Search for: All records

Abstract We describe four ancient polyploidy events where the descendant taxa retain many more duplicated gene copies than has been seen in other paleopolyploidies of similar ages. Using POInT (the Polyploidy Orthology Inference Tool), we modeled the evolution of these four events, showing that they do not represent recent independent polyploidies despite the rarity of shared gene losses. We find that these events have elevated rates of interlocus gene conversion and that these gene conversion events are spatially clustered in the genomes. Regions of gene conversion also show very low synonymous divergence between the corresponding paralogous genes. We suggest that these genomes have experienced a delay in the return to a diploid state after their polyploidies. Under this hypothesis, homoeologous exchanges between the duplicated regions created by the polyploidy persist to this day, explaining the high rates of duplicate retention. Genomes with these characteristics arguably represent a new class of paleopolyploid taxa because they possess evolutionary patterns distinct from the more common and well-known paradigm of the rapid loss of many of the duplicated pairs created by polyploidy. 

Abstract Insects have evolved complex and diverse visual systems in which light-sensing protein molecules called “opsins” couple with a chromophore to form photopigments. Insect photopigments group into three major gene families based on wavelength sensitivity: long wavelength (LW), short wavelength (SW), and ultraviolet wavelength (UV). In this study, we identified 123 opsin sequences from whole-genome assemblies across 25 caddisfly species (Insecta: Trichoptera). We discovered the LW opsins have the most diversity across species and form two separate clades in the opsin gene tree. Conversely, we observed a loss of the SW opsin in half of the trichopteran species in this study, which might be associated with the fact that caddisflies are active during low-light conditions. Lastly, we found a single copy of the UV opsin in all the species in this study, with one exception: Athripsodes cinereus has two copies of the UV opsin and resides within a clade of caddisflies with colorful wing patterns. 

Abstract 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 for a Hoplonemertea species is crucial. Such data will be highly useful for future investigations toward a better understanding of molecular ecology, venom evolution, and regeneration not only in Nemertea but also in other marine invertebrate phyla. 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 has an assembly size of 157.9 Mb. Hi-C scaffolding yielded chromosome-level scaffolds, with a scaffold N50 of 10.0 Mb and a score of 95.1% for complete BUSCO genes found as a single copy. Annotation predicted 20,684 protein-coding genes. The high-quality reference genome reaches an Earth BioGenome standard level of 7.C.Q50.