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!

Karyotype conservation in the fellowship of the ring

The ringtail, Bassariscus astutus, gets it's name from its striking black and white tail. Although known also as the ring-tailed cat or the miner's cat, the ringtail is not a true cat [1]. The ringtail is a member of the Procyonidae family alongside the raccoon and cacomistle. Ringtails are native to the south-west United States and Mexico. Although they are very common throughout these areas, they are rarely seen due to their nocturnal nature [2].

Ringtail in Phoenix, Arizona by Robertbody, [CC BY-SA 3.0], via Wikimedia Commons

Today, we share the chromosome-length assembly for the ring-tailed cat, Bassariscus astutus. We thank the San Antonio Zoo for providing the sample that made this assembly possible. This is another $1K de novo genome, with a contig n50 = 40 Kb and a scaffold n50 = 102 Mb. For assembly procedure details, check out Dudchenko et al., 2018.

In the DNA Zoo collection, we already have a close relative to the ringtail, a cacomistle Bassariscus sumichrasti genome assembly. Some studies have suggested that the sister species are quite divergent from each other, with a last common ancestor shared a full 10MYA (Koepfli et al., 2007). Karyotypically however, the two species appear to be almost identical, see the whole genome alignment between the genome assemblies below.

Whole-genome alignment plot between the cacomistle (Bassariscus_sumichrasti_HiC) and the ringtail (Bassariscus_astutus_HiC).

Interestingly, a previous study (Nash et al.,2008) suggested that ringtails may have the ancestral karyotype of all Carnivora. As such, the ringtail karyotype has been extensively studied, including with cross-species painting probes of domestic cat. The latter have suggested three major rearrangement events between the species (Nash et al.,2008), captured now in the chromosome-length genome assembly. Specifically, chromosome 1 of the ringtail corresponds to the fusion of chromosome arm A2p and chromosome C2 in the domestic cat (circled in yellow). Chromosome 3 of the ringtail corresponds to the fusion of the chromosome arms A1p and C1q of the domestic cat (circled in orange). Finally, the third fusion event of chromosome F2 and chromosome arm C1p in the domestic cat together correspond to chromosome 4 of the ringtail (circled in green).

Left: Whole-genome alignment plot between the ringtail (Bassariscus_astutus_HiC) and the domestic cat (felCat9). Right: Results of chromosome painting probes of domestic cat- (FCA) on ringtail-BAS metaphase spread (taken from Nash et al.,2008).

This is the 5th member of the Procyonidae family that we have released here on the DNAZoo blog! Check out these tails about the cacomistle, the white-nosed coati, and the kinkajou as well as the assembly page for the common raccoon and stay tuned for more!

Citations:

Koepfli, K. P., Gompper, M. E., Eizirik, E., Ho, C. C., Linden, L., Maldonado, J. E., & Wayne, R. K. (2007). Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange. Molecular phylogenetics and evolution, 43(3), 1076–1095. https://doi.org/10.1016/j.ympev.2006.10.003

Nash, W. G., Menninger, J. C., Padilla-Nash, H. M., Stone, G., Perelman, P. L., & O'Brien, S. J. (2008). The ancestral carnivore karyotype (2n = 38) lives today in ringtails. The Journal of heredity, 99(3), 241–253. https://doi.org/10.1093/jhered/esm130