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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).

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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

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This Valentine's Day, love is not only in the air but also along the coastal shores of Australia and New Zealand, where the world's smallest penguin species, the Fairy Penguins, prepare for the final month of their annual mating rituals. This year there's one more thing to celebrate on February 14th as DNA Zoo Australia team unveils the first chromosome-length assembly and a 3D genome map for these waddly symbols of love and commitment (even though their real-life social and courtship relationships are rather complicated).



The chromosome-length genome assembly shared today was generated using a sample from the Perth Zoo (Western Australia) provided by Dr. Matyas Liptovszky, Director Life Sciences, Perth Zoo. The assembly is based on previous work published by Pan et. al., 2020 in GigascienceWe thank the Pawsey Supercomputing Centre for computational support for this genome assembly. See theDNA Zoo Methods page for more detail on the procedure, and check out the interactive contact map on the assembly page.


Dr. Matyas Liptovszky, Perth Zoo's Life Sciences Director, stresses the importance of using genetic resources to help guide Little Penguin conservation as it faces challenges such as overfishing and predation. The zoo's Penguin Plunge exhibit, since 1999, provides a safe haven. Through breeding programs and daily Penguin Feeds, visitors engage in crucial conservation support. "Utilising 3D DNA maps in our conservation program marks a pivotal moment for Perth Zoo. The advanced genetic tools created through the partnership between DNA Zoo Australia and Perth Zoo will enable crafting a robust strategy that will ensure the survival of these enigmatic creatures against looming threats," says Dr. Matyas Liptovszky.


This work has been enabled and conducted under Western Australian Genome Atlas (WAGA) initiative generously funded through Lotterywest. Our sincere thanks to the Lotterywest for their ongoing support through funding the WA Genome Atlas initiative and to the collective expertise and support of our WA partner organisations.


As we celebrate love in all its forms this Valentine's Day, let us take a moment to appreciate the wonders of the natural world and the extraordinary creatures that inhabit it. Every 20 minutes, a species goes extinct from our planet. So, whether snuggled with loved ones or admiring the courtship rituals of Fairy Penguins, please take a moment to also think about our love, commitment and collective responsibility to protect the Earth's biodiversity.

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