Biology subjects

Struck, T. H.

Publications and source records attributed to Struck, T. H..

9 recordsLinked to original sources

bioRxiv2026

The phylogenetic affinities of Chaetognathifera, with considerations of systematic error and the robusticity of macrosyntenic results

Chaetognathifera, a superphylum comprising Syndermata (Rotifera including Acanthocephala), Micrognathozoa, Gnathostomulida and Chaetognatha, is a complex grouping generally recovered as the sister to all other Lophotrochozoa. However, phylogenetic relationships within this group are controversial, in part due to poor sampling, resulting in two key questions. The first is whether Gnathostomulida or Chaetognatha represent the sister group to Syndermata+Micrognathozoa. The second is the phylogenetic position of the former phylum Acanthocephala within Syndermata. Here, we present the first study of the phylogenetic affinities of Chaetognathifera with genomic representation from all major phyla, and explore the potential of macrosynteny to better understand these relationships. For this latter aspect, we also developed a new jackknifing procedure to assess the robustness of linkage groups inferred by macrosyntenic analyses. We show that the phylogenetic relationships between these clades are corroborated through a variety of gene selection and analysis methodologies. This provides clear evidence of Acanthocephala as a derived clade within Syndermata as sister to Seisonidea, and that Gnathostomulida is sister to Syndermata+Micrognathozoa, with Chaetognatha as the earliest diverging clade within Chaetognathifera. On the other hand, we found that macrosyntenic patterns cannot resolve this question. Moreover, almost all possible linkage groups involving chaetognathiferan species lack robusticity and hence, should not be considered reliable. As a consequence so far, in Chaetognathifera none of the bilaterian ancestral linkage groups can be reliably found and independent massive chromosomal rearrangements occurred. We therefore strongly suggest that studies of macrosynteny should not only assess the significance of possible linkage groups, but also the robusticity of these linkage group inferences. Furthermore, we also present a script for this purpose, which can be found at: https://github.com/JFFleming/MacrosyntenicJackknife

evolutionary biology↗

bioRxiv2025

ERGA-BGE Reference Genome of Phyllidia flava (Nudibranchia: Phyllidiidae), a Relict Species Endemic to the Mediterranean Sea

Phyllidia flava, the only Mediterranean representative of the otherwise Indo-Pacific family Phyllididae, is a radula-less dorid nudibranch that feeds exclusively on toxic sponges, from which it derives defensive and camouflage compounds. Although not currently listed as endangered, this relict species remains vulnerable due to its restricted distribution and the rising temperatures of the Mediterranean Sea. A total of 13 contiguous chromosomal pseudomolecules were assembled, resulting in a chromosome-level genome spanning 1.9 Gb. This assembly comprises 2,032 contigs and 62 scaffolds, with contig and scaffold N50 values of 2.4 Mb and 169.7 Mb, respectively. This reference genome will serve as a valuable resource for conservation efforts, provide a robust calibration point for studying nudibranch phylogenetics based on the Tethys Ocean closure, and lay the groundwork for research into toxic prey diet specialisation.

genomics↗

bioRxiv2025

ERGA-BGE genome of Erebia palarica Chapman, 1905: a montane butterfly endemic to North-West Iberia

The reference genome of Erebia palarica will provide valuable insights into evolutionary and conservation genomics. On one hand, the reference genome paves the way to unravel the speciation process, reproductive barriers, and putative hybridisation of E. palarica with its closely related sister species: Erebica meolans. On the other hand, the reference genome will play an important role in the genetic monitoring of this endemic species, facilitating the use of genomics to estimate population genomics parameters. The genome was assembled into 14 contiguous chromosomal pseudomolecules (Z chromosome included). This chromosome-level assembly encompasses 0.49 Gb, composed of 38 contigs and 17 scaffolds, with contig and scaffold N50 values of 34.2 Mb and 38.4 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE genome of the Spanish Moon Moth Graellsia isabellae Graells, 1849: a nocturnal lepidopteran protected by the Habitats Directive

The reference genome of the Spanish Moon Moth, Graellsia isabellae, will be of great importance for evolutionary and conservation genomics. Firstly, this reference genome, alongside phylogenomic analyses, may finally resolve the longstanding debate regarding the scientific name of this iconic species--whether it should be Graellsia isabellae (Graells, 1849) or Actias isabellae (Graells, 1849). Secondly, the reference genome will be instrumental in the genetic monitoring of this protected species, enabling advanced methods to calculate contemporary population genomics estimates. The genome was assembled into 31 contiguous chromosomal pseudomolecules (Z chromosome included). The mitochondrial genome has also been assembled and is 15,247 bp in length. This chromosome-level assembly encompasses 0.56 Gb, composed of 38 contigs and 32 scaffolds, with contig and scaffold N50 values of 18.9 Mb and 20.4 Mb, respectively.

genomics↗

bioRxiv2024

ERGA-BGE Reference Genome of Gluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions

The reference genome of Gluvia dorsalis is the first of its order Solifugae (sun spiders), offering insights into adaptations to arid environments and the evolutionary history of arachnids. The entirety of the genome sequence was assembled into 5 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 787 Mb, composed of 51 contigs and 10 scaffolds (including the mitogenome), with contig and scaffold N50 values of 38 Mb and 199 Mb, respectively.

