A bat that grows on trees

- Fondly referred to by some of the scientists chasing them around North America as “sky lions”, hoary bats Aeorestes cinereus are the among the biggest, flashiest, and widest ranging bats on the continent.

Hoary bat (Lasiurus cinereus) - pregnant female resting in a tree during spring migration. Photo by Paul Cryan.

- Unlike a lot of the other 40+ species of bats occurring in the U.S. & Canada, they have bright markings and contrasting colors (e.g., wing spots, yellow fur on inside of underwing and ringing their face and ears, reddish pink skin on the tops of their wings).

- Unlike a lot of other bats ranging into the temperate North America, they spend most of their lives in trees, sometimes maybe hiding under leaf litter on the ground during colder months.

- These are definitely not cave bats, because they actually get lost and die within caves when they happen to wander in.

- We don’t know much about the details of their seasonal movements, but they are highly migratory and seem to always be on the move (individuals probably migrate up to a couple thousand kilometers each way).

- They may be the widest ranging of all the terrestrial mammals in North America other than humans (I say terrestrial because whales, dolphins, and other marine mammals may migrate similar or longer distances).

- We don’t really know where the bulk of the North American population spends the winter, probably because they migrate to wintering grounds and then hibernate, which is typical bat weird/amazing.

- Our best guess is that females migrate about a month before males in spring out of wintering grounds in coastal California and Mexico, then move to summering grounds east of the Rockies where they birth and raise their pups.

- This is one of the few bats in North America in which females consistently gives birth to more than a single pup each year---twins seem to be the norm, but triplets and quadruplets aren’t that unusual.

- A mother an her pups is about as big a social groups get with hoary bats, which is why we in the business refer to them as ‘solitary tree bats.’

- Males are typical and migrate about a month later than females in the spring, mostly stop in the Rocky Mountains for the early summer, and don’t seem to travel nearly as far as the females during the spring and early summer.

- Things start to get strange and tragic as the females and their volant young start heading back to the wintering grounds in late summer and autumn.

- For reasons we still don’t quite understand, hoary bats compose about half of the tens of thousands of bats estimated to be dying after colliding with the blades of wind turbines each year.

- Most bat fatalities at wind turbines happen between about mid-July and early October, which is when the females and their young are heading back toward the wintering grounds and the males are dispersing out of their different summering areas to try and intercept females to mate with before they hunker down for the winter.

- Like most bats, hoary bats mate in the autumn and winter, then females store the sperm and fertilize themselves to be independent of the males in spring.

- The particular susceptibility of hoary bats to wind turbines might have something to do with their mating behaviors (and striking colors), but that is still mostly speculation, see here.

- Hoary bats mate by somehow finding each other while migrating in the dark, then the act begins in flight, with the couples falling to the ground as it commences.

- Our best guess right now is that hoary bats visually mistake (echolocation only works out to about 100 m and they have very sensitive but fuzzy night vision) the silhouettes of wind turbines for the trunks and crowns of large trees, then approach expecting to find something they need there, like insect accumulations, friends/mates, or simply places to rest.

- Some of us tracked a few hoary bats with GPS tags and followed one male making a 1000-km circular trip from the redwood forests of central California up to Oregon, Nevada, and then back to California in a few weeks during October, see here.

- We also put some custom-made dataloggers that recorded temperature, light levels, acceleration, etc. on hoary bats and caught one hibernating in a tree all winter in a redwood forest of CA (see here).

- Details of how hoary bats hibernate are not known, but their scientific name (at least the one I grew up with), Lasiurus cinereus, roughly translates to hairy tailed and ash colored; when they get really cold they roll up into a furry ball (I’ve heard anecdotes about hoary bats being found balled up under snow in mountains of Arizona, but it hasn’t been clearly documented yet…but a morphologically similar species in Japan hibernates under the snow - read here).

- As far as I can tell, the newly proposed genus name Aeorestes translates from Latin to something like ‘an eater that flits about.’

- Hoary bats made it out to Hawaii a couple times in the past, and were the only terrestrial mammal (again, marine mammals were there) occurring on the archipelago when humans arrived (read about it here).

- Today, we release a chromosome-length genome assembly for the hoary bat, based on the draft generated by the United States Geological Survey (Cornman, R., Cryan, P., Fike, J. and Oyler-Mccance, S., 2020). The sample used for Hi-C library preparation was collected in Fort Collins, Colorado in September 2019, by Paul Cryan, USGS Fort Collins Science Center under Colorado Parks and Wildlife Scientific Collection License 19TR2010 from a recently deceased bat provided by Larimer County Public Health Department.

