Biology subjects

Holovachov, O.

Publications and source records attributed to Holovachov, O..

6 recordsLinked to original sources

bioRxiv2025

Ultraconserved elements coupled with machine learning approaches resolve the systematics in model nematode species

Nematodes are among the most diverse animals, yet only around 28,000 of an estimated one million species have been morphologically described. Their small size, morphological simplicity, and cryptic diversity complicate phylogenetic analyses. Traditional morphological and single-locus molecular approaches often lack resolution for both recent and ancient divergences. To address these limitations, we developed the first ultraconserved elements (UCEs) probe sets for two nematode families: Panagrolaimidae, a group of non-model organisms with limited genomic resources when compared to model taxa, and Rhabditidae, which includes the model species Caenorhabditis elegans. Our probe sets targeted 1,612 loci for Panagrolaimidae and 100,397 for Rhabditidae. In vitro testing recovered up to 1,457 loci in Panagrolaimidae, supporting robust phylogenetic reconstruction. Results were largely consistent with previous analyses, except for one strain reclassified as Neocephalobus halophilus BSS8. Using machine learning, we determined the minimum number of loci needed for accurate genus-level classification. For Rhabditidae, XGBoost achieved high accuracy with just 46 loci. For Panagrolaimidae, 39 loci were most informative. Our UCE-based approach offers a scalable and cost-effective framework for phylogenomics, enhancing taxonomic resolution and evolutionary inference in nematodes. It is well suited for biodiversity assessments and shallow, field-based sequencing, expanding research possibilities across this ecologically important phylum.

evolutionary biology↗

bioRxiv2024

Soil biodiversity in the Atacama Desert shows distinct patterns at different diversity levels

Species diversity and distribution, in relation to how they interact with their environment is a major focus of ecological research. Particularly for soil ecosystems, information about geographical patterns of biota is scarce despite the pivotal role of soils as ecosystem service providers. The Atacama is the driest non-polar desert on earth: water is scarce, high salinity patches are frequent and water bodies have high concentrations of metals. It is believed that only specialized taxa can survive in this Desert. Accordingly, only some microbial life-forms and few plants, and vertebrates are present. Above ground invertebrates have been reported in the desert but its soils have not been comprehensively analyzed. By studying different areas in the Atacama, we aim to better understand resilience of soil organisms in times of global aridification. Nematodes are one of the most important groups of soil organisms in abundance and biodiversity. Here, we investigated diversity of soil nematodes at the genetic, taxonomic, community and life-cycle levels. We find distinct patterns and assemblages along the different habitats in the desert: dune systems, high altitude mountains, saline lakes, river valleys and fog oases. We also find that distribution of asexual taxa is more likely to occur at higher altitudes, and that the distribution of genera richness in the Atacama follows a latitudinal diversity gradient, as well as an increase with increasing precipitation. Our work shows that even under extreme environmental conditions stable, healthy soil communities can persist, but we see indicators of poor soil food webs.

ecology↗

bioRxiv2024

Comparative genomics of parasitoid lifestyle as exemplified by Mermithidae and Nematomorpha

Mermithidae and Nematomorpha are parasitoids united by the commonalities in their lifestyle - immature stages infect arthropod hosts, species from both phyla can manipulate their host to induce a similar water-seeking behaviour, and both have a final free-living non-feeding adult reproductive stage, often killing their host upon emergence. Some of these species are of great economic importance, being evaluated as biological control agents against mosquito vectors responsible for diseases like malaria, and other insect pests, but with scarce genomic resources currently available. Nematomorpha, despite being closely related to Nematoda, received insufficient attention in genomic research, leading to gaps in our understanding of their diverse genetic makeup. This study aimed to investigate the genetic features encoded in the genomes of both parasitoid taxa to identify similarities and parallels linked to their ecological lifestyles. We performed a comparative analysis of 12 genomes, comprising parasitoid, parasitic and free-living worms. The investigation revealed genomic signatures unique to parasitoid species, including expanded gene families enriched in neural transmission modulation, likely linked to the known host manipulation that both mermithids and nematomorphs exert on their hosts. The analysis also uncovered a diverse array of conserved transposable element superfamilies across both lineages. The findings from this study provide valuable insights into the potential genomic adaptations associated with parasitoidism in nematode and nematomorph worms. The identification of expanded gene families and conserved transposable element superfamilies sheds light on the molecular underpinnings of their unique biological traits. Additionally, the core set of orthologs specific to parasitoid worms offers new avenues for understanding the evolution of parasitism within these groups of organisms.