genomics↗

bioRxiv2024

First chromosome-level genome assembly of a ribbon worm from the Hoplonemertea clade, Emplectonema gracile, and its structural annotation

Genome-wide information has so far been unavailable for ribbon worms of the clade Hoplonemertea, the most species-rich class within the phylum Nemertea. While species within Pilidiophora, the sister clade of Hoplonemertea, possess a pilidium larval stage and lack stylets on their proboscis, Hoplonemertea species have a planuliform larva and are armed with stylets employed for the injection of toxins into their prey. To further compare these developmental, physiological, and behavioral differences from a genomic perspective, the availability of a reference genome of a Hoplonemertea species is crucial. To this end, we herein present the annotated chromosome-level genome assembly for Emplectonema gracile (Nemertea; Hoplonemertea; Monostilifera; Emplectonematidae), an easily collected nemertean well-suited for laboratory experimentation. The genome is 157.9 Mbp in span. Hi-C scaffolding yielded 15 putative chromosomes with a scaffold N50 of 10.0 Mbp and a BUSCO completeness score of 95.3%. Structural annotation predicted 20,684 protein-coding genes. The high-quality reference genome reaches an Earth BioGenome standard level of 7.C.Q50. These data will be highly useful for future investigations towards a better understanding of the evolution, development, morphology, and toxicology of Nemertea. SignificanceThe genome of Emplectonema gracile is highly contiguous, well annotated, and shorter than those of the other two ribbon worm species sequenced to date. This genome is a valuable resource for studies on molecular ecology, venom evolution, and regeneration in marine invertebrates.

genomics↗

bioRxiv2024

Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the Gastrotrich Lepidodermella squamata (Dujardin, 1841)

BackgroundObtaining adequate DNA for long-read genome sequencing remains a roadblock to producing contiguous genomes from small-bodied organisms. Multiple displacement amplification (MDA) leverages Phi29 DNA polymerase to produce micrograms of DNA from picograms of input. Few genomes have been generated using this approach, due to concerns over biases in amplification related to GC and repeat content and chimera production. Here, we explored the utility of MDA for generating template DNA for PacBio HiFi sequencing using Caenorhabditis elegans (Nematoda) and Lepidodermella squamata (Gastrotricha). ResultsHiFi sequencing of libraries prepared from MDA DNA produced highly contiguous and complete genomes for both C. elegans (102 Mbp assembly; 336 contigs; N50 = 868 Kbp; L50 = 39; BUSCO_nematoda: S:92.2%, D:2.7%) and L. squamata (122 Mbp assembly; 157 contigs; N50 = 3.9 Mb; L50 = 13; BUSCO_metazoa: S: 78.0%, D: 2.8%). Amplified C. elegans reads mapped to the reference genome with a rate of 99.92% and coverage of 99.75% with just one read (of 708,811) inferred to be chimeric. Coverage uniformity was nearly identical for reads from MDA DNA and reads from pooled worm DNA when mapped to the reference genome. The genome of Lepidodermella squamata, the first of its phylum, was leveraged to infer the phylogenetic position of Gastrotricha, which has long been debated, as the sister taxon of Platyhelminthes. ConclusionsThis methodology will help generate contiguous genomes of microscopic taxa whose body size precludes standard long-read sequencing. L. squamata is an emerging model in evolutionary developmental biology and this genome will facilitate further work on this species.

genomics↗

bioRxiv2023

Contextualising samples: Supporting reference genomes for European biodiversity through sample and associated metadata collection

The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europes eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGAs pan- European network. To demonstrate the communitys capability and capacity to realise ERGAs ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGAs member base. SSP aims to aid participating researchers through i) establishing standards for and collecting of sample/ specimen metadata; ii) prioritisation of species for genome sequencing; and iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGAs high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.

genomics↗

bioRxiv2018

Breaking the ladder: Evolution of the ventral nerve cord in Annelida

A median, segmented, annelid nerve cord has repeatedly been compared to the arthropod and vertebrate nerve cords and became the most used textbook representation of the annelid nervous system. Recent phylogenomic analyses, however, challenge the hypothesis that a subepidermal rope-ladder-like ventral nerve cord (VNC) composed of a paired serial chain of ganglia and somata-free connectives represents neither a plesiomorphic nor a typical condition in annelids.\n\nUsing a comparative approach by combining phylogenomic analyses with morphological methods (immunohistochemistry and CLSM, histology and TEM), we compiled a comprehensive dataset to reconstruct the evolution of the annelid VNC. Our phylogenomic analyses generally support previous topologies. However, the so far hard-to-place Apistobranchidae and Psammodrilidae are now incorporated among the basally branching annelids with high support. Based on this topology we reconstruct an intraepidermal VNC as ancestral state in Annelida. Thus, a subepidermal ladder-like nerve cord clearly represents a derived condition.\n\nBased on the presented data, a ladder-like appearance of the ventral nerve cord evolved repeatedly, and independently of the transition from an intraepidermal to a subepidermal cord during annelid evolution. Our investigations thereby question a common origin of the bilaterian median ganglionated VNC and propose an alternative set of neuroanatomical characteristics of the last common ancestor of Annelida or perhaps even Spiralia.

evolutionary biology↗