• Ruqayya Khan

Naked mole-rats Heterocephalus glaber are born wrinkled and pink, with few whisker-like hairs to help them navigate their surroundings. They are quite comfortable in their own skin, and keep their birthday suits and style throughout their life span!


And that life span (>30 years) is quite considerable: naked mole-rats are extremely long-lived compared to other rodents. That's not their only superpower. They famously have an incredibly decreased risk of cancer [1]. They have reduced pain sensitivity.


They are also exceptionally built for a life underground [2]. Their lips are stationed behind their front teeth, allowing them to dig with their shovel-like teeth without filling their mouths with dirt. Interestingly, their teeth can operate similar to chopsticks, separating and moving together to aid their digging [3]. They're able to survive without or in very low oxygen concentrations for long periods of time; 18 minutes at 0% oxygen and around 5 hours at 5% oxygen! Their small eyes and poor vision aren't a hindrance, as they rarely leave the dark tunnels they dig.

Naked mole-rat by Josh More, [CC BY-NC-ND 2.0], via flickr.com

They are also social! Specifically, the naked mole-rat social structure is eusocial, operating more similar to a bee-hive than other rodent colonies. One queen mole-rat rules the colony while producing offspring. Like a well-oiled machine, each mole-rat has a purpose in the colony. "Workers" spend their lives digging tunnels, gathering food, and raising the pups while "soldiers" protect the colony from predators. As colonies tend to be highly inbred, "dispersers" seek to leave their native colonies in search of others to live and mate with. These dispersers are behaviorally and morphologically distinct from their peers, generally having a higher body fat content [4].


Today, we share the chromosome-length assembly for the naked mole-rat, Heterocephalus glaber. This genome assembly is a Hi-C upgrade for the draft genome assembly generated by Keane M. et al., Bioinformatics (2014). Please visit the Naked Mole-Rat Genome Resource at http://www.naked-mole-rat.org for the draft genome assembly and more existing genomic resources for this fascinating rodent! Many thanks to Kong from the Houston Zoo for providing the sample used for this chromosome-length Hi-C upgrade (check out the interactive map below).


We're no strangers to rodents here at the DNA Zoo as this is our 18th chromosome-length genome from the rodentia order! Check out the assembly page for the only other known eusocial mammal, the Damaraland mole-rat! Read also this paper by Zhou et al., 2020 with an independent assembly of a Canadian beaver (also assembled independently in our collection, here) and the naked mole-rat.


Citations:

Keane, M., Craig, T., Alföldi, J., Berlin, A. M., Johnson, J., Seluanov, A., Gorbunova, V., Di Palma, F., Lindblad-Toh, K., Church, G. M., & de Magalhães, J. P. (2014). The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. Bioinformatics (Oxford, England), 30(24), 3558–3560. https://doi.org/10.1093/bioinformatics/btu579


Blog post by Karen Holm, DVM, Klaus-Peter Koepfli, PhD, and H.C. Lim, PhD


The Eastern mountain bongo (Tragelaphus eurycerus isaaci) is the largest montane forest dwelling antelope species native to Kenya. The bongo is a member of the Bovidae family and the tribe Tragelaphini or spiral horned antelope, including eland, nyala and sitatunga (Bibi, 2013; Chen et al. 2019). They weigh-in around 200-280kg of body weight and females carry horns as well as the males. They are a rare and elusive species with fewer than 100 surviving in 5 isolated populations in Kenya. Therefore, the IUCN Red List of Threatened Species considers the Eastern mountain bongo Critically Endangered. Another subspecies, the Western bongo, differentiated by morphological and phenotypic evidence, extends across the Dahomey Gap from the Democratic Republic of the Congo to Sierra Leone and is disjunct from the Eastern subspecies.

Young bongo, image courtesy of Karen Holm [[CC]]

Conservation efforts of the Eastern subspecies have included a repatriation in 2004 of 18 animals to a semi-captive population at the Mount Kenya Conservancy. There have been many successful births and the herd is growing. In 2019, the Kenya Wildlife Service put together a national recovery and action plan for the Eastern mountain bongo for 2019-2023.


Bongos are unique in that females have 34 chromosomes and males have 33, with an acrocentric Y chromosome that is fused with one of the smaller chromosomeS. In addition, two types of X chromosomes exist, one being acrocentric and the other submetacentric, with the acrocentric X being similar to other tragelaphine antelopes (Benirschke et al., 1982).


Today we share the chromosome-length assembly for the Eastern Mountain Bongo. We thank The Wildlife Conservation Center in Virginia for providing the sample for the initial 10x Genomics Chromium linked-read and Supernova 2.0 de novo assembly, which was funded and assembled by H.C. Lim in the George Mason University Evolutionary Genomics Lab. The genome was then analyzed and annotated by Karen Holm, DVM. This draft assembly is in the process of being written up and published.


We also thank Bernadette and Howard, the two eastern bongos at the Houston Zoo who have provided samples for the chromosome-length Hi-C upgrade. (Read more exciting news from the eastern bongo family at the Houston Zoo here!)


See below how the chromosomes of the eastern bongo (2n=33/34) relate to those of cattle (2n=60).

Whole-genome alignment plot between the bongo (barney_pseudo2.1_HiC) and cattle (Bos_taurus_UMD_3.1.1) genome assemblies.

Citations:

Benirschke, K., Kumamoto, A., Esra, G., & Crocker, K. (1982). The chromosomes of the bongo, Taurotragus (Boocerus) eurycerus. Cytogenetic and Genome Research, 34(1-2), 10-18. doi:10.1159/000131788


Bibi, F. (2013). A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics. BMC Evolutionary Biology, 13(1), 166. doi:10.1186/1471-2148-13-166


Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., . . . Wang, W. (2019). Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science, 364(6446). doi:10.1126/science.aav6202

Updated: Dec 23, 2020

Weevils are one of the most diverse groups of insects with >60,000 species. Despite their prevalence few genomic resources exist for the group. Today, we report the first genome resolved to chromosome scale for the weevils, specifically, for the Easter Egg Weevil Pachyrhynchus sulphureomaculatus.

Pachyrhynchus sulphureomaculatus (photo by Ann Cabras) [CC].

Pachyrhynchus weevils are known for their brilliant colors. Many species have striking color patterns which signal to predators that they are not tasty due to their hard exoskeleton (Tseng et al. 2014). The genus is primarily restricted to the Philippines where they have diversified into about 145 species. They are an emblematic fauna of the islands and unfortunately many species are threatened due to habitat loss.


Follow the link to download the sequence of the n=11 chromosomes for the Easter Egg Weevil Pachyrhynchus sulphureomaculatus. At ~2 Gbp, the P. sulphureomaculatus genome is roughly 1.8 times as large as the next largest weevil genome published to date, the 1.11 Gbp Listronotus bonariensis, the Argentine Stem Weevil (Harrop et al. 2020), and 2.6 times the next largest, the 782 Mbp Red Palm Weevil, Rhynchophorus ferrugineus (Hazzouri et al. 2020) genome. Finally, it is more than 13.5 times the size of the coffee berry borer (Hypothenemus hampei), also a weevil. The extreme size appears to be due to the expansion of repetitive elements in P. sulphureomaculatus (~76% of the genome).


We hope that the new assembly will provide a resource for more research on this remarkable genus as well as conservation planning for the threatened Pachyrhynchus species. Read more about the genome in our paper (Van Dam et al. 2020) here: https://biorxiv.org/cgi/content/short/2020.12.18.422986v1!


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