Biology subjects

Novakova, M.

Publications and source records attributed to Novakova, M..

6 recordsLinked to original sources

bioRxiv2025

Immunogenetic diversity and haemosporidian parasitization in European bluethroats (Luscinia svecica): do diverse genes warrant fewer parasites?

The health and fitness of vertebrates are constantly challenged by environmental stresses, which include exposure to diseases that pose significant evolutionary pressures on immune genes. The bluethroat (Luscinia svecica), has been extensively studied for its haemosporidian parasite diversity across Europe showing a high diversity and prevalence rate. Given possible evolutionary pressure exerted by these pathogens, the present study used high-throughput amplicon sequencing to explore the genetic diversity and selection mechanisms of three immunity genes (MHC I exon 3, TLR3 and TLR4) in three European bluethroat populations. Specifically, we seek to (1) characterize the genetic diversity of these immunity genes, (2) detect selection signatures shaping their diversity, and (3) investigate the relationship between these immunity genes and haemosporidian parasites (Plasmodium and Leucocytozoon). Selection analysis was conducted using FUBAR and SLAC methods, whereas GLM regression was employed to explore the correlation between MHC genes and haemosporidian parasites. Despite geographical and ecological differences, nucleotide and haplotype diversities were similar across all populations. Most frequent haplotypes were found to be shared by both red-spotted (L. s. svecica) and white-spotted (L. s. cyanecula) bluethroat subspecies. The "insular" Krkono[s]e population, despite being biogeographically peripheral and experiencing minor inbreeding, did not show significantly reduced immunogenetic diversity. Selection analysis revealed a higher presence of purifying selection in TLR genes and a combination of purifying and diversifying selection in the MHC gene, reflecting their evolutionary constraints and functional importance, while haemosporidian parasite pressure was not a major driver of genetic diversity.

zoology↗

bioRxiv2024

Host-associated genetic differentiation in the face of ongoing gene flow: ecological speciation in a pathogenic parasite of freshwater fish

Adaptation to varying environments, leading to population divergence, is one of the key processes of natural selection. However, its effectiveness amidst ongoing gene flow remains controversial. Our study explores this phenomenon by focusing on a tapeworm parasite (Ligula intestinalis), which is capable of parasitising a wide spectrum of fish species, overcoming their immunological defence and having a highly pathogenic impact. We analysed the population genetic structure, the degree of gene flow, and the level of genomic divergence between sympatrically occurring parasites from different cyprinid fish hosts. Utilising genome-wide Single Nucleotide Polymorphisms (SNPs) and transcriptome data, we investigated whether individual host species impose selection pressures on the parasite populations. Genetic clustering analyses indicated a divergence between the parasites infecting breams and those in roaches, bleaks and rudds. Historical demography modelling suggested that the most plausible scenario for this divergence is isolation with continuous gene flow. Selection analysis identified 896 SNPs under selection, exhibiting higher nucleotide diversity and genetic divergence compared to neutral loci. Transcriptome profiling corroborated these results, revealing distinct gene expression profiles for the two parasite populations. An in-depth examination of the selected SNPs and differentially expressed genes revealed specific genes and their physiological functions, as candidates for the molecular mechanisms of immune evasion and, thus, for driving ecological speciation in the parasite. This study showcases the interplay between host specificity, population demography and disruptive selection in ecological speciation. By dissecting the genomic factors at play, we gain a better understanding of the mechanisms facilitating population divergence in the presence of gene flow.

evolutionary biology↗

bioRxiv2023

Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of the tapeworm Ligula intestinalis

