Tag Archives: population genomics

Postdoc: Population genomics and speciation in fungal pathogens

Post-doc position in genomics of introgressions in fungal pathogens

[from EvolDir]

We invite applications for a postdoctoral position in the Research Institute of Horticulture and Seeds. The position is for 1 year starting as soon as January 2016.

The Postdoc will conduct his research in the field of population genomics of secondary contacts and introgression in two fungal pathogens: Venturia inaequalis, an ascomycete responsible of the apple scab, and the Scedosporium apiospermum species complex which is responsible for pulmonary infections in children with cystic fibrosis.

The Postdoc will have to identify genomics regions involved in introgression between divergent populations of Venturia inaequalis and Scedosporium species. Indeed, secondary contacts between divergent genomics pools may favour the creation of new genetic combination of loci involved in pathogenicity. New hybrids should then exhibit hitherto unseen epidemiological properties. The Postdoc will work in a team involved in several projects of genetics or genomics, functional genomics, and evolutionary epidemiology (IRHS – ECOFUN team).

Using resequenced genomes (89 for V. inaequalis and 23 for the Scedosporium species complex), the Postdoc will be in charge of the assembling, genome aligning and SNP calling, prior to population genomics analyses. The Postdoc will have to infer evolutionary histories at the interspecies and species levels for both datasets, identify and characterise genomic regions involved in introgressions. He [or she] will possibly collaborate with all the researchers involved in this project : population geneticists, microbiologists, functional genomicists, phytopathologists.

We are looking for a candidate with a keen interest for population genomics and evolutionary history in structured populations. The candidate must hold a PhD in population genomics with strong skills in bioinformatics (manipulation of NGS data, assembling, demographic inferences). Good written communication skill and ability to work as part of a team are required.

How to apply:
Applicants should submit

  1.  a cover letter describing their research interests and background,
  2.  a detailed CV (including list of publications), and
  3. the contact details of three references to bruno.lecam@angers.inra.fr or christophe.lemaire@univ-angers.fr. The cover letter should also include possible starting dates.

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

Postdoc: Fungal Comparative and Population Genomics

The Corradi Lab is currently seeking a Postdoctoral Fellow in the field of Fungal 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.

The position will be initially funded for one year, with the possibility of renewal for up to three years depending on performance. The candidate is expected to contribute to several ongoing projects that focus on the population genomics of two evolutionary unrelated groups of fungi: the Arbuscular Mycorrhizal Fungi (AMF) and the Microsporidia. Enquiries about specific projects can be sent to Dr. Nicolas Corradi (ncorradi@uottawa.ca).

Applicants are expected to have a background in comparative genomics or populations genomics. A strong experience in either Population Genetics, Environmental Genomics, Metagenomics, or ab-initio gene annotation and programming will be seen as an strong asset for the final selection of the candidate. Basic knowledge of Linux is required.

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. Evaluation of applications starts immediately and 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 (http://www.science.uottawa.ca/fac/welcome.html). Ottawa is a vibrant, multicultural city with a very high quality of life (http://www.ottawatourism.ca/fr/)

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

Representative publications:

  •  Riley R. et al. 2014. Extreme Diversification of the MATA-HMG Gene Family in the Plant – Associated Arbuscular Mycorrhizal Fungi. New Phytologist. 201: 254–268
  •  James T.Y et al. 2013. Shared signatures of parasitism and phylogenomics unite the Cryptomycota and Microsporidia. Current Biology. 23 (16), 1548–1553
  • Tisserant E. et al. The arbuscular mycorrhizal Glomus genome provides insights into the evolution of the oldest plant symbiosis. Proceedings of the National Academy of Sciences – USA. 110 (50), 20117-20122R576-R577
  •  Pombert J.F. et al. 2012. Gain and loss of multiple functionally-related horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proceedings of the National Academy of Sciences – USA 109(31):12638-43
  •  Selman M. et al. 2011. Acquisition of an animal gene by two microsporidia. 2011. Current Biology 21: R576-R577

Yeast population genomics

ResearchBlogging.org
I have cheered the Sanger-Wellcome SGRP group work to generate multiple Saccharomyces cerevisiae and S. paradoxus strain genome sequences.   The group had previously submitted a version of the manuscript to Nature precedings and it is now published in Nature AOP showing that submitting to a preprint server doesn’t necessarily hurt your manuscript getting published…  The research groups explored the impact of domestication (as was also recently done for the sake and soy sauce worker fungus, Aspergillus oryzae) on the Saccharomyces genome by comparing individuals from wild strains of S. paradoxus.

This paper addressed several challenges including methodology for light genome sequencing for population genomics. This data represents in a way, a pilot project on for genome resequencing projects and using draft genome sequencing with next generation sequencing tools. Of course with the pace of sequencing technology development, any project more than a couple months old will be using outdated technology it seems, but this work represents some important progress.  Tools like MAQ were also developed and tuned as part of the project.  In addition to the methods development it also provided a new look at evolutionary dynamics of a well-studied fungus.

