Biology subjects

Schiffer, P. H.

Publications and source records attributed to Schiffer, P. H..

At least 19 recordsLinked to original sources

bioRxiv2026

Cavalcade-Mediated Resistance Alters Tomato-Root-Knot Nematode Interactions and Limits Nematode Infection

Meloidogyne incognita is a major plant-parasitic nematode responsible for substantial yield losses in tomato worldwide. Current control strategies rely heavily on chemical nematicides, which raise environmental concerns and face increasing regulatory restrictions, underscoring the need for sustainable alternatives. Here, we show that foliar application of an aqueous extract from cavalcade (Centrosema pascuorum) enhances tomato resistance against M. incognita. Pre-inoculation treatment with cavalcade extract prior to inoculation with root-knot nematodes (RKN) significantly reduced root gall formation, delayed nematode development, and limited second-stage juvenile penetration compared with untreated infected controls, whereas post-inoculation application conferred partial protection. Transcriptomic analyses revealed the activation of multiple defense-related pathways, including salicylic acid- and jasmonic acid-associated signaling and phenylpropanoid metabolism, supported by the upregulation of PR1 and PAL. Additional induction of lipid transfer proteins, leucine-rich repeat receptor-like kinases, resistance proteins, mitochondrial calcium uniporter, and GA2ox5 suggests coordinated activation of pathogen recognition, calcium signaling, and hormone-regulated defense networks. These findings demonstrate that cavalcade extract primes broad-spectrum defense responses in tomato and highlight its potential as an environmentally sustainable strategy for nematode management.

plant biology↗

bioRxiv2026

Chromosome-level genome assembly and annotation of the parthenogenetic nematode Acrobeloides nanus

Acrobeloides nanus is a species of widely distributed bacteria-feeding nematodes belonging to the family Cephalobidae. It reproduces parthenogenetically, making it a valuable system for studying the consequences of obligate asexuality, and exhibits early developmental processes that differ significantly from the model organism Caenorhabditis elegans. Additionally, the species has demonstrated remarkable resistance in extreme conditions, surviving near-complete desiccation through anhydrobiosis. This new chromosome-level genome assembly provides a high-quality reference to study these traits. Combining Nanopore, amplified PacBio HiFi, and Hi-C sequencing, we generated a chromosome-level assembly spanning 188.9 Mb over six chromosomes. The genome features a 48.1% repeat content, dominated by Mutator-like elements, and contains 24,912 predicted genes. Structural analysis reveals the conservation of ancestral nematode linkage groups. This resource significantly improves upon previous fragmented assemblies, offering a new framework for identifying genomic adaptations in the family Cephalobidae.

genomics↗

bioRxiv2026

Panagrolaimus einhardi sp. nov. and two sisters of fortune

Identifying nematodes to the species level is known to be complicated due to their morphological plasticity and limited number of taxonomically important characters. This is especially apparent in the genus Panagrolaimus, which comprises many cryptic species that are morphologically difficult to distinguish but differ genetically. These roundworms are particularly notable for their adaptation to extreme environments that are inhospitable to many other forms of life. Traditional morphological identification methods often fail at distinguishing genetically divergent populations due to high morphological plasticity in Panagrolaimus, limiting the efficacy of species discovery. High-quality genome assemblies overcome these challenges, offering a comprehensive blueprint of an organisms genetic structure that can be used for species identification. The analysis of ultra-conserved elements across multiple loci harvested from genome assemblies provides robust phylogenetic resolution. In this study, we integrate genome sequencing, ultra-conserved element analysis, and morphological assessment to identify and describe three novel species: Panagrolaimus einhardi sp. nov., formerly Panagrolaimus sp. ES5 from Germany; Panagrolaimus shuimeiren sp. nov. from the Namib Desert; and Panagrolaimus nebliphilus sp. nov. from the Atacama Desert. P. einhardi sp. nov. is named after Prof. Einhard Schierenberg, a renowned expert in roundworm development and cherished member of the nematode community, who isolated this species himself. All three species originate from different geographical locations, and their respective identification are supported by high-quality genome assemblies from either PacBio HiFi or Oxford Nanopore long-read data. The P. einhardi sp. nov. genome was scaffolded using Hi-C technology, which resulted in a 116 Mb collapsed assembly composed of 44 scaffolds (N50: 28 Mb). P. shuimeiren sp. nov. has an assembly size of 69 Mb with 49 scaffolds and a N50 of 13 Mb. P. nebliphilus sp. nov. assembly is 70 Mb with 24 scaffolds (N50: 13 Mb). The capacity of Panagrolaimus to adapt to extreme environments is driving research into their survival mechanisms, requiring comprehensive genomic resources. By combining morphology and genomics, we can gain a more comprehensive understanding of the rich biological diversity in lineages with numerous cryptic species, such as the Panagrolaimidae, thereby clarifying relationships where morphological data alone are ambiguous or confounded.