Ligula intestinalis (Cestoda: Diphyllobothriidae) is an emerging model organism for studies on parasite population biology and host-parasite interactions. However, a well resolved genome and catalogue of its gene content has not been previously developed. Here, we present the first genome assembly of L. intestinalis, based on Oxford Nanopore Technologies, Illumina and Omni-C sequencing methodologies. We use transcriptome profiling to compare plerocercoid larvae and adult worms and identify differentially expressed genes associated with these life stages. The genome assembly is 775.5 Mbp in size, with scaffold N50 value of 118 Mbp and encodes 27,256 predicted protein-coding sequences. Over 60% of the genome consists of repetitive sequences. Synteny analyses showed that the 10 largest scaffolds representing 75% of the genome display high correspondence to full chromosomes of cyclophyllidean tapeworms. Mapping RNA-seq data to the new reference genome we identified 3,922 differentially expressed genes in adults compared to plerocercoids. Gene Ontology analyses revealed overrepresented genes involved in reproductive development of the adult stage (e.g. sperm production) and significantly enriched DEGs associated with immune evasion of plerocercoids in their fish host. This study provides the first insights into the molecular biology of L. intestinalis and provides the most highly contiguous assembly to date of a diphyllobothriid tapeworm useful for population and comparative genomic investigations of parasitic flatworms.

genomics↗

bioRxiv2023

Early embryogenesis in CHDFIDD mouse model reveals facial clefts and altered craniofacial neurogenesis

Congenital heart defects, facial dysmorphism and intellectual development disorder (CHDFIDD) is associated with mutations in CDK13 gene which encodes a transcription regulating Cyclin-dependent kinase 13 (CDK13). Here we analyzed early embryonic stages of CHDFIDD mouse models with hypomorphic mutation in Cdk13 gene with very similar phenotypic manifestations plus cleft lip/palate and knockout of Cdk13 which exhibits robust phenotype with midfacial cleft. Cdk13 is strongly expressed in the mouse embryonic craniofacial structures, namely in the forebrain, nasal epithelium and maxillary mesenchyme. In vitro, CDK13 protein is located not only in nuclear region but also in the cellular protrusions in cultured mesenchymal cells and cells isolated from dorsal root ganglia. In Cdk13-deficient embryos, we found hypoplastic branches of the trigeminal nerve including maxillary branch and additionally we detected significant gene expression changes of molecules involved in neurogenesis (Mef2c, Pou4f1, Sod1, Cdk5rap2, Nrcam) within the developing palatal shelves. Key palate-associated molecules (Msx1 and Meis2) were downregulated during early craniofacial development in mutant embryos. These results demonstrate the role of CDK13 in regulation of facial morphogenesis and also growth of craniofacial peripheral nerves.

developmental biology↗

bioRxiv2022

Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite - the Ligula intestinalis species complex

Studies on parasite biogeography and host spectrum provide insights into the processes driving parasite diversification. Global geographical distribution and a multi-host spectrum make the tapeworm Ligula intestinalis a promising model for studying both the vicariant and ecological modes of speciation in parasites. To understand the relative importance of host association and biogeography in the evolutionary history of this tapeworm, we analysed mtDNA and reduced-represented genomic SNP data for a total of 139 specimens collected from 18 fish-host genera across a distribution range representing 21 countries. Our results strongly supported the existence of at least 10 evolutionary lineages and estimated the deepest divergence at approximately 4.99-5.05 Mya, which is much younger than the diversification of the fish host genera and orders. Historical biogeography analyses revealed that the ancestor of the parasite diversified following multiple vicariance events and was widespread throughout the Palearctic, Afrotropical, and Nearctic between the late Miocene and early Pliocene. Cyprinoids were inferred as the ancestral hosts for the parasite. Later, from the late Pliocene to Pleistocene, new lineages emerged following a series of biogeographic dispersal and host-switching events. Although only a few of the current Ligula lineages show narrow host-specificity (to a single host genus), almost no host genera, even those that live in sympatry, overlapped between different Ligula lineages. Our analyses uncovered the impact of historical distribution shifts on host switching and the evolution of host specificity without parallel host-parasite co-speciation. Historical biogeography reconstructions also found that the parasite colonized several areas (Afrotropical and Australasian) much earlier than was suggested by only recent faunistic data.

evolutionary biology↗

bioRxiv2020

High syphilis seropositivity in European brown hares, Lower Saxony, Germany

Treponema paraluisleporidarum infects lagomorphs and is a close relative of the human syphilis-bacterium Treponema pallidum. There is paucity of information on the epidemiology of hare syphilis and its relationship to rabbit- and human-infecting Treponema. We have found a high seropositivity (405/734) for Treponema paraluisleporidarum-infection in hares of Lower Saxony, Germany.

ecology↗