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

Little penguins, big love

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).

Little Penguin Eudyptula minor. Photo Credits & acknowledgements – Parwinder Kaur, [CC BY 2.0]

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 Gigascience. We 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.

Ignoble purrsuits

Frustratingly few people know about fishers (Pekania pennanti). This cat-sized North American mustelid used to be classified in the genus Martes, but never quite fit in. The fisher used to inhabit the whole boreal forest belt of North America, but their populations began to decline in the first half of the 20th century due to a combination of overtrapping for their fur, and timber logging, which shrunk and fragmented its range. In fact, the fisher was nearly exterminated from the southern and eastern part of its range. However, thanks to conservation efforts and sustainable trapping management, fishers are making a splendid comeback in many states, lifting it out of many local endangered species lists (and even eating unsupervised pet cats as they proceed).

US Forest Service [CC BY 2.0 DEED], via flickr.com

While sharing the range, habitat and many dietary and behavioral traits with true martens such as the American marten (Martes americana) and Pacific marten (Martes caurina), the fisher is a bigger, burlier animal with a longer tail, coarser fur and heavier head; it oddly resembles a fuzzy otter with a bear’s head. Not only its looks are confusing. Fishers may look a bit clumsy, yet they are excellent tree climbers and are among the very few mammals able to descend trees head-first. Their climbing abilities are facilitated by being able to rotate their hind paws nearly 180°. Fishers are considered omnivorous, but their primary prey are snowshoe hares and North American porcupines (one of the very few predators known to hunt this species). Fishers have even been documented to be predators of Canada lynx! Fishers are sexually dimorphic, with males larger than females, and they are mostly solitary except during the mating season. Like some other carnivoran species, female fishers show embryonic diapause (also known as delayed implantation).

Even their name is misleading – fishers do not catch fish! The name is in fact a corruption of the word “fitch”, which is an old-fashioned term for the European polecat; the word “fitch”, in turn, goes back to Late Latin vissiō "foul smell from a noiseless fart". So much for nomenclatural dignity! The lasting taxonomic hassle among scholars, bouncing the fisher between different genera, was finally settled in 2008, when the fisher got assigned a genus of its own, Pekania, as one of the earliest branching lineages of the Guloninae clade, just like its similarly-sized South American relative, the tayra (Eira barbara).

Today, we release the chormosome-length genome assembly for the fisher, generated from a sample shared by the New York State Department of Environmental Conservation. We acknowledge Timothy Watson for providing fisher samples for sequencing and Roger Powell for making this genome assembly possible. Check out the interactive contact map below!