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.

Anotter day, anotter genome

The North American river otters (Lontra canadensis) are extremely adaptable to their environments, which explains their wide range of habitats across the North American continent. Hot or cold, low or high elevations, these semi-aquatic mammals can be found in most waterways. Even more, they don’t let the “river” in their name limit them, these otters are happy to also take up residence in lakes, ponds, and marshes [1].

Otter-able, by Valerie [CC BY-NC-ND 2.0], via flickr.com

In the early 19th and 20th century, river otters were trapped and traded for their valuable fur. As the fur trade declined, North American river otters’ populations have increased and stabilized with the help of reintroduction programs [2]. Today, their habitats in some areas are still under threat of destruction and water pollution.

These otter-ly adorable animals are well-known for their playful antics. Though amusing to watch, chasing and wrestling are thought to be an integral part of teaching survival skills to their young. North American river otters are often seen sliding down, rolling around, and rubbing themselves onto surfaces. While it may look silly, this behavior is a way to mark their territory, as their scent glands are located near the base of their tails.

Interestingly, whether the North American river otter is loyal to one significant otter or if they see otter-people, is still up for debate. Some research indicates that otters may mate for life with one partner, while other studies have identified polygamy among river otter populations [3].

Today, we are releasing a chromosome-length genome assembly for the species. This is an upgrade for the genome generated by the Canada’s Genomic Enterprise (available here). The sample for the Hi-C upgrade was donated by Belle, a female North American river otter living at the Houston zoo.

This is the fifth member of the weasel (Mustelidae) family in our collection. See below how the new genome compares to the Eurasian otter Lutra lutra. We generated the Eurasian otter genome assembly together with the Wellcome Sanger Institute and shared it a blog post from October, here. A formal paper describing this assembly is now out, read it here!

Whole genome alignment plot between GSC_riverotter_1.0_HiC, the new chromosome-length genome assembly for the North American river otter, and mLutLut1.1, the chromosome-length Eurasian otter genome assembly.