Biology subjects

Kaymak, E.

Publications and source records attributed to Kaymak, E..

8 recordsLinked to original sources

bioRxiv2026

The ancestral endosymbiont Blattabacterium was lost ten times independently in Blattellidae, Pseudophyllodromiidae and Anaplectidae cockroaches

Most cockroaches and the termite Mastotermes darwiniensis are associated with Blattabacterium, an ancient obligate endosymbiont that participates in the nitrogen metabolism of its host. Blattabacterium has been vertically transmitted since it was acquired by the common ancestor of cockroaches and termites and was reportedly lost twice, once in the cockroach genus Nocticola and once in all termites except Mastotermes darwiniensis. Here, we acquired cockroach specimens spanning most of the cockroach phylogenetic tree to study Blattabacterium using shotgun sequencing. We found no traces of Blattabacterium in 64 specimens from ten independent lineages of cockroaches across three families: Blattellidae, Pseudophyllodromiidae, and Anaplectidae. The absence of Blattabacterium was confirmed with three PCR amplifications targeting the 16S and 23S ribosomal genes with primers specific to Blattabacterium. Notably, cockroaches lacking Blattabacterium were often infected by Rickettsia and Wolbachia, many of which were related to the mutualistic Wolbachia strain of Cimex lectularius, the common bed bug. These results indicate that cockroaches from Blattellidae, Pseudophyllodromiidae and Anaplectidae have lost their ancestral Blattabacterium endosymbiont at least ten times independently, with many of these losses possibly facilitated and compensated by new associations with mutualistic Wolbachia strains that may help provision the host with B vitamins.

evolutionary biology↗

bioRxiv2026

Social caste switching triggers emergence of novel cellular identities in Zootermopsis termites

A hallmark of eusocial insects is the specialisation of individuals into castes that share the same genome but present distinct phenotypes. Caste switching can affect gene expression1,2, but can it give rise to entirely new cell types? Here, we generated single-cell transcriptomic atlases of a king, a queen, a soldier, and six workers of the termite Zootermopsis nevadensis to understand whether caste differentiation is accompanied by the emergence of novel cellular identities. Out of 24 annotated termite cell types, 18 of which mirrored homologous Drosophila cell types, one was unique for king, one was almost entirely restricted to the queen, and none were exclusive to nonreproductives. Instead, nonreproductive termites possessed more muscle and neuronal cells and less fat cells than reproductives. Caste-linked transcriptional signatures were detected in most cell types, including rare genes expressed with dual specificity for both cell type and caste. Despite the emergence of new cell types in reproductives, expression of hormones, immune genes, carbohydrate-active enzymes3, and rapidly adapting genes4 were only weakly altered by caste. These findings show that cellular differentiation can be induced anew in adult organisms without dysregulating their key physiologic pathways.

evolutionary biology↗

bioRxiv2025

Deciphering the evolution of sex determination across the termite tree of life using high-quality genome assemblies

Most termites exhibit a unique sex-determining system, featuring multiple X and Y chromosomes that fuse into large complexes during male meiosis. The evolutionary origins of such complexes remain largely unknown. Using the genomes of 45 termites and two cockroaches, we investigated the evolution of sex determination systems in an entire insect lineage. We found that termite sex chromosomes are largely undifferentiated, likely reflecting extensive ongoing recombination. Evolving from the X0 system of cockroaches, most early-diverging termites exhibit a Y chromosome bearing the sex-determining gene doublesex, whereas doublesex is autosomal in most other termites. In contrast, other species exhibit multiple sex chromosomes that have undergone frequent turnover, except for Termitidae, which harbor conserved sex chromosomes. Our findings reveal important reworkings of the ancestral transformer-doublesex pathway in termites and suggest a potential role of doublesex in the formation of meiotic chromosomal complexes and caste differentiation.

evolutionary biology↗

bioRxiv2025

Deep exploration of transcriptomic cellular identities over evolutionary time

Whole-organism cell atlases have painted the cellular landscapes of individual species; however, comparing cells across the tree of life remains challenging. Most cross-species analyses are restricted to orthologous genes, while the complexity of atlas data constitutes an access barrier for many researchers. We developed a computational strategy to accelerate the exploration of cellular identities at scale. We integrated 30 atlases detailing the expression of 861,013 genes by 2,645,508 animal and plant cells and trained a universal model of cellular transcriptomes to track cell type diversification over evolutionary times. Transfer learning achieved cell type annotation of a de novo atlas of the insect Cryptocercus punctulatus within minutes. We devised a generative artificial intelligence approach to construct virtual cell atlases from genome sequences and used it to synthesise an atlas of the Tasmanian tiger, extinct since 1936. We then reduced the footprint of extant atlases by 100 times while retaining crucial information and developed interfaces to answer dozens of query types within seconds, boosting atlas exploration by [~]50,000 times.

evolutionary biology↗

bioRxiv2024

Orchids, hawkmoths and Darwin revisited: How adaptation to pollination by hawkmoths spurred the speciation of Old and New World angraecoids