zoology↗

bioRxiv2025

Genomes of ancient asexual mites appear streamlined in their architecture

The long-term persistence of obligate asexual lineages represents one of the most enduring and critical paradoxes in evolutionary biology. Sexual reproduction, through meiotic recombination and segregation, enables the efficient removal of deleterious mutations and facilitates rapid adaptation to shifting environmental pressures. Lineages that lose sex are therefore classically predicted to experience genomic decay and face rapid extinction. Oribatid mites (Acari, Sarcoptiformes) represent a unique system for testing these predictions, as they feature multiple, ancient, and independent transitions to asexuality, providing a natural experiment on the evolutionary fate of asexual genomes. We compared four sets of sister sexual and asexual species using high-quality nuclear genome assemblies to investigate the genomic consequences of long-term asexuality. Our study revealed a profound, reproductive-mode-dependent dichotomy in the evolution of genome architecture. Contrary to their expected genomic decay, asexual species have mostly streamlined genomes with less novel genes than their sexual sister species. In contrast, sexual species have acquired genetic innovations, encompassing both gene and transposable element content. These results challenge classical expectations of genomic deterioration in asexual species and might explain the long-term evolutionary persistence of oribatid mites.

genomics↗

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

Phasing or purging: tackling the genome assembly of a highly heterozygous animal species in the era of high-accuracy long reads

The technological shift brought by high-accuracy long reads is transforming the genomic landscape and bringing forth chromosome-scale reference assemblies across the tree of life. Large-scale initiatives have emerged to encourage the production of such reference genomes, with the Earth BioGenome Project (EBP) establishing rigorous quality standards, while consortia like the Vertebrate Genome Project (VGP), Darwin Tree of Life (DToL), and European Reference Genome Atlas (ERGA) focus on large-scale sequencing and assembly production. By precisely discriminating alternative alleles and spanning multiple heterozygous regions, high-accuracy long reads enable assembly phasing, a more accurate representation of genomes than traditional collapsed assemblies. However, phasing assemblies remains challenging when access to long-read sequencing is restricted by low DNA material, or limited access to high-end sequencing facilities. To address these limitations, we evaluate three distinct long-read strategies: the established PacBio HiFi standard, the portable and more accessible Nanopore R10.4.1 technology, and the PacBio HiFi ultra-low input protocol designed for samples with only nanograms of DNA. We benchmarked five assemblers using empirical reads of these three technologies for the genome of the parthenogenetic nematode Plectus sambesii. Through a comprehensive assessment of contiguity, structural correctness, and gene and transposable element content, we identified substantial differences in haplotype separation, further validated across five additional non-model animal species for which reads from one sequencing technology were available. This study provides critical guidelines for de novo phased assembly. Ultimately, we show that the feasibility of haplotype-resolved assembly does not lie in the choice of sequencing technology, but in the selection of the appropriate assembler.

genomics↗

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↗

bioRxiv2022

Parthenogenetic Panagrolaimus species evolve at lower mutation rates, but show increased nucleotide diversity

Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus Panagrolaimus, and hermaphroditism in Propanagrolaimus. Here, we compared genomic features of free-living nematode populations in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic Panagrolaimus population, and a diploid hermaphroditic Propanagrolaimus species via long-term mutation-accumulation-lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (FST) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing Panagrolaimus populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Mullers ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.

