Stone on the beech

The stone marten, or beech marten (Martes foina), is a medium-sized animal from the weasel family (Mustelidae). Its range covers most of Europe and extends towards the Far East, with two major zones (IUCN 2020) separated by Central Asia. In Europe, the stone marten inhabits a variety of habitats – forests, open areas and mountain ranges, but often lives close to human dwelling, including big cities. Its range partially overlaps the range of the more arboreal pine marten (Martes martes), and hybrids are not uncommon in regions where the two species are sympatric. Stone martens are agile predators, but their diet also includes a variety of fruit and insects; they are mostly nocturnal. In 2016, a stone marten caused a shutdown of the Large Hadron Collider in Switzerland.

Martes foina by Bohuš Číčel, [CC BY-SA 3.0], via wikimedia.org

In a way, the stone marten is a cornerstone of carnivore genetics. Sorting chromosomes of this species were used as probes in Zoo-FISH experiments on dozens of species and will be used in many more. The stone marten itself is well-studied from the cytogenetic point of view. Zoo-FISHs with dog, cat and human probes (Figure 1) were done for this species (Graphodatsky, Perelman, and O’Brien 2020; Nie et al. 2012). This data was used to study genome architecture and rearrangements in carnivores (Nie et al. 2012) and can be used to connect assembly and karyotype, building one more bridge between genomics and cytogenetics.

Figure 1. Martes foina karyotype and Zoo-FISH with dog (CFA), cat (FCA) and human (HSA) (Graphodatsky, Perelman, and O’Brien 2020; Nie et al. 2012).

We present the chromosome-length assembly for the stone marten with all C-scaffolds (Lewin et al. 2019) assigned to the corresponding chromosomes. This genome is a first in many ways: it is the first genome assembly of such integrity within the genus Martes; the first genome generated by the Marten Genome Team; and last but not least, it is the first genome for the DNA Zoo Novosibirsk! The initial analysis of whole-genome alignment between this assembly and the domestic cat genome demonstrated strict agreement with ZooFISH in three Robertson translocations and revealed many inversions (Figure 2).

Figure 2. Dotplot for whole genome alignment of stone marten genome to domestic cat assembly (Felis_catus_9.0).

We thank Dr. Rogell Powell (North Carolina State University) for funding 10x Genomics linked-read sequencing for the draft assembly and Dr. Klaus Koepfli for organizing this sequencing and bringing all of the collaborators together. The cell culture of an individual used both for the linked read and HiC sequencing was provided by Kunming Cell Bank of the Chinese Academy of Sciences, Kunming, Yunnan, China through Drs. Malcolm Ferguson-Smith and Fengtang Yang at Department of Veterinary Medicine, University of Cambridge, UK to Animal Cytogenetics Laboratory at the Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Dr. Alexander Graphodatsky).

The initial assembly was performed by Sergei Kliver (DNA Zoo Novosibirsk, Institute of Molecular and Cellular Biology). Hi-C experiments and scaffolding to chromosomes was done by Polina Perelman, Ruqayya Khan and Olga Dudchenko. The genome annotation and a paper describing this research is in progress.

New marten genomes coming soon!

Blog post by Sergei Kliver, Tatiana Bulyonkova, Aleksandra Mironova

References:

Graphodatsky, Alexander, Polina Perelman, and Stephen J. O’Brien. 2020. Atlas of Mammalian Chromosomes. John Wiley & Sons, Incorporated.

IUCN. 2020. “IUCN 2020. The IUCN Red List of Threatened Species. Version 2020-2.”

Lewin, Harris A et al. 2019. “Precision Nomenclature for the New Genomics.” GigaScience 8(8): giz086.

Nie, W et al. 2012. “Chromosomal Rearrangements and Karyotype Evolution in Carnivores Revealed by Chromosome Painting.” Heredity 108(1): 17–27.

Hot off the volcano

The Mexican volcano mouse (Neotomodon alstoni, Merriam 1898), is the only species within the monotypic genus Neotomodon, and is endemic to the Transverse Neovolcanic Ridge of central Mexico. Its geographic range spans high-elevation Sacaton grasslands of seven Mexican states (Michoacán, Hidalgo, Tlaxcala, Morelos, Puebla, Veracruz, and Estado de México), with different mountain tops hosting morphologically distinct geographic races.

Neotomodon alstoni by aguilargm, via naturalista.mx, [CC-BY-NC]

Similar to some of their deer mouse relatives (genus Peromyscus), Mexican volcano mice are monogamous and have been used as models to better understand the molecular and physiological underpinnings of both monogamy and paternal care (Luis et al. 2000; Luis et al. 2017). The species is also an emerging biomedical model for studies of both obesity and circadian biology (Miranda-Anaya et al. 2019).

