The wingless flight club

We have some exciting news to share with you. Our paper, in collaboration with a team at Princeton University led by Ricardo Mallarino and Jorge Moreno, is out today in Nature!

In this work, we harness the power of comparative analysis across 15 marsupial genomes coupled with some excellent forward genomics to figure out how marsupials develop patagia - a skin flap between for front and hind paws that allows them to glide. Turns out it is not a superpower from a fallen meteorite (@SugarGliderJM) but from a gene called Emx2! Check out excellent summaries on the research on the Baylor website and on Scientific American. Check out also Ricardo's X writeup.

Thank you to all the excellent collaborators spanning Princeton, Baylor College of Medicine, the University of Melbourne, SeaWorld, Houston Zoo, UC Irvine, Cornell and the University of Western Australia. And a special thank you to the museum community of Australia and the Australian Biological Tissue Collection at the South Australian Museum for providing tissue samples.

Visit the assembly pages for the chromosome-length genomes published as part of the work for the common wombat, the ground cuscus, the Eastern grey kangaroo, the Western grey kangaroo, the greater glider, common ringtail possum, golden ringtail possum, green ringtail possum, feathertail glider, Western ringtail possum, feather-tailed possum, coppery ringtail possum and the sugar glider to browse the corresponding interactive contact maps!

Citation:

Moreno, J.A., Dudchenko, O., Feigin, C.Y. et al. Emx2 underlies the development and evolution of marsupial gliding membranes. Nature (2024). https://doi.org/10.1038/s41586-024-07305-3

Largest Stonefly in the Western U.S.

Pteronarcys californica is a member of the stonefly family Pteronarcyidae and is commonly referred to as the giant salmonfly by anglers. P. californica is the largest species of stonefly in the western United States and is of ecological, cultural, and economical importance. Their large body size (>6 cm in length) makes them an essential prey item for aquatic consumers like fish, and their highly synchronous emergence to adulthood provides an important seasonal food resource for terrestrial consumers, including birds, spiders, amphibians, and small mammals.

Stoneflies are indicators of freshwater quality and mediate nutrient cycling and energy flow. Most stoneflies are stenothermic, meaning they are only able to survive within a narrow temperature range and are generally susceptible to warming. Because of their environmental sensitivity, they are a focal macroinvertebrate group for aquatic biomonitoring.

Pteronarcys californica – the giant salmonfly. Photo credits – Anna Eichert

Giant salmonfly populations have experienced a substantial decline in the past few decades – becoming regionally extinct in numerous rivers in Utah, Colorado, and Montana. They are incredibly sensitive to pollution, warming temperatures, flow modification, land-use change, sedimentation, and other environmental stressors on energy flows. Ecological variables pertaining to the subsistence of giant salmonfly populations have been well-recorded, but the genomic features of this species (or family) had not been explored before this.

The chromosome-length genome assembly shared today was generated using a flash-frozen individual collected from the Diamond Fork River in Utah, provided by PhD candidate Anna Eichert at the American Museum of Natural History. See the DNAZoo Methods page for more details on the procedure and check out the interactive contact map below and on the assembly page. This genome is a Hi-C upgrade of a PacBio draft generated with help from Dr. Paul Frandsen at Brigham Young University (BYU) and the BYU DNA Sequencing Center. We thank Drs. Jessica Ware, Scott Hotaling, and C. Riley Nelson for their assistance with the analyses, providing funding to complete this project, and for their general support.

Conservation attention is immediately required to prevent P. californica from going extinct. Because P. californica has adapted to fast-flowing rivers with historical temperature and flow regimes that are now being altered by human activity in many different ways, there is limited habitat availability for these essential insects. With this being only the 9th genome produced for stoneflies, stonefly genomics is an emerging field of study. Genetic tools will provide more information on the evolutionary responses of stoneflies to habitat alteration. This, in combination with environmental data, can provide structure to prompt conservation efforts.

We hope to continually raise awareness of the ecological importance of this species in freshwater environments and rally for resources to aid in their preservation. We support and commend the work of organizations such as The Salmonfly Project that aim to monitor and generate population data for P. californica in the western United States (see https://www.salmonflyproject.org/ for more information).

Weaving together the threads of the genome of the silk-spinning caddisfly

Caddisflies are miniature underwater architects. As adults, these insects resemble small brown moths, but as larvae, they are busy building underwater homes and cases (Fig. 1). While not as well-known as their closest relatives, the butterflies and moths, caddisflies have long captured the imaginations of amateur naturalists and fly-fishers. They’re important participants in aquatic food webs and, because larvae of different species have varying levels of sensitivity to environmental pollutants, they are used extensively in freshwater biomonitoring initiatives.

Fig. 1. Arctopsyche grandis larva.

Arctopsyche grandis belongs to the family Hydropsychidae, or the net-spinning caddisflies. Members of this family use silk to build retreats, complete with capture nets, that are fixed to the bottom of rocks in the stream (Fig. 2). The silk they use to build these structures is specially adapted for underwater use and adheres to a variety of substrates. The properties of these silks are of interest to biomedical engineers who seek to create bio-inspired adhesives. The variation in the primary silk gene of Arctopsyche grandis was recently described (Frandsen et al. 2023). We aim to use the chromosome-length genome assembly we release today to further understand the genetic processes underlying this extraordinary underwater silk.

Fig. 2. Illustration of an Arctopsyche grandis fixed-retreat and net.

The assembly was done using PacBio HiFi assembled with hifiasm, followed by purge_dups, and scaffolding using Hi-C. Check out the resulting interactive contact map below to browse through the 13 chromosomes of Arctophsyche grandis, and visit the assembly page for more details on the assembly!

References:

P. B. Frandsen, et al., Allelic resolution of insect and spider silk genes reveals hidden genetic diversity. Proc. Natl. Acad. Sci. 120, e2221528120 (2023) https://doi.org/10.1073/pnas.2221528120