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!


Updated: Dec 8, 2020

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


The Eastern Yellow Robin (EYR) is a small insectivorous passerine bird native to eastern Australia [1], a member of the Australo-Papuan robin family Petroicidae. They are relatively unafraid of humans, often seen perched sideways on tree trunks in a range of habitats from dry woodland to rainforest. Their distinctive piping call is one of the first to be heard in the morning chorus, often beginning before light. They are mostly perch-and-pounce predators, grabbing invertebrates and some other small animals such as lizards out of leaf litter on the ground. The sexes are similar in appearance, but females are typically slightly smaller.

Eastern Yellow Robin (Eopsaltria australis). Photo credits and acknowledgements – Geoff Park [CC].

At 15 to 16 cm (6 in) in length, the eastern yellow robin is one of the larger Australasian robins, and one of the most easily observed. Pairs and small family parties establish a territory—sometimes year-round, sometimes for a season—and appear not to migrate any great distance, but will make local movements with the seasons, particularly to higher and lower ground. The species lives mainly in territorial pairs, sometimes with a ‘helper’, usually a son from an earlier year. During breeding season from about July to January nests are woven, mostly by females, as small cups of bark, grass, lichen and moss, tied together with spider web. It is normally built in an upright tree fork.


Eastern Yellow Robins have distribution spanning thousands of kilometres along north-south axis and across a large range of climates. Southern birds have an olive rump, different from the brighter yellow of northern birds [2].Surprisingly, there is a major genetic distinction perpendicular to this geographic colour variation [3]. Genetically the species appears to be split approximately into ‘inland’ and ‘coastal’ forms (respectively red and blue dots on the map shown here), thought to be caused by two ecologically relevant adaptive sweeps in the mitochondrial genome (mitochondria are the powerhouses of cells which bear their own small genome) [4, 5].

From Morales et al, 2017

Inland and coastal Eastern Yellow Robins seem not to interbreed freely where they occur side-by-side at a limited number of special locations. There is particular resistance to exchange of genomic material between the species in the part of the genome harbouring the greatest density of nuclear-encoded mitochondrial genes. This ‘mitonuclear cluster’ has been implicated in environmental adaptation by mitonuclear co-evolution in EYR [6]. So, the species may be in fact on its way to becoming two species, suited to different environments and conferring different metabolisms [7].


Stunning new evidence has revealed that the mitonuclear cluster in Eastern Yellow Robins and some relatives is located on a female-limited (neo-W) chromosome proposed to be formed by the fusion of the ancestral W sex chromosome with an autosome, and is also inherited in a neo-Z fashion (one copy in females, two copies in males) [8]. This genome reorganization occurred relatively recently compared to the age of the ancestral W chromosome, hence the use of the terms neo-W and neo-Z). Detailed genetic analysis of Eastern Yellow Robins revealed that while there are no apparent physical barriers preventing gene flow between the two mitochondrial types, there is almost no gene flow in mitochondrial genes between the two lineages shown on the map above [7]. This means that very few or no females move and successfully breed between the coastal and inland areas. In contrast, there is some flow of nuclear genes, which tells us that some males manage to meet and breed successfully with females of the other lineage. These contrasting patterns between mitochondrial and nuclear genomes indicate that there are strong barriers to females and their genes from moving between the two environments [3, 7].


Such wildlife species that have genomic variation distributed heterogeneously through environmental and geographic space can be excellent models for studying evolutionary processes under natural conditions. To support ongoing scientific efforts, DNA Zoo has been working with Paul Sunnucks, Alexandra Pavlova and Gabriel Low at Monash University to obtain chromosome-length genome assemblies for one inland- and one coastal-lineage female EYRs.


The chromosome-length assembly we share today is based on a draft assembly generated by Han Ming Gan and others at the Deakin Genomics Centre, with assembly by Gabriel Low. The draft genome assembly was created using MaSuRCA v3.2.8 (Zimin et al. 2013), using Oxford Nanopore MinION and PacBio reads polished with short-insert size Illumina NovaSeq reads. This work was enabled by wildlife authorities including the Victorian Department of Environment, Land, Water and Planning, Parks Victoria, and the Australian Bird and Bat Banding Scheme. The research has been funded by the Holsworth Wildlife Endowment Fund, Australian Research Council grant DP180102359, and Monash University.


The above draft was scaffolded with 172M PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!


The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.


The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.


Blog by: Parwinder Kaur and Paul Sunnucks


Citations

1. https://www.birdlife.org.au/bird-profile/eastern-yellow-robin

2. Morales HE, Pavlova A, Sunnucks P, Major R, Amos JN, Joseph L, Wang B, Lemmon AR, Endler JA, Delhey K. (2017a) Neutral and selective drivers of colour evolution in a widespread Australian passerine. Journal of Biogeography 44, 522–536.

3. Pavlova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS, Stone GN, Nicholls JA and Sunnucks P (2013). Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird. Evolution 67, 3412–3428.

4. Morales, H., P. Sunnucks, L. Joseph, and A. Pavlova. (2017b). Perpendicular axes of differentiation generated by mitochondrial introgression. Molecular Ecology 26:3241–3255.

5. Morales HE, Pavlova A, Joseph L, Sunnucks P (2015) Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance. Molecular Ecology 24, 2820–2837.

6. Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C (2017). Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Frontiers in Genetics 8:25. doi:10.3389/fgene.2017.00025

7. Morales HE, Pavlova A, Amos JN, Major R, Kilian A, Greening C and Sunnucks P (2018) Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nature Ecology & Evolution 2, 1258–1267.

8. Gan HM, Falk S, Morales HE, Austin CM, Sunnucks P, Pavlova A. (2019) Genomic evidence of neo-sex chromosomes in the Eastern Yellow Robin Gigascience 8, 1–10.

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