Biology subjects

Frenkel, Z.

Publications and source records attributed to Frenkel, Z..

6 recordsLinked to original sources

bioRxiv2026

Large-scale genomic rearrangements are a potential explanation for reproductive isolation in the Pogonomyrmex dependent-lineage system

Genetic variation is the raw material for evolution. One source of variation is chromosomal rearrangements, which can bring genes together and form genetic linkage. Rearrangements can also suppress recombination and gene flow, as in the case of sex chromosome evolution. We conducted the first population genomic study of the red harvester ant Pogonomyrmex barbatus to investigate genomic rearrangements that differentiate the lineages J1 and J2 in the "dependent-lineage system" (also known as "social hybridogenesis"). In this unusual reproductive system, males and females from different lineages mate to create hybrids, yet these hybrids develop into sterile offspring (workers), and so the two lineages remain reproductively isolated. We sequenced high-quality reference genomes for the two lineages to search for a potential explanation of the suppression of gene flow between them. Comparison of the two genome assemblies revealed multiple large-scale genomic rearrangements, all of which occurred in the J1 lineage. The rearrangements formed some of the largest J1 chromosomes, including the largest scaffold in the assembly that was formed by at least two translocation events and additional intra-chromosomal rearrangements. The translocations brought together 118 odorant receptor (OR) genes on this rearranged chromosome, 44 of which are 9-exon ORs, which are implicated in chemical communication in ants. We also identified an enrichment of transposable elements in a large synteny gap between the translocated segments. The discovery of multiple translocations that formed large rearranged chromosomes provides a potential explanation for the reproductive isolation between the pair of dependent lineages in this system, and opens the way for the study of the molecular genetic basis of an intriguing evolutionary phenomenon in these and in other ant lineages.

evolutionary biology↗

bioRxiv2025

Genetic basis of cuticular hydrocarbon variation in the desert ant

Cuticluar hydrocarbons (CHCs) are a ubiquitous component of insect cuticles that are used for a wide range of chemical signaling functions, especially recognition. Recognition and other signals are vital for the maintenance of insularity and cooperation in social insect colonies. Therefore, we expect natural selection on the composition and variabitlity of social insect CHC profiles. Selection on these signals may result in the evolution of genetic polymorphism affecting variation in CHC profiles. Here we tested for a genetic basis of CHC variation in the desert ant Cataglyphis niger. We applied a genomic mapping appraoch to a cohort of brothers from the same nest to reduce noise from environmental effects and achieve a clear statistical signal for association between the variation of CHCs and quantitative trait loci (QTL). This analysis identified 19 QTLs associated with 8 out of the 31 CHCs identified, and one QTL associated with total CHC quantity. These QTLs are located on 11 different chromosomes, including two cases where QTLs of different CHCs overlap. Each QTL explains between 13-25% of the variation in a specific CHC. We highlight several candidate genes in the QTLs identified, including fatty acid elongase and reductase genes. Our results reveal a polygenic genomic architecture underlying CHC variation in a population of the desert ant and open new research avenues into the genetic basis and evolution of chemical signaling in social insects.

ecology↗

bioRxiv2024

Repeated evolution of supergenes on an ancient social chromosome

Supergenes are non-recombining chromosomal regions that code for complex polymorphic traits. Advances in population genomics have uncovered supergenes associated with diverse traits, ranging from butterfly wing patterns to floral morphs. In ants, two supergenes on non-homologous "social chromosomes" in Solenopsis and Formica are associated with social polymorphism, with either single queen (monogyne) or multiple queens (polygyne) colonies. We discovered a new supergene associated with similar polymorphism in the desert ant Cataglyphis niger. Despite Cataglyphis being more closely related to Formica than Solenopsis, its social chromosome is homologous to that of Solenopsis, with conservation of synteny in gene content and order. This suggests that the social chromosome is ancient, dating back to the common ancestor of Solenopsis and Cataglyphis, at least 90 million years ago. Low sequence divergence between supergene haplotypes in both Solenopsis and Cataglyphis suggests that the two supergenes evolved recently and independently in the two divergent lineages on this ancient social chromosome. Comparative analysis of hymenopteran genomes further revealed a bee chromosome homologous to the ants social chromosome. The ant social chromosome contains the largest set of genes that are conserved as a linkage group across ant and bee genomes. This conserved gene set is enriched for olfactory functions, most notably a large number of odorant-binding proteins. The conservation of this gene set suggests that this chromosome plays an important role in social behavior across social Hymenoptera. We propose that the conserved gene set in the social chromosome was repeatedly used as a pre-adapted toolkit for the evolution of social traits in general, and specifically in the evolution of polygyne social structure in ants.

evolutionary biology↗

bioRxiv2022

Statistical analysis and simulation allowing simultaneously positive, negative, and no crossover interference in multilocus recombination data

Crossover interference (COI) is a widespread feature of homologous meiotic recombination. It can be quantified by the classical coefficient of coincidence (CoC) `but this characteristic is highly variable and specific to the pair of chromosomal intervals considered. Several models were proposed to characterize COI on a chromosome-wise level. In the gamma model, the strength of interference is characterized by a shape parameter{nu} , while the gamma-sprinkled two-pathway model (GS) accounts for both interference-dependent and independent crossover (CO) events by fitting a mixture of gamma distributions with v>1 and v=1, correspondingly, and mixture proportions 1-p and p. In reality, COI can vary along chromosomes resulting in low compliance of the fitted model to real data. Additional inconsistency can be caused by common neglecting of possible negative COI in the model, earlier reported for several organisms. In this work, we propose an extension of the GS-model to take possible negative COI into account. We propose a way for data simulation and parameter estimation for such situations.

bioinformatics↗

bioRxiv2020

Seasonal changes in recombination rate, crossover interference, and their response to desiccation stress in a natural population of Drosophila melanogaster from India

Environmental seasonality is a potent evolutionary force, capable to maintain polymorphism, promote phenotypic plasticity, and cause bet-hedging. In Drosophila, it has been reported to affect life-history traits, tolerance to abiotic stressors, and immunity. Oscillations in frequencies of alleles underlying fitness-related traits were also documented alongside SNP alleles across genome. Here, we test for seasonal changes in recombination in a natural D. melanogaster population from India using morphological markers of the three major chromosomes. We show that winter flies (collected after the dry season) have significantly higher desiccation tolerance than their autumn counterparts. This difference proved to hold also for hybrids with three independent marker stocks, suggesting its genetic rather than plastic nature. Significant segment-specific changes are documented for recombination rate (in five of 13 intervals) and crossover interference (in five of 16 studied pairs of intervals); both single- and double-crossover rates tended to increase in the winter cohort. The winter flies also display weaker plasticity of recombination characteristics to desiccation. We ascribe the observed differences to indirect selection on recombination caused by directional selection on desiccation tolerance. Our findings suggest that changes in recombination can arise even after a short period of seasonal adaptation (~8-10 generations).

evolutionary biology↗

bioRxiv2018

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.\n\nResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.\n\nConclusionsSufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

genomics↗