Biology subjects

Roberts, N. G.

Publications and source records attributed to Roberts, N. G..

3 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↗

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↗