Species

Objectives

The origin of sex chromosomes remains a central challenge in evolutionary genetics both because they are conspicuous features of many eukaryotic genomes and because of their central role in determining the reproductive potential of a species. Dimorphic sex chromosomes have evolved independently in diverse groups of animals, plants, and even fungi, where recent studies show convergent patterns of differentiation from ancestral autosome pairs (Charlesworth et al. 2005; Nicolas et al. 2005). From such broadly comparative analyses, we are uncovering the evolutionary forces fundamental to humans, and perhaps all sexual eukaryotes, that drive major features of genetic systems (Hood et al. 2004, Fraser et al. 2005).

Sex chromosome evolution involves factors that both decrease genome fluidity (recombination suppression) and factors that increase it (a consequential invasion by transposable elements leading to non-homologous recombination and structural rearrangements). A combination of these factors is thought to be responsible for the sometimes drastic size dimorphism of sex chromosomes. The most plausible model for the recombination suppression is the selection for linkage around an original sex determination region involving several genes that are relatively more beneficial in one sex than the other (Charlesworth et al. 2005). In several plants and animals, "evolutionary strata" have been found on the sex chromosomes, representing different stages of recombination suppression, starting from the essential sex determining region and extending to encompass most of the sex chromosome length (Nicolas et al. 2005; Handley et al. 2004).

Fungi provide perhaps the most exceptional models for sex chromosome evolution because of their tractable genome sizes and the relatively rapid rates of karyotypic change (fraser et al. 2005, Hood et al. 2004). The genetic and developmental simplicity of mating in fungi also makes more transparent the selective forces responsible for the sex chromosome characteristic, which fungi share with diverse other taxa. Fungi, despite representing a major division of frequently sexual eukaryotes, are still little studied on these aspects, and so far no phylogenetically well-resolved group have been employed to resolve the evolution of large non-recombining regions of sex chromosomes.

Furthermore, the structure and evolution of mating type loci in itself is highly interesting in basidiomycete fungi: they are composed of two loci, that may possess a pair of alternate alleles or multiple alleles. Systems where the two mating type loci are unlinked (called “tetrapolar) often have multiple alleles, yielding thousands of different mating types. Bipolar systems have only two mating types, which has been shown to be derived from tetrapolarity either by linkage of the two loci and fixation of alleles or by the loss of function in mating discrimination of one of the two loci (Bakkeren et al. 1994).

Microbotryum species carry dimorphic sex chromosomes (Hood 2002), that can be readily identified in eletrophoretic karyotypes by hybridization with linked genes or that the chromosome size variation co-segregates during meiosis with the alternate haploid mating types called A1 and A2. The observation that Microbotryum sex chromosomes range from largest to smallest in the genome, and exhibit size dimorphism between mating types, indicates a dynamic evolutionary process affecting their structure and composition. We will perform i) structural annotation ii) functional annotation on predicted genes and iii) gene content/syntheny comparisons between the sex chromosomes. Using comparative genomics and phylogenetic approaches, we will determine the following:

- Structure of mating type loci: Is bipolarity a result of linkage of the two mating type loci or has one lost its mating type function? Are genes linked to mating type in Microbotryum homologous to those in other fungi, in particular genes involved in pathogenicity and mitochondrial transmission?

- Genic and non-coding changes in evolutionary transitions between large and small sex chromosomes, or the generation of size dimorphism: What genes are necessarily retained among sex chromosomes?

- Patterns of recombination suppression (evolutionary strata) associated with regions adjacent to the mating type locus: How have karyotypic rearrangements contributed to these dynamics?

In 2009, the French National Sequencing Center, Genoscope funded the project for sequencing the sex chromosomes of 6 strains from 5 different Microbotryum species.

Results

• The gene prediction pipeline has been processed through ab initio gene finding softwares and similarity methods. All results have been then gathered and processed by Eugene.
• Previously obtained cDNA libraries for four Microbotryum species, available in MICROBASE (Yockteng et al 2007; Aguileta et al. 2010), have been used to train the software.
• The automated functional annotation pipeline has been performed predicted by EuGene, This pipeline uses the protein domain identifier InterProScan.
• Access to private secure server only for Microbotryum consortium members.