Biology subjects

Laumer, C. E.

Publications and source records attributed to Laumer, C. E..

5 recordsLinked to original sources

bioRxiv2026

Portable, multilocus DNA barcoding across the diversity of meiofauna

Molecular data have revolutionised taxonomic and ecological research on the hyperdiverse communities of aquatic benthic microinvertebrates known as meiofauna. However, reference sequence databases remain highly incomplete, with variable barcode genes or fragments studied from taxon to taxon. Furthermore, there is a typical tradeoff between universality of primers and phylogenetic resolution, with rRNA markers being robustly recoverable but failing to resolve species-level divergences, and mitochondrial markers showing the reverse trend. Here, we introduce Oxford Nanopore rRNA and COI amplicon sequencing (OrCa-seq), a rapid, low-cost protocol for parallel long-range PCR amplification and multiplexed sequencing of four amplicons, spanning the nearly-complete rRNA cistron ([~]7-8 kb) and the widely studied Folmer region of COI (represented as overlapping 313 and 658 bp amplicons). This protocol, with its associated bioinformatic workflow, was designed for conducting biodiversity inventories of meiofauna and can be easily carried out in field research and educational contexts, with data available from 96-well plates of specimens within a day of lysis. To validate the method, we processed six plates of student-isolated freshwater and limno-terrestrial meiofauna, characterising the recovery of target genes and taxa with both automated and human-curated BLAST database comparisons. These data demonstrate the universal applicability of OrCa-seq across effectively all meiofauna, including the very smallest species. Nonetheless, recovery efficiency for each amplicon shows variation by taxon, with the full-length Folmer COI amplicon standing out as the most challenging. We present exemplar phylogenetic trees integrating reference sequences, demonstrating the utility of these data in confirming morphological determinations and in identifying anonymous specimens in a reverse taxonomy context. While developed in a specific educational context for use on meiofauna, the OrCa-seq approach should be readily scalable to larger research datasets, adaptable to many specimen types, and to any combination of taxon-or target-specific primers. As such, it represents a compelling multi-locus extension to the ever-growing repertoire of nanopore DNA barcoding protocols.

zoology↗

bioRxiv2025

Phylogenetic discordance and genic innovation at the emergence of modern cephalochordates

Cephalochordates (also known as amphioxus or lancelets) are a group of marine invertebrates occupying a critical phylogenetic position as the sister group to the remaining members of the chordate phylum (vertebrates and tunicates). As such, amphioxus have been key to help understanding the origin and evolution of vertebrate genomes, the evolution of their development and the diversification of their anatomy. However, out of the three genera of amphioxus currently known (Branchiostoma, Asymmetron and Epigonichthys), most studies have focused exclusively on Branchiostoma species. Indeed, all amphioxus genomes published to date belong to the Branchiostoma genus. This implies that our understanding of cephalochordate biology is limited to findings from Branchiostoma alone. It is consequently difficult to infer from the currently available Branchiostoma genomes, what aspects of their gene composition and structure are genus-specific or ancestral to cephalochordates. Here, we provide new high-quality genome assemblies and annotations from representatives of both Asymmetron and Epigonichthys. Genome-wide phylogenetic analyses reveal that, in contrast to previous mitogenomic studies, Branchiostoma is the sister group to Asymmetron and Epigonichthys. We further uncover discordant gene histories between these three genera, with notable asymmetry in the distribution of gene trees with minority topologies. Lastly, we find that extensive gene births and duplications preceded the origin of modern cephalochordates.

evolutionary biology↗

bioRxiv2025

The genome of the charismatic sea star Linckia laevigata

Linckia laevigata is a tropical sea star commonly found throughout the Indian and Pacific Oceans, and is one of the top ten-most collected invertebrates, often encountered in the aquarium trade. It has been the subject of investigations into population structure, biodiversity and ecology, particularly regarding gene flow among populations throughout its range, the status of different colour morphs and its relationship with its putative sister species, L. multifora. Here we present and describe a high-quality genome assembly for L. laevigata. Our assembly is 585.97 Mb in length, with a scaffold N50 of 3 Mb. The genome has a typical repeat (36.99%) and GC content (41.33%), when compared with other echinoderm datasets. Our genome annotation recovers 16,178 genes, with high (89.4%) recovery of the metazoan BUSCO set. This novel resource will provide a model organism for studying the biogeography of the tropical Indo-West Pacific region, and more specifically facilitate the investigation of a range of sea star traits at the genomic level. SignificanceSea stars remain poorly characterised at a genomic level. Data from the charismatic tropical sea star Linckia laevigata will enable future studies into the biology, population structure and evolution of these ecologically important species.

genetics↗

bioRxiv2020

Transposable element expression at unique loci in single cells with CELLO-seq

The role of Transposable Elements (TEs) in regulating diverse biological processes, from early development to cancer, is becoming increasing appreciated. However, unlike other biological processes, next generation single-cell sequencing technologies are ill-suited for assaying TE expression: in particular, their highly repetitive nature means that short cDNA reads cannot be unambiguously mapped to a specific locus. Consequently, it is extremely challenging to understand the mechanisms by which TE expression is regulated and how they might themselves regulate other protein coding genes. To resolve this, we introduce CELLO-seq, a novel method and computational framework for performing long-read RNA sequencing at single cell resolution. CELLO-seq allows for full-length RNA sequencing and enables measurement of allelic, isoform and TE expression at unique loci. We use CELLO-seq to assess the widespread expression of TEs in 2-cell mouse blastomeres as well as human induced pluripotent stem cells (hiPSCs). Across both species, old and young TEs showed evidence of locus-specific expression, with simulations demonstrating that only a small number of very young elements in the mouse could not be mapped back to with high confidence. Exploring the relationship between the expression of individual elements and putative regulators revealed surprising heterogeneity, with TEs within a class showing different patterns of correlation, suggesting distinct regulatory mechanisms.

molecular biology↗

bioRxiv2017

Placozoans are eumetazoans related to Cnidaria

The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria (=Planulozoa), also seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that the support for Planulozoa can be assigned to this source of systematic error. In interpreting this placozoan-cnidarian clade, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.

zoology↗