The battiest of them all

Urban areas across the U.S. and Canada are often dominated by big brown bats, Eptesicus fuscus. These bats represent one of the very few US/Canada species with a distribution that spans the entire US. They are everywhere!

Big brown bat, photo by Paul Cryan.

The “big brown bat” name really does not capture how amazing this commensal bat can be. It does truthfully reflect one thing though: the bats are indeed bigger than most of the other hibernating North American bats of the ultra-diverse bat family Vespertilionidae, with over 400 species [1]!

In the spring and early summer, the females of the species come out of the wild to form temporary maternity colonies for giving birth to the young. Historically, maternity colonies were probably in tree cavities. In modern, human-dominated landscapes, however, many maternity colonies are in buildings and residential properties.

In the winter, the bats go into hibernation. Importantly, the big brown bat hibernates in smaller groups, and in colder and drier conditions than many of the other North American bats. This behavior likely contributes to their ability to survive the white-nose syndrome, a disease that has been decimating other hibernating bats on the continent. (By contrast, read about the little brown bat Myotis lucifugus and its struggle with the white-nose in one of our previous blog post.)

As an insectivore, big brown bats play a crucial role in maintaining bug populations and are an agriculturally valuable species. These bats are often sought out by corn farmers, as they consume cucumber beetles that are capable of destroying an entire season’s crop [2]. Farmers can build bat boxes stable place to roost, encouraging these bats to move in and provide their services. Instructions on how to construct your own bat box can be found on the National Wildlife Federation’s website.

Because they are so willing to share buildings with us, big brown bats have historically been a species that scientists study a lot. For example, one of the closest looks yet into the details of a hibernating bat’s life was the Fort Collins Bat Project, a 5-year study that scientists from USGS, Colorado State University, and CDC collaborated on from about 2001-2006 to study population dynamics of big brown bats in Fort Collins, CO, and the dynamics of rabies viruses circulating in this population. The findings of that study were many and profound, but one of the coolest aspects was that they marked over 4,000 individual big brown bats with passive integrated transponder (PIT) tags and followed their movements and gave them occasional health check-ups over the years of the project. Read this paper for a summary of the project!

Today, we share the chromosome length assembly of the big brown bat based on the EptFus1.0 draft generated by the Broad Institute. In order to do the upgrade, we generated a Hi-C library using a sample donated by one of the tagged bats from the Fort Collins Bat Project. (Sample collected under Colorado Parks and Wildlife Scientific Collection License 14TR2010 issued to Paul Cryan. Protocols approved by the Institutional Animal Care and Use Committee of the USGS Fort Collins Science Center (FORT-IACUC #2014-08).

The bat, who was at least 10 years old when she died, had successfully birthed a pup during the four years of the study when the scientists were regularly checking in on her health. Like a good proportion of the big brown bats in Fort Collins, they detected rabies virus neutralizing antibodies in her blood in multiple years, so she was presumably immune!

This is the third Vespertilionidae bat family genome assembly at the DNA Zoo, after the little brown bat Myotis lucifigus and the North American long-eared bat Myotis septentrionalis. See how the genome assemblies relate to each other below!

DNA Zoo Vespertilionidae whole genome alignments: bit brown bat (EptFul1.0_HiC); little brown bat (Myoluc2.0_HiC) and North American long-eared bat (myse_ont_racon_pilon_HiC).

Blot post by Ruqayya Khan & Olga Dudchenko

A Primo Berry Genome!

Caneberries, including blackberries (Rubus subgenus Rubus) and raspberries (R. idaeus), are botanically unique in that they have perennial root systems and crowns and biennial canes. Typically, first-year vegetative canes (primocanes) must overwinter and accumulate chilling hours before flowering and fruiting in their second year after becoming floricanes (Clark et al., 2007). The development and adoption of primocane-fruiting raspberry and blackberry cultivars that fruit on first year canes has revolutionized the caneberry industry. Now growers can produce a summer crop on floricanes and a second fall crop on primocanes, extending the growing season and producing two crops in one year!

Tetraploid primocane-fruiting breeding selection from the University of Arkansas fruit breeding program that has Hillquist blackberry is in the pedigree! Photo by Margaret Worthington.

Today, we share the chromosome-length genome assembly for the diploid blackberry ‘Hillquist’ (R. argutus, PI 553951), generated using plants donated by the USDA-ARS National Clonal Germplasm Repository in Corvallis, OR.

