Biology subjects

Palinauskas, V.

Publications and source records attributed to Palinauskas, V..

3 recordsLinked to original sources

bioRxiv2026

Parasite epigenetic memory and blood barriers dictate host transcriptional responses during generalist host-shifts

The evolutionary success of generalist parasites is often attributed to their capacity to rapidly navigate divergent host environments through transcriptional plasticity. While host-parasite dynamics are frequently studied in avian models, the immunogenic impact of the heterologous blood matrix, a critical variable in cross-species inoculation experiments, is rarely accounted for. In this study, we investigated the host-transcriptomic landscape of domestic canaries (Serinus canaria) infected with the avian malaria parasite Plasmodium homocircumflexum (lineage COLL4), employing a crosswise infection design to differentiate between homologous and heterologous donor sources. By implementing a factorial experimental framework, we successfully isolated the transcriptional noise induced by the heterologous blood matrix per se, revealing that mismatched transfusions trigger significant, non-specific innate immune activation independently of parasite presence. Upon correcting for this background effect, we observed distinct transcriptional trajectories: while adapted (homologous) infections induced a metabolic catalytic overload driven by key kinase hubs (e.g., AKT1, CDK6), heterologous infections were characterized by a shift toward structural and ribosomal regulation. These divergence patterns in the host, combined with the strain-specific transcription of the parasite, suggest that early infection phases are heavily constrained by recent host-switching events. Our results demonstrate that this epigenetic memory acts as a fundamental determinant of virulence, providing a new systems-based framework for understanding how pathogen history and host-donor compatibility reshape infection dynamics and host molecular outcomes during the colonization of novel ecological frontiers.

evolutionary biology↗

bioRxiv2025

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the [~]4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.

genomics↗

bioRxiv2025

Generalist malaria parasites and host imprinting: Unveiling transcriptional memory

Generalist parasites must rapidly adapt to diverse host environments to ensure their survival and transmission. Parasites may employ fixed genetic responses, transcriptional plasticity, or epigenetic mechanisms to optimize survival. The avian malaria parasite Plasmodium homocircumflexum serves as an ideal model for studying transcriptional variation and adaptive strategies. We experimentally inoculated P. homocircumflexum into different bird hosts, bypassing vector recombination, to investigate whether parasite gene expression remains stable across hosts, resets in response to new environments, or reflects epigenetic inheritance. Our study evaluates four potential mechanisms: (1) A universal gene expression profile ("one key fits all"), where expression remains stable across hosts. Our outcomes revealed that gene expression differed significantly depending on the host species and time post-infection, thus rejecting this hypothesis. (2) Complete transcriptional plasticity, where gene expression is fully determined by the recipient host. Contrary to this hypothesis, we observed that gene expression was primarily influenced by the donor at 8 days post-infection (dpi), whereas gene expression was more aligned with the recipient host at 16 dpi. (3) Epigenetic inheritance, where early-stage gene expression reflects the donor host but gradually adjusts to the recipient. Our results support this mechanism, as 2,647 differentially expressed genes (DEGs) were associated with donors at 8 dpi, whereas 271 DEGs were linked to the recipient by 16 dpi. (4) Selection-driven differentiation favoring specific haplotypes. This latter hypothesis was not supported since SNP analyses showed low genetic differentiation. These findings suggest a P. homocircumflexum transition from donor-dependent to recipient-dependent gene expression, likely mediated by epigenetic regulation and transcriptional plasticity.

genomics↗