Genome assembly
The authors apply several different quality controls and utilize a new tool called PALAS (Parallel ALignment and ASsembly)  to assemble all the strains at the same time using a graph-based approach that utilized the reference genome sequences for each species. This is different than a full-blown WGA approach like PCAP, Phusion or Arachne because this is deliberately low-coverage sequencing pass.  The authors are trying impute missing sequence via Ancestral Recombination Graphs as implemented in the Margarita system.   They also use MAQ to align sequence from Illumina/Solexa sequencing to these assemblies made by PALAS.

Since this project was on two species of SaccharomycesS. cerevisiae and S. paradoxus they needed good reference assemblies for each of these species. The previously availably S.paradoxus assembly wasn’t complete enough for this study so they did an addition 4.3 X coverage with sanger/ABI sequencing and 80X coverage with Illumina.

Population genomics and domestication

The sequencing data also provided a framework for population genetic investigations. Some simple findings showed that geographic isolates within each species were more genetically similar to each other.  The main geographic regions of samples for S.paradoxus data included the UK, American, and Far East samples, some of which had been analyzed in a very nice study on Chromosome III.  For the S. cerevisiae samples there were individuals from around Europe, at least 10 European wine strains, Malaysian, Sake brewing strains, West Africa, and North America. From these data it was possible to discover that there are several of strains with mosiac genomes meaning that pieces of the genome match best with the sake fermentation strains and other parts from the wine/European samples.

Efforts to detect the effects of natural selection that may be linked to domestication of these strains explored two different approaches. The McDonald-Kreitman test did not identify any loci under positive selection while Tajima’s D was negative in the S.cerevisiae global and wine strain populations indicating an excess of singleton polymorphisms – though they draw little conclusions from that.  The authors also observed a sharper decay of linkage disequilibrium in S.cerevisiae (half maximum of 3kb) than S.paradoxus (half maximum 9kb) suggesting that S.cerevisiae is recombining more, either due to increased opportunities or a great frequency of recombination events when it does.

In context of the paper title and the idea of exploring the effects of domestication on the genome, the authors observe that the standard paradigm that ‘domesticated’ species have lower diversity levels is simply not the case in these samples.  This isn’t to say there isn’t evidence of the selection for fermentation production from these strains based on the stress response conditions they were tested on, but that there is still ample evidence of maintaining diversity within the populations presumably through various amounts of outcrossing.

We are also interested in these results as we apply similar questions to population genomics of the human pathogenic fungus Coccidioides where 14 strains have been sequenced with sanger sequencing technology.  Hopefully some of these lessons will resonate in our analyses and also that this era of population genomics will see ever more extensive collections to address aspects of migration, phylogeography, and local adaptations within populations of fungi and other microbes.

Gianni Liti, David M. Carter, Alan M. Moses, Jonas Warringer, Leopold Parts, Stephen A. James, Robert P. Davey, Ian N. Roberts, Austin Burt, Vassiliki Koufopanou, Isheng J. Tsai, Casey M. Bergman, Douda Bensasson, Michael J. T. O’Kelly, Alexander van Oudenaarden, David B. H. Barton, Elizabeth Bailes, Alex N. Nguyen, Matthew Jones, Michael A. Quail, Ian Goodhead, Sarah Sims, Frances Smith, Anders Blomberg, Richard Durbin, Edward J. Louis (2009). Population genomics of domestic and wild yeasts Nature DOI: 10.1038/nature07743

More updates on Saccharomyces resequencing project at Sanger

I’ve paraphrased an email sent by David Carter to folks interested in Saccharomyces resequencing project.

The latest version of the SGRP data is on the web site and ftp site. This release is somewhat provisional, and motivated more by the fact that we have a paper deadline coming up than by any claim to finality. It should be quite a bit better than what was there before, but doesn’t have a correct treatment of transposons.

You can get the data by starting here:
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/datadoc.shtml

There is also a new version of the browser:
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/browser.shtml

There are a few new features in the browser which [David] is going to document over the next couple of days.

Major new features of the data are that there should be much better consistency between alignments; Solexa/Illumina data has been incorporated for the strains that had it; and the S. paradoxus alignments are based on a new assembly that created a few weeks ago and which covers about 95% of the genome; a description is at
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/spara_assembly.shtml

Yeast resequencing update

Ed Louis at Nottingham sent out an email today outlining plans for publishing analyses of the Saccharomyces Genome Resequencing Project.  They are in process of analyzing the data and ask that people respect their use of the data, but also invite collaborations and companion papers.

“If anyone has done or plans on doing a global analysis with a tight clean result which you think should be included in the overview paper, please contact us [Richard Durbin and Ed Louis; emails available through above links]. The analysis would have to be complete by 14 December and you would have to be willing to have the details transparently displayed on the web pages associated with the project.”