Cell fate specification modes shape transcriptome evolution in the highly conserved spiral cleavage.

Early animal development can be remarkably variable, influenced by lineage-specific reproductive strategies and adaptations. Yet, early embryogenesis is also strikingly conserved in certain groups, such as Spiralia. In this clade, a shared cleavage program (i.

Chromosome-scale genome assembly and gene annotation of the hydrothermal vent annelid Alvinella pompejana yield insight into animal evolution in extreme environments.

Background: The Pompeii worm Alvinella pompejana, a terebellid annelid, has long been an exemplar of a metazoan that lives in an extreme environment, on the chimney wall of deep-sea hydrothermal vents, but this very environment has made it difficult to study. Comprehensive assessment of Alvinella pompejana genome content, and the factors that could explain its ability to thrive in seemingly hostile conditions has been lacking.

Results: We report the chromosome-level genome sequence of Alvinella pompejana and population-level sequence variants.

The genomic origin of the unique chaetognath body plan.

The emergence of animal phyla, each with their unique body plan, was a rapid event in the history of animal life, yet its genomic underpinnings are still poorly understood. Here we investigate at the genomic, regulatory and cellular levels, the origin of one of the most distinctive animal phyla, the chaetognaths, whose organismal characteristics have historically complicated their phylogenetic placement. We show that these characteristics are reflected at the cell-type level by the expression of genes that originated in the chaetognath lineage, contributing to adaptation to planktonic life at the sensory and structural levels.

The chromosomal genome sequence of the marine leech, Moore, 1952 and its associated microbial metagenome sequences.

We present a genome assembly from an individual (the marine leech; Annelida; Clitellata; Hirudinida; Piscicolidae). The genome sequence is 174.1 megabases in span.

A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade.

Background: The dynamic addition and removal of posttranslational modifications on eukaryotic histones define regulatory regions that play a central role in genome and chromatin biology. However, our understanding of these regulatory mechanisms in animals is primarily based on a few model systems, preventing a general understanding of how histone-based regulation directs and promotes phenotypic variation during animal embryogenesis.

Results: Here, we apply a comprehensive multi-omics approach to dissect the histone-based regulatory complement in Annelida, one of the largest invertebrate clades.

Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles.

Background: Characterizing genetic and epigenetic diversity is crucial for assessing the adaptive potential of threatened populations and species in the face of climate change. Sea turtles are particularly vulnerable due to their temperature-dependent sex determination (TSD) system, which heightens the risk of extreme sex ratio bias and extinction under future climate scenarios. High-quality genomic and epigenomic resources will therefore support conservation efforts for these endangered flagship species with such plastic traits.

The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the Tree of Life.

We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbioses. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms - both the "hosts" and the microbial symbionts with which they associate.

Fundamental questions in meiofauna research highlight how small but ubiquitous animals can improve our understanding of Nature.

This paper identifies the top-50 priority questions for meiofaunal research, highlighting their critical roles in biogeochemical cycles and biodiversity. It calls for a balanced research agenda, international cooperation, and advances in technology to overcome current challenges and unlock meiofauna’s full potential.

Preservation and early evolution of scalidophoran ventral nerve cord.

Ecdysozoan worms (Nematoida + Scalidophora) are typified by disparate grades of neural organization reflecting a complex evolutionary history. The fossil record offers a unique opportunity to reconstruct the early character evolution of the nervous system via the exceptional preservation of extinct representatives. We focus on their nervous system as it appears in early and mid-Cambrian fossils.

Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning.

Background: Wnt signaling pathways play crucial roles in animal development. They establish embryonic axes, specify cell fates, and regulate tissue morphogenesis from the early embryo to organogenesis. It is becoming increasingly recognized that these distinct developmental outcomes depend upon dynamic interactions between multiple ligands, receptors, antagonists, and other pathway modulators, consolidating the view that a combinatorial "code" controls the output of Wnt signaling.

DNA Methylation Carries Signatures of Sublethal Effects Under Thermal Stress in Loggerhead Sea Turtles.

