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.

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