Morphologically intermediate to deer mice (Peromyscus) and voles (Microtus), the genus Neotomodon is named for their morphologically distinct teeth which resemble those of wood rats in the genus Neotoma. Genetically however, Neotomodon are more closely allied with deer mice (Peromyscus) and Florida mice (Podomys) (Bradley et al. 2007; Miller and Engstrom 2008; Platt et al. 2015), with a long history of systematic uncertainty.

Today, we share a chromosome-length genome assembly for the Mexican volcano mouse, Neotomodon alstoni (see also the contact map for the 24 chromosomes below). This assembly has a contig N50 of 45 KB and a scaffold N50 of 92 MB. The individual sequenced here was collected by David Ribble and Victor Sanchez-Cordero near Cuernavaca, Mexico in Morelos. The chromosome-length genome assembly was created in collaboration with the MacManes lab, University of New Hampshire. The draft assembly was generated using 10X data and was scaffolded using Oxford Nanopore data. The resulting assembly was misjoin-corrected, ordered and oriented into chromosomes using Hi-C data. See Methods for more details!

Interested in more mice genomes? Check out these blog posts on the cactus mouse and the Northern rock mouse, also created in collaboration with between the MacManes Lab and the DNA Zoo!

REFERENCES

R. D. Bradley, N. D. Durish, D. S. Rogers, J. R. Miller, M. D. Engstrom, C. W. Kilpatrick. Toward a molecular phylogeny for Peromyscus: Evidence from mitochondrial cytochrome-b sequences. J. Mamm., 88(5) (2007), pp. 1146-1159.

O. Dudchenko, M. S. Shamim, S. S. Batra, N. C. Durand, N. T. Musial, R. Mostofa, M. Pham, B. Glenn St. Hilaire, W. Yao, E. Stamenova, M. Hoeger, S. K. Nyquist, V. Jorchina, K. Pletch, J. P. Flanagan, A. Tomaszewicz, D. McAloose, C. Pérez Estrada, B. J. Novak, A. D. Omer, E. L. Aiden. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. 2018. Biorxiv: https://dio,org/10.1101/254797.

J. Luis, A. Carmona, J. Delgado, F. Cervantes, R. Cardenas. Paternal Behavior of the Volcano Mouse, *Neotomodon alstoni* (Rodentia: Muridae), in Captivity. J. Mammal., 81 (2) (2000), pp. 600-605

J. Luis, G. Ramos, M. Martínez-Torres, A. Carmona, B. Cedillo, J. Delgado. Testosterone induces paternal behavior in sexually inexperienced males of Neotomodon alstoni (Rodentia: Muridae). Revista de Biologia Tropical, 65 (4) (2017), pp. 1419-1427

J. R. Miller, M. D. Engstrom. The relationship of major lineages within Peromyscine rodents: a molecular phylogenetic hypothesis and systematic reappraisal. J. Mamm., 89 (2008), 1279-1295.

M. Miranda-Anaya, M. Pérez-Mendoza, C. R. Juárez-Tapia, A. Carmona-Castro. The volcano mouse Neotomodon alstoni of central Mexico, a biological model in the study of breeding, obesity, and circadian rhythms. General and Comparative Endocrinology, 273 (2019), 61-66.

Koala hugs for Australia Day!

The koala is recognized worldwide as a symbol of Australia, who got their name from the word Dharug gula, meaning no water. It was at one time thought, since the animals were not observed to come down from trees often, that they were able to survive without drinking. The secret lay in their diet: the eucalyptus leaves. The leaves have a high-water content, so the koala does not need to drink often. But the notion that they do not need to drink water at all is a myth [1].

Koala (Phascolarctos cinereus) Photo Credits & acknowledgements – Parwinder Kaur, [CC BY 2.0]

Koalas typically inhabit open eucalyptus woodlands. They are super cute, cuddly and fluffy, yet very territorial wild species. Koalas are evolutionarily and biologically distinct from other marsupials. The modern koala is the only living representative of the marsupial family Phascolarctidae, a family that once included several genera and species. During the Oligocene and Miocene, koalas lived in rainforests and had less specialised diets [2]. During the Miocene, the Australian continent began drying out, leading to the decline of rainforests and the spread of open Eucalyptus woodlands. The genus Phascolarctos split from Litokoala in the late Miocene [2][3] and had several adaptations that allowed it to live on a specialised eucalyptus diet [4].