genomics↗

bioRxiv2023

Phylogenomic Insights into the Evolution and Origin of Nematoda

The phylum Nematoda represents one of the most cosmopolitan and abundant metazoan groups on Earth. In this study, we reconstructed the phylogenomic tree for phylum Nematoda. A total of 60 genomes, belonging to eight nematode orders, were newly sequenced, providing the first low-coverage genomes for the orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, and Enoplida. The resulting phylogeny is well-resolved across most clades, with topologies remaining consistent across various reconstruction parameters. The subclass Enoplia is placed as a sister group to the rest of Nematoda, agrees with previous published phylogenies. While the order Triplonchida is monophyletic, it is not well-supported, and the order Enoplida is paraphyletic. Taxa possessing a stomatostylet form a monophyletic group; however, the superfamily Aphelenchoidea does not constitute a monophyletic clade. The genera Trichinella and Trichuris are inferred to have shared a common ancestor approximately 202 mya, a considerably later period than previously suggested. All stomatostylet-bearing nematodes are proposed to have originated [~]305 mya, corresponding to the transition from the Devonian to the Permian period. The genus Thornia is placed outside of Dorylaimina and Nygolaimina, disagreeing with its position in previous studies. Additionally, we tested the whole genome amplification method and demonstrated that it is a promising strategy for obtaining sufficient DNA for phylogenomic studies of microscopic eukaryotes. This study significantly expanded the current nematode genome dataset, and the well-resolved phylogeny enhances our understanding of the evolution of Nematoda.

genomics↗

bioRxiv2023

Revisiting Hox gene evolution and Hox clusterlinkage across Nematoda

Hox genes are central to metazoan body plan formation, patterning and evolution, playing a critical role in cell fate decisions early in embryonic development in invertebrates and vertebrates. While the archetypical Hox gene cluster consists of members of nine ortholog groups (HOX1-HOX9), arrayed in close linkage in the order in which they have their anterior-posterior patterning effects, nematode Hox gene sets do not fit this model. The Caenorhabditis elegans Hox gene set is not clustered and contains only six Hox genes from four of the ancestral groups. The pattern observed in C. elegans is not typical of the phylum, and variation in orthologue set presence and absence and in genomic organisation has been reported. Recent advances in genome sequencing have resulted in the availability of many novel genome assemblies in Nematoda, especially from taxonomic groups that had not been analysed previously. Here, we explored Hox gene complements in high-quality genomes of 80 species from all major clades of Nematoda to understand the evolution of this key set of body pattern genes and especially to probe the origins of the "dispersed" cluster observed in C. elegans. We also included the recently available high-quality genomes of some Nematomorpha as an outgroup. We find that nematodes can have Hox genes from up to six orthology groups. While nematode Hox "clusters" are often interrupted by unrelated genes we identify species in which the cluster is intact and not dispersed.

developmental biology↗

bioRxiv2023

Spatio-temporal diversity and genetic architecture of pyrantel resistance in Cylicocyclus nassatus, the most abundant horse parasite

Cyathostomins are a complex of 50 intestinal parasite species infecting horses and wild equids. The massive administration of modern anthelmintic drugs has increased their relative abundance in horse helminth communities and selected drug-resistant isolates worldwide. Cylicocyclus nassatus is the most prevalent and the most abundant species. The tedious identification and isolation of these worms have hampered studies of their biology that remain largely uncharacterised. Here we have leveraged ultra-low input sequencing protocols to build a reference genome for the most prevalent horse strongyle species. Using this resource, we have established the first estimates of its genetic diversity and population structure on a gradient ranging from Ukraine (close to modern horse domestication area) to North America, while capturing a 19th-century snapshot of C. nassatus diversity in Egypt. Our results support a diverse and lowly structured global population. Modern populations displayed lower nucleotide diversity relative to the old North African isolate. We identified the first genetic candidates upon which pyrantel (an anthelmintic drug used in companion animals) selection likely applied in field populations, highlighting previously suspected genes coding for nicotinic acetylcholine receptor subunits, and identifying new candidates showing differential expression in independently evolved Caenorhabditis elegans lines. These results offer a first resource to widen current knowledge on cyathostomin biology, unravel novel aspects of pyrantel resistance mechanisms and provide candidate genes to track pyrantel resistance in the field.

genomics↗