evolutionary biology↗

bioRxiv2022

The slow evolving genome of the xenacoelomorph worm Xenoturbella bocki

The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data can help to elucidate phylogenetic relationships and provide important comparative data. Here we assemble and analyse the genome of the simple, marine xenacoelomorph Xenoturbella bocki, a key species for our understanding of early bilaterian and deuterostome evolution. Our highly contiguous genome assembly of X. bocki has a size of [~]111 Mbp in 18 chromosome like scaffolds, with repeat content and intron, exon and intergenic space comparable to other bilaterian invertebrates. We find X. bocki to have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signalling pathways are also largely complete and most bilaterian miRNAs are present. We conclude that X. bocki has a complex genome typical of bilaterians, in contrast to the apparent simplicity of its body plan. Overall, our data do not provide evidence supporting the idea that Xenacoelomorpha are a primitively simple outgroup to other bilaterians and gene presence/absence data support a relationship with Ambulacraria.

evolutionary biology↗

bioRxiv2022

Nematodes can survive in a suspended form of life for indefinite time

Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis1 when environmental conditions are unfavorable. This state-transition requires execution of a combination of genetic and biochemical pathways1,2,3 that enable the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera Panagrolaimus and Plectus4. Here, we present precise radiocarbon dating indicating that the Panagrolaimus individuals have remained in cryptobiosis since the late Pleistocene ([~]46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named Panagrolaimus n. sp. Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in Panagrolaimus n. sp. and in C. elegans is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.

genomics↗

bioRxiv2020

Systematic errors in orthology inference: a bug or a feature for evolutionary analyses?

Introductory paragraphThe availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; to identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy - identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs which experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction which mimic expected patterns of gene evolution.

evolutionary biology↗

bioRxiv2020

Evolutionary dynamics of transposable elements in bdelloid rotifers

Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates where males are thus far unknown. Contrary to expectations, we find a diverse range of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms, but we report that bdelloids share a large and unusual expansion of genes involved in RNAi-mediated TE suppression. This suggests that enhanced cellular defence mechanisms might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

evolutionary biology↗

bioRxiv2019

Concordant developmental expression profiles of orthologues in highly divergent Bilateria

Bilateria are the predominant clade of animals on earth. Despite having evolved a large variety of body-plans and developmental modes, they are characterized by common morphological traits. However, it is not clear if clade-specific genes can be linked to these traits, distinguishing bilaterians from non-bilaterians, with their less complex body morphology. Comparing proteomes of bilaterian and non-bilaterian species in an elaborate computational pipeline we aimed to find and define a set of of bilaterian-specific genes. Finding no high-confidence set of such genes, we nevertheless detected an evolutionary signal possibly uniting the highly diverse bilaterian taxa. Using a novel multi-species GO-enrichment method, we determined the functional repertoire of genes that are widely conserved among Bilateria. We found that these genes contribute to morphogenesis, neuronal-system and muscle development, processes that have been described as different between bilaterians and non-bilaterians. Analyzing gene expression profiles in three very distantly related bilaterina species, we find characteristic peaks at comparable stages of development and a delayed onset of expression in embryos. In particular, the expression of the conserved genes appears to peak at the phylotypic stage of different bilaterian phyla. In summary, our data underpin the orthologue conjecture and illustrate how development connects distantly related Bilateria after millions of years of divergence, pointing to processes potentially separating them from non-bilaterians.

evolutionary biology↗

bioRxiv2019

Computational discovery of hidden breaks in 28S rRNA across eukaryotes and consequences for RNA Integrity Numbers

In some eukaryotes, a hidden break has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break is common in protostome animals (arthropods, molluscs, annelids etc.) but a break has also been reported in some vertebrates and non-metazoan eukaryotes. We present a new computational approach to determine the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. We find a homologous break is present across protostomes although has been lost in a small number of taxa. We show that rare breaks in vertebrate 28S rRNAs are not homologous to the protostome break. A break is found in just 4 out of 331 species of non-animal eukaryotes studied and three of these are located in the same position as the protostome break suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28s rRNA and will be consistently underestimated in the great majority of animal species with a break.

