Marching to the beat of the Bongo

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

Fear no weevil

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!

Pick a peck of peppers

Just about everyone is familiar with the sweet Bell pepper (Capsicum annuum) found in grocery stores. Likewise, most of us have tasted (like it or not) one of its ‘hot’ cousins like the jalapeno (C. annuum), the tabasco (C. frutescens) or the very hot habanero (C. chinense). Varieties of these large-fruited most-always pungent peppers are favored worldwide as a spice and a vegetable. However, the genus also contains many primitive species of pepper that are rarely seen. These wild types are typically found in ecologically unique (often fragile) environments that are geographically isolated. Most produce very small, but still pungent, fruit.

C. rhomboideum fruit, photo courtesy of G. Barboza

All of the cultivated species of pepper (there are 5 of them) share a common chromosome number of 2n=24. Most of the wild species also share this 2n=24 chromosome number – but there are exceptions. Certain of these wild types may contain 2n=26 chromosomes. A phylogenetic tree of Capsicum species indicates that the chromosome number of wild species has changed over time flip-flopping from 2n=24 to 2n=26, and back again on more than one occasion. The DNA content (genome size) in Capsicum species also varies 3-fold with wild species having 1/2X and 2X the genome size of C. annuum.

The origin and subsequent fate of the 13th chromosome pair in wild Capsicum species remains unclear as does the basis for the large shifts in genome size. The independent evolution of 2n=24 and 2n=26 species makes them particularly useful in the study of chromosome/genome evolution and genome architecture in the genus Capsicum. A better understanding of genome evolution in Capsicum, using wild species, many of which contain agriculturally important traits, will enable the use of such information to trace the evolution of genes and gene complex in this important genus.

We report here the genome sequence of the n=13 chromosome Capsicum rhomboideum (Dunal) Kuntze, a species bearing small, red, non-pungent fruit and having a characteristic yellow corolla. This species is native to Mexico, Central America and northwestern South America to northern Peru. A phylogenetic tree places C. rhomboideum near the base of that tree making this species one of the species most distantly related to C. annum.

Count the 13 chromosomes for yourself in the map below, and don't forget to check out the assembly page!