To date, studies of the impacts of climate warming on individuals and populations have mostly focused on mortality and thermal tolerance. In contrast, much less is known about the consequences of sublethal effects, which are more challenging to detect, particularly in wild species with cryptic life histories. This necessitates the development of molecular tools to identify their signatures.

Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria.

Background: DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. While vertebrate genomes are hypermethylated, in most invertebrates, 5mC concentrates on constantly and highly transcribed genes (gene body methylation; GbM) and, in some species, on transposable elements (TEs), a pattern known as "mosaic".

Developmental toxicity of pre-production plastic pellets affects a large swathe of invertebrate taxa.

Microplastics pose risks to marine organisms through ingestion, entanglement, and as carriers of toxic additives and environmental pollutants. Plastic pre-production pellet leachates have been shown to affect the development of sea urchins and, to some extent, mussels. The extent of those developmental effects on other animal phyla remains unknown.

The development of the adult nervous system in the annelid Owenia fusiformis.

Background: The evolutionary origins of animal nervous systems remain contentious because we still have a limited understanding of neural development in most major animal clades. Annelids - a species-rich group with centralised nervous systems - have played central roles in hypotheses about the origins of animal nervous systems. However, most studies have focused on adults of deeply nested species in the annelid tree.

Functional genomics in Spiralia.

Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact.

Emerging trends in the study of spiralian larvae.

Many animals undergo indirect development, where their embryogenesis produces an intermediate life stage, or larva, that is often free-living and later metamorphoses into an adult. As their adult counterparts, larvae can have unique and diverse morphologies and occupy various ecological niches. Given their broad phylogenetic distribution, larvae have been central to hypotheses about animal evolution.

A dynamic epibiont community associated with the bone-eating polychaete genus .

the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of , which change over time as the whale carcass degrades on the sea floor.

Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms.

Bacterial symbioses allow annelids to colonise extreme ecological niches, such as hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbioses remain unclear. Here, we show that different genomic adaptations underpin the symbioses of phylogenetically related annelids with distinct nutritional strategies.

Annelid functional genomics reveal the origins of bilaterian life cycles.

Indirect development with an intermediate larva exists in all major animal lineages, which makes larvae central to most scenarios of animal evolution. Yet how larvae evolved remains disputed. Here we show that temporal shifts (that is, heterochronies) in trunk formation underpin the diversification of larvae and bilaterian life cycles.

The Fox Gene Repertoire in the Annelid Owenia fusiformis Reveals Multiple Expansions of the foxQ2 Class in Spiralia.

Fox genes are a large and conserved family of transcription factors involved in many key biological processes, including embryogenesis and body patterning. Although the role of Fox genes has been studied in an array of model systems, comprehensive comparative studies in Spiralia-a large clade of invertebrate animals including molluscs and annelids-are scarce but much needed to better understand the evolutionary history of this gene family. Here, we reconstruct and functionally characterize the Fox gene complement in the annelid Owenia fusiformis, a slow evolving species and member of the sister group to all remaining annelids.

ERK1/2 is an ancestral organising signal in spiral cleavage.

Animal development is classified as conditional or autonomous based on whether cell fates are specified through inductive signals or maternal determinants, respectively. Yet how these two major developmental modes evolved remains unclear. During spiral cleavage-a stereotypic embryogenesis ancestral to 15 invertebrate groups, including molluscs and annelids-most lineages specify cell fates conditionally, while some define the primary axial fates autonomously.

Early embryogenesis and organogenesis in the annelid Owenia fusiformis.

Background: Annelids are a diverse group of segmented worms within Spiralia, whose embryos exhibit spiral cleavage and a variety of larval forms. While most modern embryological studies focus on species with unequal spiral cleavage nested in Pleistoannelida (Sedentaria + Errantia), a few recent studies looked into Owenia fusiformis, a member of the sister group to all remaining annelids and thus a key lineage to understand annelid and spiralian evolution and development. However, the timing of early cleavage and detailed morphogenetic events leading to the formation of the idiosyncratic mitraria larva of O.

Conservative route to genome compaction in a miniature annelid.

The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8-megabase genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm.