Fungi. The ITS region (Intergenic Internal Transcribed Spacer) has been proposed as the best molecule for this based on a variety of analyses and has been deployed in labs for many years. Other marker sequences (such as intron and COX1/COI) have been proposed but so far it appears that ITS is the blessed marker for fungi by the Barcode of Life project for the time being (see the fungal barcoding site too). The recent Amsterdam declaration proposed we could name fungi with a single name based on this marker sequence and perhaps simplify life for new students learning to memorize two names for a fungus which has a sexual and asexual lifecycle.

A summary of the history and challenges here can be found in a recent paper in IMA Fungus by John Taylor One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR (available pre-print here). In particular we can see that at least two papers have gone ahead and taken the Amsterdam proposal to heart and had already starting named one name for groups of fungi (perhaps predating the proposal) and removing what may seem confusing and perhaps outdated approach of teleomorph and anamorph naming. See Houbraken et al and also Crous et al where the authors state “Separate teleomorph and anamorph names are not provided for newly introduced genera, even where both morphs are known”.

Many mycologists are looking on as to what will happen next as to the naming of future species and how we unify this. We also hope to have better approaches to naming Environmental sequences which are only known by the sequence of ITS obtained from a soil, water, air, plant material sequencing experiment. A discussion held at the MSA meeting in Fairbanks will produce a more mature position paper lead by David Hibbett that can be discussed and vetted by the community as to how to proceed with deluge of new unidentified species that will emerge from large scale pyrosequencing of environments. If you have ideas, concerns, or want to read and comment on the current ideas in the proposal, please contact David. Hopefully we can surf this wave and get new names in the system lest we be swept away by it!

John W Taylor (2011). One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR IMA Fungus, 2 (2) : 10.5598/imafungus.2011.02.02.01

Houbraken, J., Frisvad, J., & Samson, R. (2010). Taxonomy of Penicillium citrinum and related species Fungal Diversity, 44 (1), 117-133 DOI: 10.1007/s13225-010-0047-z

Still time to sign up for EMBO Comparative Genomics meeting

[via Teun Boekhout]

This year looks like another great lineup of speakers for the EMBO Comparative Genomics of Microorganisms: ‘Understanding the Complexity of Diversity’ 15-20 Oct 2011 Sant Feliu de Guixols, Spain.

Andrew Allen J. Craig Venter Institute US
Anders Blomberg Göteborg University SE
Chris Bowler École Normale Supérieure FR
Gertraud Burger University of Montreal CA
Bernard Dujon Institut Pasteur FR
Toni Gabaldón CRG, Barcelona ES
Ursula Goodenough Washington University US
Michael Gray Dalhousie University CA
Joseph Heitman Duke University US
Christiane Hertz-Fowler University of Liverpool UK
Regine Kahmann Max Planck Institute DE
Patrick Keeling University of British Columbia CA
Nicole King UC, Berkeley US
Edda Klipp Humboldt University DE
Veronique Leh Louis University of Strasbourg FR
Jan Pawlowski University of Geneva CH
Jure Piskur Lund University SE
Tom Richards University of Exeter UK
Andrew J. Roger Dalhousie University CA
David Roos University of Pennsylvania US
Iñaki Ruiz-Trillo University of Barcelona ES
Joseph Schacherer University of Strasbourg FR
Artur Scherf Institut Pasteur FR
Joey Spatafora Oregon State University US
Nicholas Talbot University of Exeter UK
Kevin Verstrepen University of Leuven BE
Eric Westhof University of Strasbourg FR
Patrick Wincker Genoscope FR
Ken Wolfe Smurfit Institute of Genetics IE
Alexandra Z. Worden University of California US

Some comments from former participants:

Comments from 2009 meeting

Overall rating

Based on responses from 80% of participants:

Excellent 50%; Very Good 44%; Good 6%.

 

Comments:

It is hard to improve the meeting. It’s a good mixture of conference and workshop with a lot of input from expert of adjacent field.

I strongly support the idea the meeting is organized in the future at a regular basis.

Very high quality, open minded with presentations ranging from pure genomics to implementation in the field of ecology; plenty of novelties. Plenty of time to discuss and to establish potential collaborations

I hope to have the possibility to go in the future to this meeting. We learn a lot, and also the size is well, the students have the possibility to talk of discuss with senior

Great work!

Thanks to the organizers for an extremely interesting and productive meeting.

Great meeting. This is a unique meeting because it brings together a group of scientists that dont normally interact with each other. Thus, great opportunities for cross-interactions. This meeting has the potential to fill a very unique niche. I enjoyed meeting new people from diverse fields. I plan to attend again and encourage my colleagues to do so.

This meeting was a great match to my interests but also challenged me to think outside of my normal sphere.  I applaud the organizers and the participants in making this a useful meeting.

The meeting was very well organized and at a very good location. I enjoyed it very much.

I hope this meeting continues as it was a valuable forum for the field of comparative genomics.

This meeting is unique in its broad organism focus. Please keep supporting it.

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.