bioinformatics↗

bioRxiv2018

Fitness Landscape of the Fission Yeast Genome

BackgroundNon-protein-coding regions of eukaryotic genomes remain poorly understood. Diversity studies, comparative genomics and biochemical outputs of genomic sites can be indicators of functional elements, but none produce fine-scale genome-wide descriptions of all functional elements.\n\nResultsTowards the generation of a comprehensive description of functional elements in the haploid Schizosaccharomyces pombe genome, we generated transposon mutagenesis libraries to a density of one insertion per 13 nucleotides of the genome. We applied a five-state hidden Markov model (HMM) to characterise insertion-depleted regions at nucleotide-level resolution. HMM-defined functional constraint was consistent with genetic diversity, comparative genomics, gene-expression data and genome annotation.\n\nConclusionsWe infer that transposon insertions lead to fitness consequences in 90% of the genome, including 80% of the non-protein-coding regions, reflecting the presence of numerous non-coding elements in this compact genome that have functional roles. Display of this data in genome browsers provides fine-scale views of structure-function relationships within specific genes.

genomics↗

bioRxiv2017

Differences in the genetic control of early egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus

BackgroundThe free-living nematode Diploscapter coronatus is the closest known relative of C. elegans with parthenogenetic reproduction. It shows several developmental idiosyncracies, for example concerning the control of meiosis and embryonic axis formation [1]. Our recent genome analysis [2] provided some support for the view that D. coronatus is a product of interspecies hybridization. Here we present additional data towards this assumption. Based on genomic and transcriptomic data we try to better understand the molecular basis of developmental idiosyncrasies in this species in an evolutionary context by comparison with selected other nematodes.\n\nResultsIn a genomic comparison between D. coronatus, C. elegans, other representatives of the genus Caenorhabditis and the more distantly related Pristionchus pacificus and Panagrellus redivivus, certain genes required for normal embryogenesis in C. elegans were found to be restricted to the genus Caenorhabditis. The mRNA content of early D. coronatus embryos was sequenced and compared with similar stages in C. elegans and Ascaris suum. We identified 350 gene families transcribed in the early embryo of D. coronatus but not in the other two nematodes. Looking at individual genes transcribed early in D. coronatus but not in C. elegans and A. suum we found that orthologs of most of these are present in the genomes of the latter species as well, suggesting heterochronic shifts with respect to expression behavior. Considerable divergence between alleles lends further support to the view that D. coronatus may be the result of an interspecies hybridization. Expression analysis of early acting single copy genes yield no indication for silencing of one parental genome.\n\nConclusionsOur comparative cellular and molecular studies support the view that the genus Caenorhabditis differs considerably from the other studied nematodes in its control of development and reproduction. The easy-to-culture parthenogenetic D. coronatus, with its high quality draft genome and only a single chromosome when haploid, offers many new starting points on the cellular, molecular, and genomic level to better understand alternative routes of nematode development and reproduction.

evolutionary biology↗

bioRxiv2017

Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes

Most animal species reproduce sexually, but parthenogenesis, asexual reproduction of various forms, has arisen repeatedly. Parthenogenetic lineages are usually short lived in evolution; though in some environments parthenogenesis may be advantageous, avoiding the cost of sex. Panagrolaimus nematodes have colonised environments ranging from arid deserts to arctic and antarctic biomes. Many are parthenogenetic, and most have cryptobiotic abilities, being able to survive repeated complete desiccation and freezing. It is not clear which genomic and molecular mechanisms led to the successful establishment of parthenogenesis and the evolution of cryptobiosis in animals in general. At the same time, model systems to study these traits in the laboratory are missing.\n\nWe compared the genomes and transcriptomes of parthenogenetic and sexual Panagrolaimus able to survive crybtobiosis, as well as a non-cryptobiotic Propanogrolaimus species, to identify systems that contribute to these striking abilities. The parthenogens are most probably tripoids originating from hybridisation (allopolyploids). We identified genomic singularities like expansion of gene families, and selection on genes that could be linked to the adaptation to cryptobiosis. All Panagrolaimus have acquired genes through horizontal transfer, some of which are likely to contribute to cryptobiosis. Many genes acting in C. elegans reproduction and development were absent in distant nematode species (including the Panagrolaimids), suggesting molecular pathways cannot directly be transferred from the model system.\n\nThe easily cultured Panagrolaimus nematodes offer a system to study developmental diversity in Nematoda, the molecular evolution of parthenogens, the effects of triploidy on genomes stability, and the origin and biology of cryptobiosis.

evolutionary biology↗