Unlike kangaroos and eucalyptus-eating possums, koalas are hindgut fermenters, and their digestive retention can last for up to 100 hours in the wild, or up to 200 hours in captivity. They can eat highly toxic eucalyptus leaves that would kill most other mammals, but they are picky eaters, so very prone to habitat loss. They are able to digest the toxins present in eucalyptus leaves due to their expansion of cytochrome P450 gene family of metabolic enzymes, which breaks down these poisons in the liver [5].

Koalas are listed as a vulnerable species by the International Union for Conservation of Nature [6]. The animal was hunted heavily in the early 20th century for its fur, and large-scale cullings in Queensland resulted in a public outcry that initiated a movement to protect the species. Sanctuaries were established, and translocation efforts moved to new regions koalas whose habitat had become fragmented or reduced. Among the many threats to their existence are habitat destruction caused by agriculture, urbanization, droughts and associated bushfires, some related to climate change.

The animals are particularly vulnerable to bushfires due to their slow movements and the flammability of eucalyptus trees. The koala instinctively seeks refuge in the higher branches, where it is vulnerable to intense heat and flames. Bushfires also fragment the animal's habitat, which restricts their movement and leads to population decline and loss of genetic diversity [7].

This koala mum and her joey were rescued during a wildfire by Jimboomba Police and Wildcare volunteers in the Gold Coast Hinterland Bushfires. Photo Credits and acknowledgements – Darren, Jimboomba Police

The chromosome-length assembly we share today is based on a draft assembly phaCin_unsw_v4.1 submitted to NCBI by The Earlham Institute, UK with full refseq representative genome data (Johnson et al., Nat. Genet. 2018). Please visit The Koala Genome Consortium website and learn about the efforts by the Koala Genome Project, a pioneering collaborative research led by Australian geneticist Rebecca Nicole Johnson AM, with far-reaching and significant implications for the conservation of Australian koalas!

The above draft was scaffolded with in situ 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.

We gratefully acknowledge the collaboration with Natasha Tay, Harry Butler Institute, Murdoch University, and samples provided by the Ranger Red's Zoo & Conservation park. The Hi-C work was enabled by resources provided by DNA Zoo Australia, the University of Western Australia (UWA) and by DNA Zoo, Aiden Lab at the 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.

A high-quality genome sequence is an essential resource required to implement genomics data into conservation management initiatives. More than 80% of the current 200 Australian national vertebrate recovery plans have genetic action listed in the species recovery plan with only less than 15% with any genomic data available. The genomic resources for understanding genetic diversity is of utmost importance in species conservation.

This chromosome-length genome assembly enables a highly detailed 3D view of the genome architecture for koala, karyotype evolution studies, identification of new genome linked markers and learning how the overall structure of genes evolve from a zoonotic point of view. Having koala DNA organized into 8 chromosomes (see map below) in the present release provides a cost-effective method for fast and reliable analyses options for conservation management initiatives. We hope the improved assembly will also offer further insights into the species’ genetic susceptibility to diseases like koala retrovirus (KoRV) and Chlamydia, serve as a basis for innovative vaccines, and facilitate new conservation management solutions that incorporate the species’ population and genetic structure, such as facilitating gene flow via habitat connectivity or translocations.

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

Citations

1. "Bigger and better 'Blinky Drinkers' to quench koalas' thirst this summer". NSW Environment & Heritage. Archived from the original on 22 July 2019.

2. Louys, J.; Aplin, K.; Beck, R. M. D.; Archer, M. (2009). "Cranial anatomy of Oligo-Miocene koalas (Diprotodontia: Phascolarctidae): Stages in the evolution of an extreme leaf-eating specialization". Journal of Vertebrate Paleontology. 29 (4): 981–92. doi:10.1671/039.029.0412. S2CID 86356713.

3. Black, K.; Archer, M.; Hand, S. J. (2012). "New Tertiary koala (Marsupialia, Phascolarctidae) from Riversleigh, Australia, with a revision of phascolarctid phylogenetics, paleoecology, and paleobiodiversity". Journal of Vertebrate Paleontology. 32 (1): 125–38. doi:10.1080/02724634.2012.626825. S2CID 86152273.

4. Tyndale-Biscoe, p. 226 Archived 3 June 2016 at the Wayback Machine.

5. Koalas are eating their forests into extinction — even feasting on poisonous eucalyptus plants National Post, 4 July 2018.

6. Woinarski, J. & Burbidge, A.A. 2020. Phascolarctos cinereus (amended version of 2016 assessment). The IUCN Red List of Threatened Species 2020.

7. Moyal, pp. 209–11 Archived 11 June 2016 at the Wayback Machine.