Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000–12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was accompanied by structural rearrangements in the small dispensable chromosomes, while footprints of positive selection were present in only a small number of protein coding genes

A novel high channel-count system for acute multi-site neuronal recordings

Multisite recording represents a suitable condition to study microphysiology and network, interactions in the central nervous system and; therefore, to understand brain functions. Several different materials and array configurations have been proposed for the development of new probes utilized to record brain activity from experimental animal models. We describe new multisite silicon probes that broaden the currently available application base for neuroscientists. The array arrangement of the probes recording sites was extended to increase their spatial resolution. Probes were integrated with a newly developed electronic hardware and novel software for advanced real-time processing and analysis. The new system, based on 32- and 64-electrode silicon probes, proved very valuable to record field potentials and single unit activity from the olfactory-limbic cortex of the in vitro isolated guinea-pig brain preparation and to acutely record unit activity at multiple sites from the cerebellar cortex in vivo. The potential advantages of the new system in comparison to the currently available technology are discussed