A new kind of monograph – online

C. pruinosa

A critical part of understanding and documenting the diversity is formal descriptions of species and their relatives. This can be a laborious task and is usually captured in the form of a monograph of a species where a group of species are described in careful detail along with the phylogenetic relationships of them.  This has served as the basis for documentation of the the natural history and morphological descriptions of species.  The information is typically presented in the form of a book that goes to a library or your shelf which can be pulled down and poured over when trying to determine traits for a group of organisms.  Books are great but sharing images and the

Ryan Kepler, a PhD student at Oregon State, is writing a monograph about the ever so cool Cordyceps fungi which have intimate and quite manipulative relationship with insects. However, he’s doing it as an electronic monograph that he is publishing on the web. This is a great way to share this technical and visual information. By publishing it online he is making it searchable and so that it can be a living document that can be updated over time. He’s also willing to publish it as he goes along so the current version is a starting point, but will continue to mature as he completes his PhD thesis work and has input from other experts in the field. I really like that the is publishing it early on and truly embracing an open science approach to presenting his descriptions of the species and their relationships. This is akin to other efforts putting information about species on the web, from the Encyclopedia of Life to Mushroom observer, but I really like that this is a site dedicated to capturing the expert level information that Ryan is gathering as part of this thesis in a searchable and interactive form.

Cordyceps are an interesting group of fungi not only because of their insect association, but their variety of colors and morphologies. The ability to manipulate their insect hosts also suggests a wide variety of secondary metabolites are probably produced by these fungi to enable them to change behavior of infected individuals.

Will be great to see this resource mature and also additional monographs and species descriptions to embrace an online and freely available form. I suspect there could be a (tiny) market for better web software here for making this easier so that one doesn’t have to be or have an expert web development team to deploy these for individual projects.

Where can I get orthologs?

There are several databases that include orthology prediction for fungi. These all have pros and cons. Some are more comprehensive and have many more species. Some are curated orthologies and paralogy which should be pretty stable. Some are automated and groupings and ortholog group IDs change at each iteration.

  • A phylogenetic approach from a Saccharomyces perspective is at PhylomeDB.
  • Fungal Orthogroups is based on Synergy algorithm from I. Wapinski formerly of the Regev group at the Broad Institutue.
  • Yeast gene order browser (YGOB) for Saccharomyces spp and CGOB for Candida spp.
  • OrthoMCL database based on whole genomes, not a ton of fungi but useful starting set.
  • Ensembl Genomes provides ortholog prediction as part of the Compara pipeline though there is a limited phylogenetic diversity in the current Ensembl Fungal genomes.
  • TreeFam has Saccharomyces cerevisiae and Schizosaccharomyces pombe as the two fungi included in the curated ortholog assignments and phylogenies.
  • SIMAP provides pre-computed similarities among all proteins in UniProt.
  • InParanoid provides a pretty comprehensive of available 100 whole genomes and many fungal genomes which I tried to help select.
  • JGI’s Mycocosm attempts to provide a fungal focused paralog/gene family look at clusters of genes based on whole genomes
  • E-Fungi is also an attempt at automated clustering with some fancy webservices logic.
  • Fungal Transcription Factor database focused just on families of transcription factors.

Some of these tools are better than others in terms of providing downloadable tables.  Another problem is what Identifiers are used. Many biologists are using gene names or Locus identifiers not UniProt/GenPept IDs to identify genes or proteins of interest.  So tools that just cluster UniProt data aren’t as useful as those which refer to the gene or locus names. Also, providing a way to download all the data from a comparison is important for further mining and grouping of the data or cross-referencing local datasets.  One-by-one plugging in geneids is not really a tool that respects the idea that your user wants to ask sophisticated queries.

Also – beware that some approaches are very much pairwise comparisons lists whereas others are finding orthologous groupings.  So if you want to fine the Rad59 ortholog from all fungi it may be easier or harder depending on the source.

[I may make this a static page in the future to allow for more detailed updating since I know the available resources wax and wane]

Horizontal gene transfer from Zygo to pea aphid

Pea AphidAnother result from the analysis of the recently published genome of the pea aphid, Acyrthosiphon pisum. Nancy Moran and Tyler Jarvik present a study of the origin of the carotenoid production gene in pea aphid. Animals typically cannot make carotenoids so they sought to discover how this is possible. They find that it is derived from a horizontal gene transfer event of a fungal gene into the aphid lineage. This gene is responsible for the red-green color polymorphism in the aphid. It appears the gene is derived from a ‘zygomycete’ or relative in the early branching lineage of the fungi. One gene, a carotenoid desaturase, is encoded in a 30kb genomic region that is missing in green aphids but present in the red morphs. The region is apparently maintained in the population by frequency dependent selection since each color has an advantage or disadvantage for evading detection by predators in different environments.

The reports of eukaryotic HGT event from fungi to animals is quite rare so this finding is surprising in that sense, but the authors argue that the important ecological role of carotenoids suggest we might see even more examples if we look harder.

Moran, N., & Jarvik, T. (2010). Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids Science, 328 (5978), 624-627 DOI: 10.1126/science.1187113