Moves like jaguar

The jaguar (Panthera onca) is a large felid species, and the only remaining member of the Panthera genus native to the Americas [1]. These amazing animals have the most powerful bite of all big cats, and are aptly named. The word ‘jaguar’ comes from the Tupian word ‘yaguara’ which means ‘beast of prey’. The jaguar is listed as near threatened on the ICUN’s red list due to loss of habitat [2]. Read more about the jaguar on panthera.org website and learn about the Jaguar Corridor Initiative to preserve the genetic integrity and future of the jaguar by connecting and protecting core jaguar populations from Mexico to Argentina!

Today, we share the chromosome-length assembly for the jaguar named Cocoy from the Houston Zoo. Sadly, Cocoy passed away in 2015, but her genome lives on in the digital form and will hopefully help the jaguar species in the years to come. This is a $1K genome assembly, see Dudchenko et al., 2018 for strategy details.

This is the sixth felid assembly in our collection alongside the cheetah, leopard, tiger, cougar, and clouded leopard. As pointed out before (see, e.g. this blog post) the Felidae karyotype is very highly conserved, confirmed once again in the whole-genome alignment plot between the domestic cat genome assembly, from Pontius et al., Genome Res., 2007, and the new jaguar genome assembly.

Whole genome alignment between the new jaguar genome assembly (Panthera_onca_HiC) and the domestic cat genome assembly (felCat9, NCBI accession number GCF_000181335.3).

Selfish genes, or shellfish genes?

Often known as the Great Scallop, King Scallop or Coquille St Jacques, the scallop Pecten maximus is widespread around northern Europe, and is an important human food source.

The genome of this species has just been made available (see Kenny et al. 2020 and this dnazoo.org webpage) as part of a collaboration with the Wellcome Sanger 25 Genomes project. As well as being the best assembled bivalve genome to date, it contains a large number of surprises. Approximately 70,000 of them, in fact - an exceptionally high number of genes packed into a relatively normal (circa 1.1 Gbp) sized genome. This is more than double the number of genes found in humans and in most commonly studied species!

These genes have been generated from widespread gene duplication, together with relatively little gene loss. The cause of this is not yet known, but echos what has been seen in some other mollusk genomes (e.g. Li et al 2018). Scallops therefore seem to need lots of new genes!

The genome contains a number of clues that will be useful for managing fisheries of this species. For example, Scallops are resistant to domoic acid, which they can accumulate when filter feeding. A potential cause of this resistance has been identified in our data, which could stop people from getting sick with Amnesic shellfish poisoning.

Scallops also have beautiful and unique eyes, and are some of the most mobile shellfish (able to swim surprisingly big distances). The Pecten maximus genome will therefore be interesting to evolutionary biologists, pharmaceutical companies, and anyone who likes to eat seafood. It is sure to be the basis for many sorts of work in the future - the world is its oyster (oops, no, scallop!).

References:

Kenny et al. 2020 Scallop preprint: https://www.biorxiv.org/content/10.1101/2020.01.08.887828v1.full

Li, C., Liu, X., Liu, B., Ma, B., Liu, F., Liu, G., Shi, Q. and Wang, C., 2018. Draft genome of the Peruvian scallop Argopecten purpuratus. GigaScience, 7(4), p.giy031.

Tools to solve a thorny problem

The global blackberry (Rubus subgenus Rubus) industry has experienced rapid growth during the past 15 years, driven by increased consumer demand, advanced production methods, year-round product availability, and new cultivars. Despite the growing economic importance of blackberries and their excellent nutritional properties, few genomic resources exist to facilitate molecular breeding.

Blackberries!

The application of molecular breeding in blackberry is a ‘thorny’ problem due to polyploidy, multisomic inheritance, and heterozygosity. While the red and black raspberries in subgenus Idaeobatus are diploids (2n = 2x = 14), cultivated blackberries in the subgenus Rubus are bred at the tetraploid (2n = 4x = 28) and higher order polyploid levels (Clark et al., 2007).

Today, we share the chromosome-length genome assembly for the diploid blackberry ‘Burbank Thornless’ (R. ulmifolius inermis, PI 554060), generated using plants donated by the USDA-ARS National Clonal Germplasm Repository in Corvallis, OR. The assembly was created 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).

‘Burbank Thornless’ was chosen because it is believed to be closely related to ‘John Innes’, the source of the recessive gene for thornlessness in ‘Merton Thornless’, which has been used widely in fresh-market blackberry breeding programs (Coyner et al., 2005; Scott et al., 1957). Botanically speaking, it would be more accurate to describe this accession as prickle-free than thornless. Blackberries have prickles, outgrowths from epidermal tissue, instead of thorns or spines, which are connected to the vascular systems of the plant (more details on this here). Regardless of what they are called, anyone who has spent time picking berries in wild bramble patches can appreciate that picking from thornless cultivars is a much smoother experience!

Thorny vs thornless blackberry canes.

This work is part of a collaborative effort between the University of Arkansas, USDA-ARS, North Carolina State University, DNA Zoo, NIAB-EMR, Pairwise Plants, and the Wellcome Sanger Institute. Thanks to all involved: Erez Aiden, Rishi Aryal, Hamid Ashrafi, Nahla Bassil, Mario Caccamo, Brian Crawford, Michael Dossett, Olga Dudchenko, Felicidad Fernandez-Fernandez, Gina Fernandez, Jodi Humann, Sook Jung, Dorrie Main, Dan Mead, Cherie Ochsenfeld, Gina Pham, Melanie Pham, Tom Poorten, Dan Sargent, Aabid Shariff, Margaret Worthington, Xiaoyu Zhang. Find out more on the Genome Database for Rosaceae (GDR) webpage dedicated to the 'Burbank Thornless' blackberry genome assembly, here!

See below the whole-genome alignment plots that compare the genomes of the Burbank Thornless (R. ulmifolius) to the black raspberry (R. occidentalis V. 3, VanBuren et al., 2018) and woodland strawberry (Fragaria vesca V. 4, Edger et al., 2017). All three genomes are highly collinear. Inversions on chromosomes 1 and 7 were found between woodland strawberry and both Rubus species. Interestingly, the inversions between R. occidentalis and F. vesca previously documented on chromosomes 4 and 6 were not seen in the new assembly of Burbank thornless. These inversions likely represent errors in the chromosome-scale assembly of R. occidentalis.

Whole-genome alignment plots between the new genome assembly for Burbank thornless blackberry (Burbank_HiC aka Burbank_genome_v1_purged_primary_contigs_HiC) and the genome assemblies of woodland strawberry (Fragaria vesca v.4, from Edger et al., 2017) and black raspberry (R. occidentalis v.3, from VanBuren et al., 2018). The new chromosome scale Burbank thornless assembly, as well woodland strawberry and black raspberry genomes, are publicly available at the Genome Database for Rosaceae (https://www.rosaceae.org/).

Citations:

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.

Coyner, M.A., Skirvin, R.M., Norton, M.A., and Otterbacher, A.G. (2005). Thornlessness in blackberries: a review. Small Fruits Rev. 4, 83–106.

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.

Scott, D.H., Darrrow G.M., and Ink D.P. (1957). ‘Merton Thornless’ as a parent in breeding thornless blackberries. Proc. Amer. Soc. Hort. Sci. 69,268-277.

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.