These findings underscore the importance of considering dorsal and ventral hippocampus separately when conducting high-throughput molecular analyses, which has important implications for fundamental research as well as clinical studies.

Microbial pathogens can rapidly adapt to changing environments such as the application of pesticides or host resistance. Copy number variations (CNV) are a major source of adaptive genetic variation for recent adaptation. Here, we analyze how a major fungal pathogen of barley, Rhynchosporium commune, has adapted to host environment, fungicide and temperature challenges.We screen the genomes of 126 isolates sampled across a worldwide set of populations and identify a total of 7'879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. We find that genes showing recent gains or losses are enriched in functions related to host exploitation (i.e. effectors and cell wall degrading enzymes). We perform a phylogeny-informed genome-wide association study (GWAS) and identify 191 copy-number variants associated with different pathogenesis and temperature related traits, including a large segmental duplication of CYP51A that has contributed to the emergence of azole resistance. Additionally, we use a genome-wide SNP dataset to replicate the GWAS and contrast it with the CNV-focused analysis.We find that frequencies of adaptive CNV alleles show high variation among populations for traits under strong selection such as fungicide resistance. In contrast, adaptive CNV alleles underpinning temperature adaptation tend to be near fixation. Finally, we show that transposable elements are important drivers of recent gene copy-number variation. Loci showing signatures of recent positive selection are enriched in miniature inverted repeat transposons. Our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.

Understanding the conservation and evolution of protein complexes is of critical value to decode their function in physiological and pathological processes. One prominent proposal posits gene duplication as a potential mechanism for protein complex evolution. In this study we take advantage of large-scale proteome expression datasets to systematically investigate the role of paralogues, and specifically self-interacting paralogues, in shaping the evolutionary trajectories of protein complexes. First, we show that protein co-expression derived from quantitative proteomic matrices is a good indicator for complex membership and is conserved across species. Second, we suggest that paralogues are commonly strongly co-expressed and that for the subset of paralogues that show diverging co-expression patterns, the divergent co-expression patterns reflect both sequence and functional divergence. Finally, on this basis, we show that homomeric paralogues known to be part of protein complexes display a unique co-expression pattern distribution, with a subset of them being highly diverging. These findings support the idea that homomeric paralogues can avoid cross-interference by diversifying their expression patterns, and corroborates the role of this mechanism as a force shaping protein complex evolution and specialization.

High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. In this study, we present a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific amplicons using PacBio circular consensus sequencing. We focus on the wheat microbiome as a proof-of-principle and demonstrate unprecedented resolution for the wheat-associatedPseudomonasmicrobiome and the ubiquitous fungal pathogenZymoseptoria tritici. Our approach achieves an order of magnitude higher phylogenetic resolution compared to existing ribosomal amplicons. We show that the designed amplicons accurately capture species and strain diversity outperforming full-length 16S and ITS amplicons. We track microbial communities in the wheat phyllosphere across time and space to establish fine-grained species and strain-specific dynamics. The high-resolution profiling provided by taxon-specific amplicons opens new avenues for studying microbial community dynamics in complex environments. Moreover, the cost-effectiveness and scalability of our approach make it applicable to diverse ecological studies. Overall, our work demonstrates the potential of long-read amplicon sequencing to overcome limitations in phylogenetic resolution and enhance our understanding of microbiome diversity and dynamics.

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