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Meiosis is generally a fair process: each chromosome has a 50% chance of being included into each gamete. However, meiosis can become aberrant with some chromosomes having a higher chance of making it into gametes than others. Yet, why and how such systems evolve remains unclear. Here, we study the unusual reproductive genetics of mealybugs, where only maternal-origin chromosomes are included in gametes during male meiosis, while paternal chromosomes are eliminated. One species— Pseudococcus viburni —has a segregating B chromosome that drives by escaping paternal genome elimination. We present whole genome and gene expression data from lines with and without B chromosomes. We identify B-linked sequences including 204 protein-coding genes and a satellite repeat that makes up a significant proportion of the chromosome. The few paralogs between the B and the core genome are distributed throughout the genome, arguing against a simple, or at least recent, chromosomal duplication of one of the autosomes to create the B. We do, however, find one 373 kb region containing 146 genes that appears to be a recent translocation. Finally, we show that while many B-linked genes are expressed during meiosis, most of these are encoded on the recently translocated region. Only a small number of B-exclusive genes are expressed during meiosis. Of these, only one was overexpressed during male meiosis, which is when the drive occurs: an acetyltransferase involved in H3K56Ac, which has a putative role in meiosis and is, therefore, a promising candidate for further studies. [ABSTRACT FROM AUTHOR]

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results; however, computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested and are hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests.

Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages. [ABSTRACT FROM AUTHOR]

Bacteria that engage in long‐standing associations with particular hosts are expected to evolve host‐specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and the underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep‐branching host‐specific phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization. In contrast, honey bee strains of divergent phylogenetic lineages were able to coexist within individual bees. This suggests that both host selection and interbacterial competition play important roles in host specialization. Using comparative genomics of 27 Firm5 isolates, we found that the genomes of honey bee strains harbour more carbohydrate‐related functions than bumble bee strains, possibly providing a competitive advantage in the honey bee gut. Remarkably, most of the genes encoding carbohydrate‐related functions were not conserved among the honey bee strains, which suggests that honey bees can support a metabolically more diverse community of Firm5 strains than bumble bees. These findings advance our understanding of the genomic changes underlying host specialization. [ABSTRACT FROM AUTHOR]

The wide array of currently available genomes displays a wonderful diversity in size, composition, and structure and is quickly expanding thanks to several global biodiversity genomics initiatives. However, sequencing of genomes, even with the latest technologies, can still be challenging for both technical (e.g., small physical size, contaminated samples, or access to appropriate sequencing platforms) and biological reasons (e.g., germline-restricted DNA, variable ploidy levels, sex chromosomes, or very large genomes). In recent years, k -mer-based techniques have become popular to overcome some of these challenges. They are based on the simple process of dividing the analyzed sequences (e.g., raw reads or genomes) into a set of subsequences of length k , called k -mers, and then analyzing the frequency or sequences of those k -mers. Analyses based on k -mers allow for a rapid and intuitive assessment of complex sequencing data sets. Here, we provide a comprehensive review to the theoretical properties and practical applications of k -mers in biodiversity genomics with a special focus on genome modeling., (© 2025 Jenike et al.; Published by Cold Spring Harbor Laboratory Press.)

We present a genome assembly from an individual female Dicyrtomina minuta (springtail; Arthropoda; Collembola; Symphypleona; Dicyrtomidae). The genome sequence is 582.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 15.59 kilobases in length., Competing Interests: No competing interests were disclosed., (Copyright: © 2024 Jaron KS et al.)

Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in microsporidia is variable, with a few species formally identified as diploid and one as polyploid. Given the increase in the number of studies sequencing microsporidian genomes, it is now possible to assess ploidy levels across all currently explored microsporidian diversity. We estimate ploidy for all microsporidian data sets available on the Sequence Read Archive using k-mer-based analyses, indicating that polyploidy is widespread in Microsporidia and that ploidy change is dynamic in the group. Using genome-wide heterozygosity estimates, we also show that polyploid microsporidian genomes are relatively homozygous, and we discuss the implications of these findings on the timing of polyploidization events and their origin.IMPORTANCEMicrosporidia are single-celled intracellular parasites, distantly related to fungi, that can infect a broad range of hosts, from humans all the way to protozoans. Exploiting the wealth of microsporidian genomic data available, we use k-mer-based analyses to assess ploidy status across the group. Understanding a genome's ploidy is crucial in order to assemble it effectively and may also be relevant for better understanding a parasite's behavior and life cycle. We show that tetraploidy is present in at least six species in Microsporidia and that these polyploidization events are likely to have occurred independently. We discuss why these findings may be paradoxical, given that Microsporidia, like other intracellular parasites, have extremely small, reduced genomes., Competing Interests: The authors declare no conflict of interest.