Post-doc position in genomics of introgressions in fungal pathogens
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
- a cover letter describing their research interests and background,
- a detailed CV (including list of publications), and
- the contact details of three references to firstname.lastname@example.org or email@example.com. The cover letter should also include possible starting dates.
Dettman, Anderson, and Kohn recently published a paper in BMC Evolutionary Biology on reproductive experimental evolution in two Neurospora crassa populations evolved under different selective conditions. This is a great study that complements work published last year in Nature on experimental evolution in Saccharomyces cerevisiae populations. Neurospora populations were evolved under high salt and low temperature and were started from either high diversity (interspecific crosses, N. crassa vs N. intermedia) or low diversity (intraspecific cross, two N. crassa isolates D143 (Louisiana, USA)and D69 (Ivory Coast)) as described in Figure 1. The experimentally evolved populations were then tested for asexual and sexual fitness (they were taken through complete meiotic cycle throughout the experiment to avoid insure there was selection on the sexual reproduction pathway.
Continue reading Neurospora speciation through experimental evolution
Perhaps not a surprise to anyone that has dabbled in evolutionary analysis of proteins, Kawahara and Imanishi (BMC Evolutionary Biology 2007) confirm that not every protein evolves via a molecular clock in Saccharomyces sensu scricto. Using everyone’s favorite evolutionary tool, PAML, the authors identify protein lineages via a whole genome scan that evolve relatively slow or fast compared to the rest of the clade. Some changes even appear to be due to the invisible hand of natural selection and independent of the complications that may have arisen during the whole genome duplication in the ancestor of this clade.
It has been previously speculated that, either upon protein duplication or change in the selective regime of the environment, a protein may rapidly evolve at speciation and then, upon obtaining a new, important function, slow down it’s evolutionary rate to a clock-like tempo. One of the black boxes in this hypothesis is whether or not closely related proteins can rapidly diverge. While the authors are not able to identify a mechanism explaining how, their study demonstrates the plausibility of this hypothesis. However, it remains uncertain if proteins that exhibit rapid divergence will subsequently slow down their evolutionary rate later in time.
It’s good to see evolutionary analysis being applied to fungal genomes. With so many sequenced species spanning a great range of phylogenetic distance, the fungal kingdom is poised to provide great insight into the evolution of eukaryotes.
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.
Continue reading Fungal Genetics 2007 details
A paper in PLoS Genetics studied what happens when individual chromosomes of S. cerevisiae are replaced with a homologous copy its sister species, S. paradoxus. Previous work from Ken Wolfe’s lab interpreted the differential loss of genes after the whole genome duplication in the Saccharomyces lineage played a role in speciation among the yeast species. Surprisingly (or not, depending on how you interpret the previous work) Greig did not find any lethality in haploid F1 offspring from a diploid synthetically constructed individuals. Certainly this is not the last word but it represents a nice experimental screen to identify interacting genotypes. What would be interesting in followup work would be more subtle dissection of epistatic interactions among the genes on the different chromosomes to score phenotypes other than complete inviability. This might help understand what pathways are operating differently.
Continue reading Mystery in the mechanism of yeast speciation