Background/Aims: To determine the structure-function relationship throughout the different stages of glaucoma. Methods Conclusion:The logarithmic and linear relationships between SAP-MS and mean RNFL thickness did not differ when individuals were stratified using the piecewise linear regressionobtained cut-off point. The curvilinear relationship between the morphologic and perimetric results may be due to the wide variability in normal morphology and limitations in the dynamic range of the morphologic tests in cases with moderate and severe defects.

Sex chromosomes and mating-type chromosomes can display large genomic regions without recombination. Recombination suppression often extended stepwise with time away from the sex- or mating-type-determining genes, generating evolutionary strata of differentiation between alternative sex or mating-type chromosomes. In anther-smut fungi of the Microbotryum genus, recombination suppression evolved repeatedly, linking the two mating-type loci and extended multiple times in regions distal to the mating-type genes. Here, we obtained high-quality genome assemblies of alternative mating types for four Microbotryum fungi. We found an additional event of independent chromosomal rearrangements bringing the two mating-type loci on the same chromosome followed by recombination suppression linking them. We also found, in a new clade analysed here, that recombination suppression between the two mating-type loci occurred in several steps, with first an ancestral recombination suppression between one of the mating-type locus and its centromere; later, completion of recombination suppression up to the second mating-type locus occurred independently in three species. The estimated dates of recombination suppression between the mating-type loci ranged from 0.15 to 3.58 million years ago. In total, this makes at least nine independent events of linkage between the mating-type loci across the Microbotryum genus. Several mating-type locus linkage events occurred through the same types of chromosomal rearrangements, where similar chromosome fissions at centromeres represent convergence in the genomic changes leading to the phenotypic convergence. These findings further highlight Microbotryum fungi as excellent models to study the evolution of recombination suppression.

Sex chromosomes and mating‐type chromosomes can display large genomic regions without recombination. Recombination suppression often extended stepwise with time away from the sex‐ or mating‐type‐determining genes, generating evolutionary strata of differentiation between alternative sex or mating‐type chromosomes. In anther‐smut fungi of the Microbotryum genus, recombination suppression evolved repeatedly, linking the two mating‐type loci and extended multiple times in regions distal to the mating‐type genes. Here, we obtained high‐quality genome assemblies of alternative mating types for four Microbotryum fungi. We found an additional event of independent chromosomal rearrangements bringing the two mating‐type loci on the same chromosome followed by recombination suppression linking them. We also found, in a new clade analysed here, that recombination suppression between the two mating‐type loci occurred in several steps, with first an ancestral recombination suppression between one of the mating‐type locus and its centromere; later, completion of recombination suppression up to the second mating‐type locus occurred independently in three species. The estimated dates of recombination suppression between the mating‐type loci ranged from 0.15 to 3.58 million years ago. In total, this makes at least nine independent events of linkage between the mating‐type loci across the Microbotryum genus. Several mating‐type locus linkage events occurred through the same types of chromosomal rearrangements, where similar chromosome fissions at centromeres represent convergence in the genomic changes leading to the phenotypic convergence. These findings further highlight Microbotryum fungi as excellent models to study the evolution of recombination suppression.

Background: Transposable element (TE) activity is generally deleterious to the host fitness, so that genomes often evolve TE control mechanisms, and TE copies are purged by recombination and selection. In the absence of recombination, the number of TE insertions usually increases, but the dynamics of such TE accumulations is unknown. Results: In this study, we investigated the tempo of TE accumulation in the non-recombining genomic regions of 15 Microbotryum species, leveraging on a unique dataset of 21 independent evolutionary strata of recombination cessation of different ages in closely related species. We show that TEs have rapidly accumulated following recombination suppression but that the TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 MY following recombination suppression. The same superfamilies repeatedly expanded in independently evolved non-recombining regions, and in particular Helitrons, despite being scarce before recombination suppression. TEs from the most abundant elements, i.e., Copia and Ty3/Gypsy retrotransposon superfamilies, have also expanded independently in the different non-recombining regions. Copia and Ty3 retrotransposons have accumulated through bursts affecting both the non-recombining regions of the mating-type chromosomes and autosomes at the same time, which supports the TE reservoir hypothesis, i.e., that the TEs accumulated in non-recombining regions have a genome-wide impact by transposing to recombining regions. Conclusion: This study sheds light on the genome-wide consequences of the accumulation of TEs in non-recombining regions, thus improving our knowledge on genome evolution.

Recombination is beneficial over the long term, allowing more effective selection. Despite long-term advantages of recombination, local recombination suppression can evolve and lead to genomic degeneration, in particular on sex chromosomes. Here, we investigated the tempo of degeneration in non-recombining regions, i.e., the function curve for the accumulation of deleterious mutations over time, leveraging on 22 independent events of recombination suppression identified on mating-type chromosomes of anther-smut fungi, including newly identified ones. Using previously available and newly generated high-quality genome assemblies of alternative mating types of 13 Microbotryum species, we estimated degeneration levels in terms of accumulation of non-optimal codons and non-synonymous substitutions in non-recombining regions. We found a reduced frequency of optimal codons in the non-recombining regions compared to autosomes, that was not due to less frequent GC-biased gene conversion or lower ancestral expression levels compared to recombining regions. The frequency of optimal codons rapidly decreased following recombination suppression and reached an asymptote after ca 3 Mya. The strength of purifying selection remained virtually constant at dN/dS = 0.55, i.e. at an intermediate level between purifying selection and neutral evolution. Accordingly, non-synonymous differences between mating-type chromosomes increased linearly with stratum age, at a rate of 0.015 per MY. We thus develop a method for disentangling effects of reduced selection efficacy from GC-biased gene conversion in the evolution of codon usage and we quantify the tempo of degeneration in non-recombining regions, which is important for our knowledge on genomic evolution and on the maintenance of regions without recombination.

Genome sequencing has affected studies into the biology of all classes of organisms and this is certainly true for filamentous fungi. The level with which biological systems can be studied since the availability of genomes and post-genomic technologies is beyond what most people could have imagined previously. The fungal genera Aspergillus and Penicillium contain some species that are amongst the most widely used industrial microorganisms and others that are serious pathogens of plants, animals and humans. These genera are also at the forefront of fungal genomics with many genome sequences available and a whole genus genome sequencing project in progress for Aspergillus.This book highlights some of the changes in the studies into these fungi, since the availability of genome sequences. The contributions vary from insights in the taxonomy of these genera, use of genomics for forward genetics and genomic adaptations, to specific stories addressing virulence, carbon starvation, sulphur metabolism, feruloyl esterases, secondary metabolism and pH modulation, to the development of novel methodology for use in parallel to genome sequencing. It therefore provides a taste of the current status of research in Penicillium and Aspergillus and a promise of many more things to come.An essential reference for everyone working with Aspergillus and Penicillium and other filamentous fungi and the book is also recommended reading for everyone with an interest in fungal genomics.

Many fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers. We studied the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, with no differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild-type conspecifics, and those of P. nalgiovense were whiter. The phenotypes of the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed evidence of multiple horizontal gene transfers, particularly between P. nalgiovense and P. salamii. Some horizontal gene transfers involving P. biforme, also found in dry-cured meat products, were also detected. We also detected positive and purifying selection based on amino-acid changes. Our genetic and phenotypic findings suggest that human selection has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense, and P. biforme, providing an interesting case of convergent adaptation to the same human-made environment.

Spark perimetry appears to show useful sensitivity and specificity, even in the first phase, and good agreement with the morphology.