Specialised pollination has often been proposed as a major driver of the unrivalled diversification of angiosperms. With its unparalleled variation in flower depth, ranging from spurless to 40 cm spurred flowers pollinated by hawkmoths, angraecoid orchids (Angraecinae) provide unique opportunities to reveal the impact of floral specialisation on diversification rates in the Afrotropics and Neotropics. We compiled floral characters for 327 angraecoid species, and assigned these species to newly formalised floral syndrome categories calibrated against pollination case studies. We then estimated ancestral character states and state-dependent speciation rates using the latest time-calibrated phylogeny of angraecoids. We found that white flowers consistent with micro-sphingophily (2 cm[≥] spurs <8.7 cm), macro-sphingophily (8.7 cm[≥] spurs <18.6 cm) and mega-sphingophily (spurs [≥]18.6 cm) evolved repeatedly in angraecoids, and are ancestral in some non-sphingophilous clades. Reversals to non-sphingophily and pigmented flowers suggest higher evolutionary lability of these traits than what is traditionally thought. Increasing floral specialisation with long spurs does not seem to enhance angraecoid orchids speciation rates, since micro-sphingophily appears to be associated with the highest speciation rates. An abundance of short-proboscid hawkmoths in Madagascar, as an ecological opportunity, may have accelerated the speciation of micro-sphingophilous taxa.

evolutionary biology↗

bioRxiv2022

Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR

Among the major classes of RNAs in the cell, tRNAs remain the most difficult to characterize via deep sequencing approaches, as tRNA secondary structure and nucleotide modifications can both interfere with cDNA synthesis by commonly-used reverse transcriptases (RTs). Here, we benchmark a recently-developed RNA cloning protocol, termed Ordered Two-Template Relay (OTTR), to characterize intact tRNAs and tRNA fragments in budding yeast and in mouse tissues. We find that OTTR robustly captures full-length tRNAs in budding yeast and in mouse testis, with relatively low levels of premature termination at known barriers - 1-methylguanine, N2,N2-dimethylguanine, and 1-methyladenine - to typical reverse transcriptases. Moreover, these and several other nucleotide modifications leave misincorporation signatures in OTTR datasets which enables their detection without any additional protocol steps. Turning to analysis of small RNAs such as tRNA cleavage products, we compare OTTR with several standard small RNA-Seq protocols, finding that OTTR provides the most accurate picture of tRNA fragment levels by comparison to "ground truth" Northern blots. Applying this protocol to mature mouse spermatozoa, our data dramatically alter our understanding of the small RNA cargo of mature mammalian sperm, revealing a far more complex population of tRFs - including both 5 and 3 tRNA halves derived from the majority of tRNAs - than previously appreciated. Taken together, our data confirm the superior performance of OTTR to commercial protocols in analysis of tRNA fragments, and force a reappraisal of potential epigenetic functions of the sperm small RNA payload.

genomics↗

bioRxiv2018

Control of noncoding RNA production and histone levels by a 5’ tRNA fragment

Small RNAs derived from mature tRNAs, referred to as tRNA fragments or \"tRFs\", are an emerging class of regulatory RNAs with poorly understood functions in cellular regulation. We recently identified a role for one specific tRF - 5 tRF-Gly-GCC, or tRFGG - in repression of genes associated with the endogenous retroelement MERVL, but the mechanistic basis for this regulation was unknown. Here, we show that tRF-GG plays a role in production of a wide variety of noncoding RNAs normally synthesized in Cajal bodies. Among these noncoding RNAs, tRF-GG regulation of the U7 snRNA modulates heterochromatin-mediated transcriptional repression of MERVL elements by supporting an adequate supply of histone proteins. Importantly, the effects of inhibiting tRF-GG on histone mRNA levels, activity of a histone 3 UTR reporter, and ultimately on MERVL regulation could all be suppressed by the U7 RNA. We show that the related RNA-binding proteins hnRNPF and H bind directly to tRF-GG, and are required for Cajal body biogenesis. Together, our data reveal a conserved mechanism for 5 tRNA fragment control of noncoding RNA biogenesis and, consequently, in global chromatin organization.

molecular biology↗

bioRxiv2018

Multi-modal regulation of C. elegans hermaphrodite spermatogenesis by the GLD-1-FOG-2 complex

Proper germ cell sex determination in Caenorhabditis nematodes requires a network of RNA-binding proteins (RBPs) and their target mRNAs. In some species, changes in this network enabled limited XX spermatogenesis, and thus self-fertility. In C. elegans, one of these selfing species, the global sex-determining gene tra-2 is regulated in germ cells by a conserved RBP, GLD-1, via the 3 untranslated region (3UTR) of its transcript. A C. elegans-specific GLD-1 cofactor, FOG-2, is also required for hermaphrodite sperm fate, but how it modifies GLD-1 function is unknown. Germline feminization in gld-1 and fog-2 null mutants has been interpreted as due to cell-autonomous elevation of TRA-2 translation. Consistent with the proposed role of FOG-2 in translational control, the abundance of nearly all GLD-1 target mRNAs (including tra-2) is unchanged in fog-2 mutants. Epitope tagging reveals abundant TRA-2 expression in somatic tissues, but an undetectably low level in wild-type germ cells. Loss of gld-1 function elevates germline TRA-2 expression to detectable levels, but loss of fog-2 function does not. A simple quantitative model of tra-2 activity constrained by these results can successfully sort genotypes into normal or feminized groups. Surprisingly, fog-2 and gld-1 activity enable the sperm fate even when GLD-1 cannot bind to the tra-2 3 UTR. This suggests the GLD-1-FOG-2 complex regulates uncharacterized sites within tra-2, or other mRNA targets. Finally, we quantify the RNA-binding capacities of dominant missense alleles of GLD-1 that act genetically as \"hyperrepressors\" of tra-2 activity. These variants bind RNA more weakly in vitro than does wild-type GLD-1. These results indicate that gld-1 and fog-2 regulate germline sex via multiple interactions, and that our understanding of the control and evolution of germ cell sex determination in the C. elegans hermaphrodite is far from complete.

developmental biology↗