Citrullus naudinianus (Sond.) Hook. f.

Just about everyone knows what a watermelon (Citrullus lanatus) looks like. They come in various sizes and shapes, and the edible interior portion in various colors (white, red, yellow, etc.), but, how many are familiar with the ancestors of the watermelon - the primitive, wild forms?

Immature fruit of Citrullus naudinianus, photo by Robert Jarret (USDA) [CC]

The genus Citrullus is small in terms of the number of recognized species – containing only 7 or so. All the members of the genus are native to xerophytic (containing little liquid water) environments and the distribution ranges of individual species includes portions of the African continent, the Middle East and South and Central Asia. Each Citrullus species possesses one or more unique characteristics that allow it to survive, and thrive, in a hostile environment.

A great example of the diversity within the genus Citrullus is the gemsbok cucumber (it’s not really a cucumber at all!). The fruit of this desert-loving plant (scientific name Citrullus naudinianus) are, in fact, eaten by gemsbok. However, the fruit are also favored by mole-rats, jackals and honey badgers. Squirrels, porcupines, crickets and other insects use the water that gathers in the skin of old fruit after rains.

The fruit of the gemsbok cucumber are bitter. This is likely due to the presence of tetracyclic terpines common in the fruit of some other members of the genus. Nonetheless, the cooked fruit are edible. The bushmen of the Kalahari eat the fruit after they have been roasted in a fire or boiled. The cooking renders the terpines harmless. The fleshy fruits are also known to serve as a source of water and have even been used to make pickles. In addition to its fleshy fruits, the gemsbok cucumber produces large underground storage roots.

We report here a chromosome-length genome sequence of the gemsbok cucumber (Citrullus naudinianus), a plant bearing small (6-12cm in length) oval-shaped fruits with rudimentary spines. This plant is native to southern Africa including Botswana, Namibia, Mozambique, Zambia, Zimbabwe and South Africa. It represents the basal branch in the taxonomic tree of Citrullus and the Citrullus species most distantly related to the common watermelon. Unlike all other members of the genus Citrullus, the gemsbok cucumber is dioecious having separate male and female plants. The genetic mechanism accounting for the conversion from dioecy (gemsbok cucumber) to monoecy (all other Citrullus species), has yet to be determined.

The genome sequence of the gemsbok cucumber serves to provide an evolutionary anchor point for a pan-genus study on genome evolution in the genus Citrullus. It also facilitates an examination of the evolution of the gemsbok cucumber’s many unique adaptive traits that allow it to survive in an environment where few other plants can.

Interior of ripening fruit of Citrullus naudinianus, photo by Robert Jarret, USDA [CC]

Check the interactive map below and explore the Hi-C contacts across the 11 chromosomes of the gemsbok cucumber, and don't forget to visit the assembly page for more details on this HiFi+Hi-C genome assembly!

References:

1. Chomicki, G. and S. Renner. 2015. Watermelon origin solved with molecular phylogenetics including Linnaean material: another example of museomics. New Phytologist (2015) 205: 526–532 doi: 10.1111/nph.13163.

2. Jeffrey, C. 1978. Cucurbitaceae. Fl. Zambes. 4:414-499. Flora Zambesiaca Managing Committee, Glasgow.

3. Retief, E. and N.L. Meyer. 2017. Cucurbitaceae. In: E. Retief and N.L. Meyer (Eds.) Plants of the Free State: Inventory and identification guide. Strelitzia 38:484-489. South African National Biodiversity Institute, Pretoria.

4. Schaefer, H. and S.S. Renner. 2011. Cucurbitaceae. Cucurbitaceae Durande (1782), nom. cons. In: K. Kubitzk (ed.) Flowering Plants. Eudicots: Sapindales, Cucurbitales, Myrtaceae. Springer. pp. 112-174.

5. Tropical Plants Database, Ken Fern. tropical.theferns.info. 2021-12-26. <tropical.theferns.info/viewtropical.php?id=Acanthosicyos+naudinianus>

6. WFO. 2021: Acanthosicyos naudinianus (Sond.) C. Jeffrey. Published on the internet; http://www.worldfloraonline.org/taxon/wfo-000051376.

A genome to blue your mind

The blue monkey, Cercopithecus mitis, is an Old World monkey species endemic to Central and East Africa. Though called blue monkeys, they are actually more gray in appearance. As frugivores, the majority of the blue monkey's diet consists of fruit but they also eat leaves and occasionally insects. Wild populations of blue monkeys display interspecies cooperation, notably with red-tailed monkeys (C. ascanius) for extra protection against predators [1].

Cercopithecus mitis by Yvonne A. de Jong, [CC BY-NC-SA], via inaturalist.org

Today, we release the genome assembly for the blue monkey, Cercopithecus mitis. The genome was generated using a sample from the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center stored all the way back in 1978! We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for their help with this sample.

There are several recognized subspecies of the blue monkey [2]. At different times in history, they may have been viewed as separate species entirely, but have been later recategorized as subspecies. Our analysis of the mitochondrial sequence for the individual monkey that donated sample for this assembly suggests it is a Cercopithecus mitis albogularis, more commonly known as the Sykes' monkey.

This is a $1K genome assembly, following the protocol outlined on out Methods page. This genome assembly has a contig N50 = 28 Kb and a scaffold N50 = 51 Mb. Check out the 36 chromosomes (2n=72) of the blue monkey in the interactive JuiceBox map session below!

Whether you're interested in Old or New World monkeys, we've got you covered. This is the sixth Old World monkey species we've released here on the DNA Zoo blog and the 18th primate overall! Check out our $1K de novo assemblies for the Guinea baboon (Papio papio), the Allen's swamp monkey (Allenopithecus nigroviridis), and the Patas monkey (Erythrocebus patas).

For the greater galago

The brown greater galago (Otolemur crassicaudatus) is also commonly known as bush babies. This cutesy name likely came from the high-pitch cries they can make as well as the large, round eyes.. The eyes of the brown greater galago are not only adorable, they provide excellent night vision as they are nocturnal like most other galago species. In addition, the oversized, bat-like ears of the greater brown galago can point in opposite directions and can furl and unfurl their ears to best track insects in the dark [1].

Otolemur crassicaudatus by Hans Hillewaert, [CC BY-NC-ND 2.0], via flickr.com

We would like to graciously thank the Duke Lemur Center for providing the material used in this genome assembly! For the past 35 years, the Duke Lemur Center has collaborated and organized conservation programs in Madagascar to protect the many precious lemur species endemic to the area. Please consider symbolically adopting a lemur help support conversation efforts!

Today, we release the chromosome-length genome for the greater brown galago, Otolemur crassicaudatus! This is a $1K genome, with a contig N50 = 74 Kb and a scaffold N50= 91 Kb.

For assembly procedure details, please see our Methods page. Explore the 31 chromosomes of the greater brown galago in the interactive Hi-C map below.

This is the 6th Lemuriforme species and the 17th primate we've released here on the DNA Zoo blog! Leaping for more lemurs? Check out the assembly pages for the Mongoose lemur (Eulemur mongoz) , the Collared lemur (Eulemur collaris) , and the Gray mouse lemur (Microcebus murinus). Don't forget to subscribe to our mailing list below and give us a follow on Twitter @thednazoo to stay up to date on our latest releases!