Biology subjects

Elkrewi, M.

Publications and source records attributed to Elkrewi, M..

5 recordsLinked to original sources

bioRxiv2026

A single locus carrying modified oogenesis genes underlies the switch to asexuality in Artemia brine shrimp

Transitions from sexual to asexual reproduction are well-documented across different taxa. However, despite extensive efforts, the regulatory changes underlying the emergence of asexuality remain largely undiscovered in the majority of species studied. Artemia brine shrimp have multiple closely related sexual and obligate parthenogenetic lineages, making them a promising model for addressing this question. While earlier work suggested that asexuals use a modified meiosis, and inferred a likely role for the Z-chromosome in its transmission, no master regulator or genetic changes have been put forward as the root causes for the shift. Here, we generate single-nucleus RNAseq data of the female reproductive system of individuals from the Aibi lake population of Artemia parthenogenetica and its closely related obligate sexual species Artemia sp. Kazakhstan. We identify the germline cell clusters in the female reproductive system and perform differential expression analysis to infer substantial transcriptional differences at genes putatively involved in cell cycle and oocyte development between the meiotic cells of the two species. Additionally, we use whole-genome sequencing of 32 individuals from two backcrossing experiments to narrow down the genomic regions associated with the transmission of asexuality to an 8 megabase region of the Z chromosome. Within the identified regions, two adjacent genes with known functions in oogenesis, ITPR and USP8, show differential expression and genetic differentiation between sexuals and asexuals, making them promising candidate drivers of asexuality in this species. Significance statementWhile most animals reproduce sexually, many do not, and why and how these shifts occur remains an open question. This paper presents a systematic investigation of the molecular changes that underlie the transition from sexual to asexual reproduction in brine shrimp. We combine multiple computational and experimental approaches to look for differences between close sexual and asexual lineages. We find that a subset of meiotic germ cells is regulated differently in the two, and that two important oogenesis genes are the likely drivers of asexuality. This work is unique in providing an in-depth characterization of the combined genetic and regulatory changes underlying this key transition in reproductive modes.

evolutionary biology↗

bioRxiv2026

Out with the Old: Contrasting Histone Marks are Associated with Dosage Compensation on the Ancient and New Z of a Moth with Complex Sex Chromosomes

Sex chromosome differentiation is often accompanied by the evolution of dosage compensation (DC) mechanisms that balance gene expression between autosomes and sex chromosomes, and consequently between the sexes. ZW systems were traditionally thought to exhibit only partial DC, but recent studies in Lepidoptera, Artemia franciscana, and Apalone spinifera suggest a diverse range of compensation strategies, challenging traditional assumptions. While DC often involves chromatin-level regulation, the specific mechanisms in most ZW systems are still poorly understood. To explore these gaps, we generated a genome assembly of Cameraria ohridella (horse-chestnut leaf miner moth, Gracillidae), and combined transcriptomic data from two tissues with CUT&Tag epigenomic profiling targeting both active (H4K16ac, H3K4me3) and repressive (H3K27me3) chromatin marks. Our findings reveal a highly dynamic landscape of sex chromosome evolution in C. ohridella, including the ancestral Z (AncZ), a NeoZ1 formed by fusion of AncZ with an autosome, and a NeoZ2 that likely arose via the fusion of another autosome to the W chromosome. We uncover distinct dosage compensation (DC) patterns across ancestral and neo-sex chromosome regions. On the Ancestral Z, DC involves repression of gene expression in males (ZZ), with a depletion of the active histone mark H4K16ac being observed in this region. In contrast, NeoZ1 regions show upregulation of gene expression in the heterogametic sex (ZW), accompanied by enrichment of H4K16ac. Together, our findings underscore the dynamic nature of sex chromosome evolution and reveal variation in dosage compensation strategies across the Z chromosome, where the NeoZ1 appears to evolve entirely new, Drosophila-like mechanisms rather than co-opting the existing Nematode-like mechanisms of AncZ. We performed simulations that suggest that cooption of ancient DC mechanisms on a neo-sex chromosome is expected when it acts through up-regulation in the heterogametic sex but not when it involves downregulation in the homogametic sex, providing a framework for understanding the different patterns observed between Drosophila and Lepidoptera neo sex chromosomes.

evolutionary biology↗

bioRxiv2025

Evidence for the major role of PH4EFB in the prolyl 4-hydroxylation of Drosophila collagen IV

Collagens are fundamental components of extracellular matrices, requiring precise intracellular post-translational modifications for proper function. Among the modifications, prolyl 4-hydroxylation is critical to stabilise the collagen triple helix. In humans, this reaction is mediated by collagen prolyl 4-hydroxylases (P4Hs). While humans possess three genes encoding these enzymes (P4Hs), Drosophila melanogaster harbour at least 26 candidates for collagen P4Hs despite its simple genome, and it is poorly understood which of them are actually working on collagen in the fly. In this study, we addressed this question by carrying out thorough bioinformatic and biochemical analyses. We demonstrate that among the 26 potential collagen P4Hs, PH4EFB shares the highest homology with vertebrate collagen P4Hs. Furthermore, while collagen P4Hs and their substrates must exist in the same cells, our transcriptomic analyses at the tissue and single cell levels showed a global co-expression of PH4EFB but not the other P4H-related genes with the collagen IV genes. Moreover, expression of PH4EFB during embryogenesis was found to precede that of collagen IV, presumably enabling efficient collagen modification by PH4EFB. Finally, biochemical assays confirm that PH4EFB binds collagen, supporting its direct role in collagen IV modification. Collectively, we identify PH4EFB as the primary and potentially constitutive prolyl 4-hydroxylase responsible for collagen IV biosynthesis in Drosophila. Our findings highlight the remarkably simple nature of Drosophila collagen IV biosynthesis, which may serve as a blueprint for defining the minimal requirements for collagen engineering.

biochemistry↗

bioRxiv2023

The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.

Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.

evolutionary biology↗

bioRxiv2022

ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp

Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this with short-read genomic data for the sexual species A. sp. Kazakhstan and several lineages of A. parthenogenetica, allowing us to perform a first in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis may be partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.

evolutionary biology↗