‘Hillquist’ was chosen for the assembly because it is the source of the recessive allele for primocane-fruiting used in modern blackberry breeding programs (Clark, 2008; Lopez Medina et al., 2000). ‘Hillquist’ was originally discovered in Ashland, VA by L.G. Hillquist, who noticed that some of the wild blackberries growing in his backyard had an unusual fruiting habit. His wife later donated the plants to the New York State Agricultural Experiment Station in 1949. Jim Moore, the founder of the University of Arkansas System Division of Agriculture fruit breeding program, first crossed ‘Brazos,’ a tetraploid, floricane-fruiting blackberry cultivar, to ‘Hillquist’ in 1967, but the first primocane-fruiting cultivars, ‘Prime-Jim’ ® and ‘Prime-Jan’® were not released until 2004, nearly 40 years later (Clark, 2008). Since then, primocane fruiting cultivars have transformed the blackberry industry and ‘Hillquist’ is now represented in the pedigree of much public and private blackberry breeding germplasm around the world.

This work is part of a collaborative effort between DNA Zoo, the University of Arkansas, USDA-ARS, North Carolina State University, NIAB-EMR, Pairwise Plants, and the Wellcome Sanger Institute. The assembly was generated using PacBio and Hi-C sequencing data. The PacBio data was assembled using FALCON software. The Falcon assembly was phased into haplotypes using FALCON-Unzip (see Chin, Peluso et al., 2016), with error correction on the phased assembly performed using Arrow. The Hi-C scaffolding was performed using the standard DNA Zoo workflow, based on in situ Hi-C (Rao, Huntley et al., 2014) prepared from fresh leaf samples. The tools used for Hi-C data processing included Juicer (Durand, Shamim et al., 2016), 3D-DNA (Dudchenko et al., 2017), and Juicebox Assembly Tools (Dudchenko et al., 2018).

See below the whole-genome alignment plots that compare the Hillquist genome to the Burbank Thornless (R. ulmifolius), available here at the DNA Zoo, black raspberry (R. occidentalis V. 3, VanBuren et al., 2018), and woodland strawberry (Fragaria vesca V. 4, Edger et al., 2017) genomes. All four genomes are highly collinear. (Note that inversions on chromosomes 4 and 6 in R. occidentalis likely represent errors in the chromosome-scale assembly of R. occidentalis.)

Whole-genome alignment plots between the new genome assembly for ‘Hillquist’ blackberry (Hillquist_HiC) and the chromosome-scale assemblies of R. ulmifolius ‘Burbank Thornless’ (Burbank_HiC) blackberry, woodland strawberry (Fragaria vesca v.4, from Edger et al., 2017) and black raspberry (R. occidentalis v.3, from VanBuren et al., 2018). The ‘Burbank Thornless’ (Burbank_HiC) genome assembly is available on DNAzoo (https://www.dnazoo.org/assemblies/Rubus_ulmifolius) and both woodland strawberry and black raspberry genomes are publicly available at the Genome Database for Rosaceae (https://www.rosaceae.org/).

All the following people contributed to the project: Erez Aiden, Rishi Aryal, Hamid Ashrafi, Nahla Bassil, Mario Caccamo, Brian Crawford, Michael Dossett, Olga Dudchenko, Felicidad Fernandez-Fernandez, Gina Fernandez, Dan Mead, Cherie Ochsenfeld, Gina Pham, Melanie Pham, Tom Poorten, Dan Sargent, Aabid Shariff, David Weisz, Margaret Worthington, Xiaoyu Zhang

Citations:

Clark, J.R. (2008). Primocane-fruiting blackberry breeding. HortScience 43, 1637–1639.

Clark, J.R., Stafne, E.T., Hall, H.K., Region, N., and Finn, C.E. (2007). Blackberry breeding and genetics. Plant Breed. Rev. 29, 19–144.

Lopez-Medina, J., Moore, J.N. and McNew, R.W.. 2000. A proposed model for inheritance of primocane fruiting in tetraploid erect blackberry. J. Am. Soc. Hortic. Sci. 125, 217–221.

Edger, P.P., VanBuren, R., Colle, M., Poorten, T.J., Wai, C.M., Niederhuth, C.E., Alger, E.I., Ou, S., Acharya, C.B., Wang, J., et al. (2017). Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience 7, 1–7.

VanBuren, R., Wai, C.M., Colle, M., Wang, J., Sullivan, S., Bushakra, J.M., Liachko, I., Vining, K.J., Dossett, M., Finn, C.E., et al. (2018). A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. Gigascience 7, 1–9.