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.

Fangtastic assembly

Meet the Northern Long-eared bat, Myotis septentrionalis (pronounced "my-oh-tis sep-ten-tree-oh-nal-is"). You may be forgiven for not recognizing the particular name, as it's also been known as the Northern bat ('septentrionalis' means "of the north"), and was previously assigned a different taxonomy (formerly a Mytois keenii subspecies). Rest assured, regardless of the nomenclature confusion, there is no mistaking this amazing bat with those distinctive long ears!

Northern Long-eared Bat, by Brookhaven National Laboratory [CC BY-NC-ND 2.0], via flickr.com

The Northern Long-eared bat shares many features with other species of other North American Myotis: these are fairly small bats with a body mass between 5-8 g, a body length of about 50 mm. The Northern's wingspan of about 200 mm is among the largest for a bat its size, and it has been suggested that the larger wing area coupled with a relatively longer tail are adaptations enabling foraging for insects occupying interior forest areas (whereas other North American Myotis bats generally forage in more open areas). And don't forget about the ears - it's likely that the extra surface area comes in handy when feeding in dense forests while stationed on a tree (known as "gleaning"). This foraging strategy is a distinctive behavior of these bats, though it can also can capture it's prey in flight (known as "aerial foraging") like other Myotis species. It's a stealthy eater too: the Northern Long-eared is able to emit an ultrasonic call to identify moth prey items that are nearly undetectable by the moth itself.

Despite a broad historic range spanning the boreal forests across Canada through eastern and north central United States, the Northern Long-eared bat is currently listed as a federally Threatened species under the Endangered Species Act [1]. Massive population declines are due primarily to a fungal pathogen causing White-nose Syndrome, a disease that has impacted many North American bats. In a grim twist of fate, these bats were previously so ubiquitous that there was little investment in understanding their natural history, thus detailed historical records regarding their ecology and behavior is limited. They have always been a tricky species to locate because they are much more solitary bats than other North American species.

In warm months these bats prefer snags tree hollows rather than more visible human structures like bridges and attics that other species like the Little Brown bat (Myotis lucifugus) or Big Brown bat (Eptesicus fuscus) are often detected. They spend the winter hibernating in caves like other North American bats, but prefer to hide in smaller crevices of instead of gathering in larger congregations. They might prefer the longest of winter naps, spending some of the longest hibernation periods of any Myotis, but they are frequently on the move in the summer with mothers moving their pup throughout the forest every 2-14 days.

Today, we share the chromosome-length genome assembly for the species. Contigging for this assembly was performed by Devon O'Rourke, Matt MacManes and Jeff Foster. Oxford Nanopore R9 flowcells were used to generate the initial raw data (5818511 total reads; 29116606101 total bases ; 8882 read length N50) from a single female adult specimen collected from West Tisbury, MA. These data were then basecalled with Albacore, reads trimmed with Porechop, and assembled into contigs with Flye (17,268 contigs, 1,998,235,525 bp, N50 217932). Illumina 150 bp PE reads were used to polish the scaffolds using three rounds of Racon and one round of Pilon. A second bat, a juvenile male, from Oak Bluffs, MA, was used for Hi-C data generation. This is the sixth chromosome-length bat genome assembly at the DNA Zoo, and the most contiguous genome assembly for common bats currently available!

Both bat specimen used for generating this assembly were collected thanks to Luanne Johnson, Director/Wildlife Biologist at BiodiversityWorks, who coordinated with the residents of the Martha's Vineyard island to make this project possible.

Despite over 1200 bat species throughout the world, only a few dozen genomes are currently available. We hope this contribution will enhance conservation management efforts that had previously relied on an alternative species (Myotis lucifugus) for population genetic investigations.

P.S.: We hear you fellow chiropterologists - bats don't have fangs, but the title was too fun!