Biology subjects

Athanasouli, M.

Publications and source records attributed to Athanasouli, M..

4 recordsLinked to original sources

bioRxiv2024

Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, behavior, and survival

All animals live in tight association with complex microbial communities, yet studying the effects of individual bacteria remains challenging. Here, we exploit the system of the bacterial feeding nematode Pristionchus pacificus, where specific interactions can be studied in isolation. We sequenced the genomes of 84 Pristionchus-associated bacteria to investigate how differences in bacterial metabolic potential affect nematode traits. Specifically, we identified the Paerucumarin biosynthesis pathway as a strong candidate for nematode survival. Hypothesizing that bacterial production of coumarin derivatives contributed to increased lethality, we demonstrated nematicidal effects of two related compounds using supplementation assays. To explore metabolic interactions at a broader scale, we generated nematode transcriptomes for 38 bacterial diets and constructed a coexpression network that revealed distinct developmental and environmental signatures. Interspecies association studies resulted in a bipartite network with more than 2,800 interactions which may assist future studies to identify metabolites affecting various biological processes.

microbiology↗

bioRxiv2024

High nutritional conditions influence feeding plasticity in Pristionchus pacificus and render worms non-predatory

Developmental plasticity, the ability of a genotype to produce different phenotypes in response to environmental conditions, has been subject to intense studies in the last four decades. The self-fertilizing nematode Pristionchus pacificus has been developed as a genetic model system for studying developmental plasticity due to its mouth-form polyphenism that results in alternative feeding strategies with a facultative predatory and a non-predatory mouth form. Many studies linked molecular aspects of the regulation of mouth-form polyphenism with investigations of its evolutionary and ecological significance. Also, several environmental factors influencing P. pacificus feeding structure expression were identified including temperature, culture condition and population density. However, the nutritional plasticity of the mouth form has never been properly investigated although polyphenisms are known to be influenced by changes in nutritional conditions. For instance, studies in eusocial insects and scarab beetles have provided significant mechanistic insights into the nutritional regulation of polyphenisms but also other forms of plasticity. Here, we study the influence of nutrition on mouth-form polyphenism in P. pacificus through experiments with monosaccharide and fatty acid supplementation. We show that in particular glucose supplementation renders worms non-predatory. Subsequent transcriptomic and mutant analyses indicate that de novo fatty acid synthesis and peroxisomal beta-oxidation pathways play an important role in the mediation of this plastic response. Finally, the analysis of fitness consequences through fecundity counts suggests that non-predatory animals have an advantage over predatory animals grown in the glucose-supplemented condition. Research highlightsThis study represents the first systematic attempt to investigate the influence of nutrition on mouth-form polyphenism in the genetic model organism Pristionchus pacificus. Through glucose and oleic acid supplementation we show that high nutritional conditions influence feeding plasticity and render worms non-predatory. Mutant analysis indicates a role of de novo fatty acid synthesis and peroxisomal beta-oxidation pathways for these responses.

evolutionary biology↗

bioRxiv2024

The genome assembly of Rhabditoides inermis from a complex microbial community reveals further evidence for parallel gene family expansions across multiple nematodes

BackgroundFree-living nematodes such as Caenorhabditis elegans and Pristionchus pacificus are powerful model systems for linking specific traits to their underlying genetic basis. To trace the evolutionary history of a candidate gene, a robust phylogenomic framework is indispensable. ResultsIn this work, we generated a near chromosome-scale genome assembly of the nematode Rhabditoides inermis which had previously been proposed as the sister group of the family Diplogastridae to which P. pacificus belongs. The genome was assembled from a complex microbial community that consists of multiple bacteria and a fungus of the genus Vanrija. The R. inermis genome has five chromosomes that likely arose from recent fusions of different Nigon elements. Phylogenomic analysis grouped R. inermis within a clade including C. elegans, Mesorhabditis belari and other rhabditids and thus, did not support a sister group relationship between R. inermis and the family Diplogastridae. Comparative genomic analyses identified abundant lineage-specific orthogroups which reveal evidence for parallel expansions of environmentally responsive gene families. ConclusionsOur work demonstrates the value of the R. inermis genome as a resource for future phylogenomic analysis and for studying gene family evolution.

genomics↗

bioRxiv2020

Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

BackgroundNematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. ResultsHere, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths and screens for atypical domain combinations and species-specific orphan genes resulted in 4,221 candidate genes that were subject to community-based curation. Corrections for 2,851 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. ConclusionsOur work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.

genomics↗